---- COMMAND EXECUTED: --------------------------------------------------------- ( export TMPDIR=/lscratch/$SLURM_JOB_ID && export SINGULARITY_BINDPATH=/gs3,/gs4,/gs5,/gs6,/gs7,/gs8,/gs9,/gs10,/gs11,/spin1,/scratch,/fdb,/data,/lscratch && mkdir -p $TMPDIR/out && mkdir -p $TMPDIR/wrk && singularity run --cleanenv /data/MBDU/singularity_images/fmriprep_1.4.1.simg /data/MBDU/midla/data/bids $TMPDIR/out participant --participant_label 23649 -w $TMPDIR/wrk --nthreads $SLURM_CPUS_PER_TASK --mem_mb $SLURM_MEM_PER_NODE --fs-license-file /data/MBDU/singularity_images/license.txt --output-spaces MNI152NLin2009cAsym fsaverage6 func --dummy-scans 4 --longitudinal --use-aroma --error-on-aroma-warnings --t2s-coreg && mv $TMPDIR/out /data/MBDU/midla/data/derivatives/fmriprep/run_aroma/sub-23649 ) -------------------------------------------------------------------------------- 1: [WARN] The recommended file /README is missing. See Section 03 (Modality agnostic files) of the BIDS specification. (code: 101 - README_FILE_MISSING)  Please visit https://neurostars.org/search?q=README_FILE_MISSING for existing conversations about this issue. Summary: Available Tasks: Available Modalities: 8547 Files, 71.06GB Monetary incentive delay T1w 166 - Subjects rest T2w 4 - Sessions bold FLAIR fieldmap  If you have any questions, please post on https://neurostars.org/tags/bids. Making sure the input data is BIDS compliant (warnings can be ignored in most cases). 190731-15:14:38,264 nipype.workflow IMPORTANT: Running fMRIPREP version 1.4.1: * BIDS dataset path: /gs11/users/MBDU/bids/mid_longitudinal_20190717. * Participant list: ['23649']. * Run identifier: 20190731-151423_2077084b-c342-47bb-938a-a6214ae8452d. 190731-15:14:41,521 nipype.workflow IMPORTANT: Creating bold processing workflow for "/gs11/users/MBDU/bids/mid_longitudinal_20190717/sub-23649/ses-01/func/sub-23649_ses-01_task-mid_bold.nii.gz" (0.06 GB / 366 TRs). Memory resampled/largemem=0.25/0.48 GB. 190731-15:14:41,566 nipype.workflow IMPORTANT: No single-band-reference found for sub-23649_ses-01_task-mid_bold.nii.gz 190731-15:14:43,113 nipype.workflow WARNING: No multiecho BOLD images found for T2* coregistration. Using standard EPI-T1 coregistration. 190731-15:14:44,272 nipype.workflow IMPORTANT: Slice-timing correction will be included. 190731-15:14:44,704 nipype.workflow IMPORTANT: SDC: fieldmap estimation of type "epi" intended for /gs11/users/MBDU/bids/mid_longitudinal_20190717/sub-23649/ses-01/func/sub-23649_ses-01_task-mid_bold.nii.gz found. 190731-15:14:46,216 nipype.workflow IMPORTANT: Creating BOLD surface-sampling workflow. 190731-15:14:50,223 nipype.workflow IMPORTANT: Creating bold processing workflow for "/gs11/users/MBDU/bids/mid_longitudinal_20190717/sub-23649/ses-01/func/sub-23649_ses-01_task-rest_echo-1_bold.nii.gz" (0.03 GB / 196 TRs). Memory resampled/largemem=0.12/0.17 GB. 190731-15:14:50,260 nipype.workflow IMPORTANT: No single-band-reference found for sub-23649_ses-01_task-rest_echo-1_bold.nii.gz 190731-15:14:51,9 nipype.workflow IMPORTANT: Slice-timing correction will be included. 190731-15:14:51,431 nipype.workflow IMPORTANT: SDC: fieldmap estimation of type "epi" intended for /gs11/users/MBDU/bids/mid_longitudinal_20190717/sub-23649/ses-01/func/sub-23649_ses-01_task-rest_echo-1_bold.nii.gz found. 190731-15:14:51,435 nipype.workflow IMPORTANT: Generating T2* map and optimally combined ME-EPI time series. 190731-15:14:53,17 nipype.workflow IMPORTANT: Creating BOLD surface-sampling workflow. 190731-15:14:56,842 nipype.workflow IMPORTANT: Creating bold processing workflow for "/gs11/users/MBDU/bids/mid_longitudinal_20190717/sub-23649/ses-02/func/sub-23649_ses-02_task-mid_bold.nii.gz" (0.06 GB / 366 TRs). Memory resampled/largemem=0.25/0.48 GB. 190731-15:14:56,880 nipype.workflow IMPORTANT: No single-band-reference found for sub-23649_ses-02_task-mid_bold.nii.gz 190731-15:14:57,380 nipype.workflow WARNING: No multiecho BOLD images found for T2* coregistration. Using standard EPI-T1 coregistration. 190731-15:14:57,791 nipype.workflow IMPORTANT: Slice-timing correction will be included. 190731-15:14:58,219 nipype.workflow IMPORTANT: SDC: fieldmap estimation of type "epi" intended for /gs11/users/MBDU/bids/mid_longitudinal_20190717/sub-23649/ses-02/func/sub-23649_ses-02_task-mid_bold.nii.gz found. 190731-15:14:59,728 nipype.workflow IMPORTANT: Creating BOLD surface-sampling workflow. 190731-15:15:04,115 nipype.workflow IMPORTANT: Creating bold processing workflow for "/gs11/users/MBDU/bids/mid_longitudinal_20190717/sub-23649/ses-02/func/sub-23649_ses-02_task-rest_echo-1_bold.nii.gz" (0.03 GB / 196 TRs). Memory resampled/largemem=0.12/0.17 GB. 190731-15:15:04,157 nipype.workflow IMPORTANT: No single-band-reference found for sub-23649_ses-02_task-rest_echo-1_bold.nii.gz 190731-15:15:04,955 nipype.workflow IMPORTANT: Slice-timing correction will be included. 190731-15:15:05,425 nipype.workflow IMPORTANT: SDC: fieldmap estimation of type "epi" intended for /gs11/users/MBDU/bids/mid_longitudinal_20190717/sub-23649/ses-02/func/sub-23649_ses-02_task-rest_echo-1_bold.nii.gz found. 190731-15:15:05,429 nipype.workflow IMPORTANT: Generating T2* map and optimally combined ME-EPI time series. 190731-15:15:06,995 nipype.workflow IMPORTANT: Creating BOLD surface-sampling workflow. 190731-15:15:11,211 nipype.workflow IMPORTANT: Creating bold processing workflow for "/gs11/users/MBDU/bids/mid_longitudinal_20190717/sub-23649/ses-03/func/sub-23649_ses-03_task-mid_run-1_bold.nii.gz" (0.04 GB / 211 TRs). Memory resampled/largemem=0.15/0.22 GB. 190731-15:15:11,253 nipype.workflow IMPORTANT: No single-band-reference found for sub-23649_ses-03_task-mid_run-1_bold.nii.gz 190731-15:15:11,782 nipype.workflow WARNING: No multiecho BOLD images found for T2* coregistration. Using standard EPI-T1 coregistration. 190731-15:15:12,240 nipype.workflow IMPORTANT: Slice-timing correction will be included. 190731-15:15:12,717 nipype.workflow IMPORTANT: SDC: fieldmap estimation of type "epi" intended for /gs11/users/MBDU/bids/mid_longitudinal_20190717/sub-23649/ses-03/func/sub-23649_ses-03_task-mid_run-1_bold.nii.gz found. 190731-15:15:14,703 nipype.workflow IMPORTANT: Creating BOLD surface-sampling workflow. 190731-15:15:18,851 nipype.workflow IMPORTANT: Creating bold processing workflow for "/gs11/users/MBDU/bids/mid_longitudinal_20190717/sub-23649/ses-03/func/sub-23649_ses-03_task-mid_run-2_bold.nii.gz" (0.06 GB / 366 TRs). Memory resampled/largemem=0.25/0.48 GB. 190731-15:15:18,893 nipype.workflow IMPORTANT: No single-band-reference found for sub-23649_ses-03_task-mid_run-2_bold.nii.gz 190731-15:15:19,411 nipype.workflow WARNING: No multiecho BOLD images found for T2* coregistration. Using standard EPI-T1 coregistration. 190731-15:15:19,860 nipype.workflow IMPORTANT: Slice-timing correction will be included. 190731-15:15:20,334 nipype.workflow IMPORTANT: SDC: fieldmap estimation of type "epi" intended for /gs11/users/MBDU/bids/mid_longitudinal_20190717/sub-23649/ses-03/func/sub-23649_ses-03_task-mid_run-2_bold.nii.gz found. 190731-15:15:21,970 nipype.workflow IMPORTANT: Creating BOLD surface-sampling workflow. 190731-15:15:26,480 nipype.workflow IMPORTANT: Creating bold processing workflow for "/gs11/users/MBDU/bids/mid_longitudinal_20190717/sub-23649/ses-03/func/sub-23649_ses-03_task-rest_echo-1_bold.nii.gz" (0.03 GB / 196 TRs). Memory resampled/largemem=0.12/0.17 GB. 190731-15:15:26,521 nipype.workflow IMPORTANT: No single-band-reference found for sub-23649_ses-03_task-rest_echo-1_bold.nii.gz 190731-15:15:27,316 nipype.workflow IMPORTANT: Slice-timing correction will be included. 190731-15:15:27,782 nipype.workflow IMPORTANT: SDC: fieldmap estimation of type "epi" intended for /gs11/users/MBDU/bids/mid_longitudinal_20190717/sub-23649/ses-03/func/sub-23649_ses-03_task-rest_echo-1_bold.nii.gz found. 190731-15:15:27,786 nipype.workflow IMPORTANT: Generating T2* map and optimally combined ME-EPI time series. 190731-15:15:29,344 nipype.workflow IMPORTANT: Creating BOLD surface-sampling workflow. 190731-15:15:33,685 nipype.workflow IMPORTANT: Creating bold processing workflow for "/gs11/users/MBDU/bids/mid_longitudinal_20190717/sub-23649/ses-04/func/sub-23649_ses-04_task-mid_bold.nii.gz" (0.06 GB / 366 TRs). Memory resampled/largemem=0.25/0.48 GB. 190731-15:15:33,748 nipype.workflow IMPORTANT: No single-band-reference found for sub-23649_ses-04_task-mid_bold.nii.gz 190731-15:15:34,273 nipype.workflow WARNING: No multiecho BOLD images found for T2* coregistration. Using standard EPI-T1 coregistration. 190731-15:15:34,722 nipype.workflow IMPORTANT: Slice-timing correction will be included. 190731-15:15:35,191 nipype.workflow IMPORTANT: SDC: fieldmap estimation of type "epi" intended for /gs11/users/MBDU/bids/mid_longitudinal_20190717/sub-23649/ses-04/func/sub-23649_ses-04_task-mid_bold.nii.gz found. 190731-15:15:36,819 nipype.workflow IMPORTANT: Creating BOLD surface-sampling workflow. 190731-15:15:41,445 nipype.workflow IMPORTANT: Creating bold processing workflow for "/gs11/users/MBDU/bids/mid_longitudinal_20190717/sub-23649/ses-04/func/sub-23649_ses-04_task-rest_echo-1_bold.nii.gz" (0.03 GB / 196 TRs). Memory resampled/largemem=0.12/0.17 GB. 190731-15:15:41,484 nipype.workflow IMPORTANT: No single-band-reference found for sub-23649_ses-04_task-rest_echo-1_bold.nii.gz 190731-15:15:42,265 nipype.workflow IMPORTANT: Slice-timing correction will be included. 190731-15:15:42,728 nipype.workflow IMPORTANT: SDC: fieldmap estimation of type "epi" intended for /gs11/users/MBDU/bids/mid_longitudinal_20190717/sub-23649/ses-04/func/sub-23649_ses-04_task-rest_echo-1_bold.nii.gz found. 190731-15:15:42,732 nipype.workflow IMPORTANT: Generating T2* map and optimally combined ME-EPI time series. 190731-15:15:44,284 nipype.workflow IMPORTANT: Creating BOLD surface-sampling workflow. 190731-15:15:58,673 nipype.workflow IMPORTANT: Works derived from this fMRIPrep execution should include the following boilerplate: Results included in this manuscript come from preprocessing performed using *fMRIPrep* 1.4.1 (@fmriprep1; @fmriprep2; RRID:SCR_016216), which is based on *Nipype* 1.2.0 (@nipype1; @nipype2; RRID:SCR_002502). Anatomical data preprocessing : A total of 4 T1-weighted (T1w) images were found within the input BIDS dataset. All of them were corrected for intensity non-uniformity (INU) with `N4BiasFieldCorrection` [@n4], distributed with ANTs 2.2.0 [@ants, RRID:SCR_004757]. The T1w-reference was then skull-stripped with a *Nipype* implementation of the `antsBrainExtraction.sh` workflow (from ANTs), using OASIS30ANTs as target template. Brain tissue segmentation of cerebrospinal fluid (CSF), white-matter (WM) and gray-matter (GM) was performed on the brain-extracted T1w using `fast` [FSL 5.0.9, RRID:SCR_002823, @fsl_fast]. A T1w-reference map was computed after registration of 4 T1w images (after INU-correction) using `mri_robust_template` [FreeSurfer 6.0.1, @fs_template]. Brain surfaces were reconstructed using `recon-all` [FreeSurfer 6.0.1, RRID:SCR_001847, @fs_reconall], and the brain mask estimated previously was refined with a custom variation of the method to reconcile ANTs-derived and FreeSurfer-derived segmentations of the cortical gray-matter of Mindboggle [RRID:SCR_002438, @mindboggle]. Volume-based spatial normalization to two standard spaces (MNI152NLin2009cAsym, MNI152NLin6Asym) was performed through nonlinear registration with `antsRegistration` (ANTs 2.2.0), using brain-extracted versions of both T1w reference and the T1w template. The following templates were selected for spatial normalization: *ICBM 152 Nonlinear Asymmetrical template version 2009c* [@mni152nlin2009casym, RRID:SCR_008796; TemplateFlow ID: MNI152NLin2009cAsym], *FSL's MNI ICBM 152 non-linear 6th Generation Asymmetric Average Brain Stereotaxic Registration Model* [@mni152nlin6asym, RRID:SCR_002823; TemplateFlow ID: MNI152NLin6Asym]. Functional data preprocessing : For each of the 9 BOLD runs found per subject (across all tasks and sessions), the following preprocessing was performed. First, a reference volume and its skull-stripped version were generated using a custom methodology of *fMRIPrep*. A deformation field to correct for susceptibility distortions was estimated based on two echo-planar imaging (EPI) references with opposing phase-encoding directions, using `3dQwarp` @afni (AFNI 20160207). Based on the estimated susceptibility distortion, an unwarped BOLD reference was calculated for a more accurate co-registration with the anatomical reference. Head-motion parameters with respect to the BOLD reference (transformation matrices, and six corresponding rotation and translation parameters) are estimated before any spatiotemporal filtering using `mcflirt` [FSL 5.0.9, @mcflirt]. BOLD runs were slice-time corrected using `3dTshift` from AFNI 20160207 [@afni, RRID:SCR_005927]. The BOLD time-series (including slice-timing correction when applied) were resampled onto their original, native space by applying a single, composite transform to correct for head-motion and susceptibility distortions. These resampled BOLD time-series will be referred to as *preprocessed BOLD in original space*, or just *preprocessed BOLD*. A T2* map was estimated from the preprocessed BOLD by fitting to a monoexponential signal decay model with log-linear regression. For each voxel, the maximal number of echoes with reliable signal in that voxel were used to fit the model. The calculated T2* map was then used to optimally combine preprocessed BOLD across echoes following the method described in [@posse_t2s]. The optimally combined time series was carried forward as the *preprocessed BOLD*, and the T2* map was also retained as the BOLD reference. The BOLD reference was then co-registered to the T1w reference using `bbregister` (FreeSurfer) which implements boundary-based registration [@bbr]. Co-registration was configured with nine degrees of freedom to account for distortions remaining in the BOLD reference. The BOLD time-series were resampled into several standard spaces, correspondingly generating the following *spatially-normalized, preprocessed BOLD runs*: MNI152NLin2009cAsym, MNI152NLin6Asym. First, a reference volume and its skull-stripped version were generated using a custom methodology of *fMRIPrep*. Automatic removal of motion artifacts using independent component analysis [ICA-AROMA, @aroma] was performed on the *preprocessed BOLD on MNI space* time-series after removal of non-steady state volumes and spatial smoothing with an isotropic, Gaussian kernel of 6mm FWHM (full-width half-maximum). Corresponding "non-aggresively" denoised runs were produced after such smoothing. Additionally, the "aggressive" noise-regressors were collected and placed in the corresponding confounds file. Several confounding time-series were calculated based on the *preprocessed BOLD*: framewise displacement (FD), DVARS and three region-wise global signals. FD and DVARS are calculated for each functional run, both using their implementations in *Nipype* [following the definitions by @power_fd_dvars]. The three global signals are extracted within the CSF, the WM, and the whole-brain masks. Additionally, a set of physiological regressors were extracted to allow for component-based noise correction [*CompCor*, @compcor]. Principal components are estimated after high-pass filtering the *preprocessed BOLD* time-series (using a discrete cosine filter with 128s cut-off) for the two *CompCor* variants: temporal (tCompCor) and anatomical (aCompCor). tCompCor components are then calculated from the top 5% variable voxels within a mask covering the subcortical regions. This subcortical mask is obtained by heavily eroding the brain mask, which ensures it does not include cortical GM regions. For aCompCor, components are calculated within the intersection of the aforementioned mask and the union of CSF and WM masks calculated in T1w space, after their projection to the native space of each functional run (using the inverse BOLD-to-T1w transformation). Components are also calculated separately within the WM and CSF masks. For each CompCor decomposition, the *k* components with the largest singular values are retained, such that the retained components' time series are sufficient to explain 50 percent of variance across the nuisance mask (CSF, WM, combined, or temporal). The remaining components are dropped from consideration. The head-motion estimates calculated in the correction step were also placed within the corresponding confounds file. The confound time series derived from head motion estimates and global signals were expanded with the inclusion of temporal derivatives and quadratic terms for each [@confounds_satterthwaite_2013]. Frames that exceeded a threshold of 0.5 mm FD or 1.5 standardised DVARS were annotated as motion outliers. The BOLD time-series, were resampled to surfaces on the following spaces: *fsaverage6*. All resamplings can be performed with *a single interpolation step* by composing all the pertinent transformations (i.e. head-motion transform matrices, susceptibility distortion correction when available, and co-registrations to anatomical and output spaces). Gridded (volumetric) resamplings were performed using `antsApplyTransforms` (ANTs), configured with Lanczos interpolation to minimize the smoothing effects of other kernels [@lanczos]. Non-gridded (surface) resamplings were performed using `mri_vol2surf` (FreeSurfer). Functional data preprocessing : For each of the 9 BOLD runs found per subject (across all tasks and sessions), the following preprocessing was performed. First, a reference volume and its skull-stripped version were generated using a custom methodology of *fMRIPrep*. A deformation field to correct for susceptibility distortions was estimated based on two echo-planar imaging (EPI) references with opposing phase-encoding directions, using `3dQwarp` @afni (AFNI 20160207). Based on the estimated susceptibility distortion, an unwarped BOLD reference was calculated for a more accurate co-registration with the anatomical reference. The BOLD reference was then co-registered to the T1w reference using `bbregister` (FreeSurfer) which implements boundary-based registration [@bbr]. Co-registration was configured with nine degrees of freedom to account for distortions remaining in the BOLD reference. Head-motion parameters with respect to the BOLD reference (transformation matrices, and six corresponding rotation and translation parameters) are estimated before any spatiotemporal filtering using `mcflirt` [FSL 5.0.9, @mcflirt]. BOLD runs were slice-time corrected using `3dTshift` from AFNI 20160207 [@afni, RRID:SCR_005927]. The BOLD time-series, were resampled to surfaces on the following spaces: *fsaverage6*. The BOLD time-series (including slice-timing correction when applied) were resampled onto their original, native space by applying a single, composite transform to correct for head-motion and susceptibility distortions. These resampled BOLD time-series will be referred to as *preprocessed BOLD in original space*, or just *preprocessed BOLD*. The BOLD time-series were resampled into several standard spaces, correspondingly generating the following *spatially-normalized, preprocessed BOLD runs*: MNI152NLin2009cAsym, MNI152NLin6Asym. First, a reference volume and its skull-stripped version were generated using a custom methodology of *fMRIPrep*. Automatic removal of motion artifacts using independent component analysis [ICA-AROMA, @aroma] was performed on the *preprocessed BOLD on MNI space* time-series after removal of non-steady state volumes and spatial smoothing with an isotropic, Gaussian kernel of 6mm FWHM (full-width half-maximum). Corresponding "non-aggresively" denoised runs were produced after such smoothing. Additionally, the "aggressive" noise-regressors were collected and placed in the corresponding confounds file. Several confounding time-series were calculated based on the *preprocessed BOLD*: framewise displacement (FD), DVARS and three region-wise global signals. FD and DVARS are calculated for each functional run, both using their implementations in *Nipype* [following the definitions by @power_fd_dvars]. The three global signals are extracted within the CSF, the WM, and the whole-brain masks. Additionally, a set of physiological regressors were extracted to allow for component-based noise correction [*CompCor*, @compcor]. Principal components are estimated after high-pass filtering the *preprocessed BOLD* time-series (using a discrete cosine filter with 128s cut-off) for the two *CompCor* variants: temporal (tCompCor) and anatomical (aCompCor). tCompCor components are then calculated from the top 5% variable voxels within a mask covering the subcortical regions. This subcortical mask is obtained by heavily eroding the brain mask, which ensures it does not include cortical GM regions. For aCompCor, components are calculated within the intersection of the aforementioned mask and the union of CSF and WM masks calculated in T1w space, after their projection to the native space of each functional run (using the inverse BOLD-to-T1w transformation). Components are also calculated separately within the WM and CSF masks. For each CompCor decomposition, the *k* components with the largest singular values are retained, such that the retained components' time series are sufficient to explain 50 percent of variance across the nuisance mask (CSF, WM, combined, or temporal). The remaining components are dropped from consideration. The head-motion estimates calculated in the correction step were also placed within the corresponding confounds file. The confound time series derived from head motion estimates and global signals were expanded with the inclusion of temporal derivatives and quadratic terms for each [@confounds_satterthwaite_2013]. Frames that exceeded a threshold of 0.5 mm FD or 1.5 standardised DVARS were annotated as motion outliers. All resamplings can be performed with *a single interpolation step* by composing all the pertinent transformations (i.e. head-motion transform matrices, susceptibility distortion correction when available, and co-registrations to anatomical and output spaces). Gridded (volumetric) resamplings were performed using `antsApplyTransforms` (ANTs), configured with Lanczos interpolation to minimize the smoothing effects of other kernels [@lanczos]. Non-gridded (surface) resamplings were performed using `mri_vol2surf` (FreeSurfer). Many internal operations of *fMRIPrep* use *Nilearn* 0.5.2 [@nilearn, RRID:SCR_001362], mostly within the functional processing workflow. For more details of the pipeline, see [the section corresponding to workflows in *fMRIPrep*'s documentation](https://fmriprep.readthedocs.io/en/latest/workflows.html "FMRIPrep's documentation"). ### References 190731-15:17:35,339 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.func_derivatives_wf.raw_sources" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/func_derivatives_wf/raw_sources". 190731-15:17:35,343 nipype.workflow INFO: [Node] Running "raw_sources" ("nipype.interfaces.utility.wrappers.Function") 190731-15:17:35,352 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.func_derivatives_wf.raw_sources". 190731-15:17:35,373 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_mid_wf.func_derivatives_wf.raw_sources" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_mid_wf/func_derivatives_wf/raw_sources". 190731-15:17:35,376 nipype.workflow INFO: [Node] Running "raw_sources" ("nipype.interfaces.utility.wrappers.Function") 190731-15:17:35,384 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_mid_wf.func_derivatives_wf.raw_sources". 190731-15:17:35,518 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_mid_wf.func_derivatives_wf.raw_sources" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_mid_wf/func_derivatives_wf/raw_sources". 190731-15:17:35,521 nipype.workflow INFO: [Node] Running "raw_sources" ("nipype.interfaces.utility.wrappers.Function") 190731-15:17:35,530 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_mid_wf.func_derivatives_wf.raw_sources". 190731-15:17:35,551 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_mid_run_1_wf.func_derivatives_wf.raw_sources" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_1_wf/func_derivatives_wf/raw_sources". 190731-15:17:35,554 nipype.workflow INFO: [Node] Running "raw_sources" ("nipype.interfaces.utility.wrappers.Function") 190731-15:17:35,563 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_mid_run_1_wf.func_derivatives_wf.raw_sources". 190731-15:17:35,655 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.func_derivatives_wf.raw_sources" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/func_derivatives_wf/raw_sources". 190731-15:17:35,658 nipype.workflow INFO: [Node] Running "raw_sources" ("nipype.interfaces.utility.wrappers.Function") 190731-15:17:35,667 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.func_derivatives_wf.raw_sources". 190731-15:17:35,822 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_opposite_wf.split" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/split". 190731-15:17:35,828 nipype.workflow INFO: [Node] Setting-up "_split0" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/split/mapflow/_split0". 190731-15:17:35,832 nipype.workflow INFO: [Node] Running "_split0" ("nipype.interfaces.fsl.utils.Split"), a CommandLine Interface with command: fslsplit /gs11/users/MBDU/bids/mid_longitudinal_20190717/sub-23649/ses-02/fmap/sub-23649_ses-02_acq-rest_dir-opp_epi.nii.gz -t 190731-15:17:35,837 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_matching_wf.split" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/split". 190731-15:17:35,841 nipype.workflow INFO: [Node] Setting-up "_split0" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/split/mapflow/_split0". 190731-15:17:35,844 nipype.workflow INFO: [Node] Running "_split0" ("nipype.interfaces.fsl.utils.Split"), a CommandLine Interface with command: fslsplit /gs11/users/MBDU/bids/mid_longitudinal_20190717/sub-23649/ses-01/fmap/sub-23649_ses-01_acq-rest_dir-match_epi.nii.gz -t 190731-15:17:35,902 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_mid_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_opposite_wf.split" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_mid_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/split". 190731-15:17:35,906 nipype.workflow INFO: [Node] Setting-up "_split0" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_mid_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/split/mapflow/_split0". 190731-15:17:35,908 nipype.workflow INFO: [Node] Running "_split0" ("nipype.interfaces.fsl.utils.Split"), a CommandLine Interface with command: fslsplit /gs11/users/MBDU/bids/mid_longitudinal_20190717/sub-23649/ses-01/fmap/sub-23649_ses-01_acq-task_dir-opp_epi.nii.gz -t 190731-15:17:35,920 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_opposite_wf.split" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/split". 190731-15:17:35,926 nipype.workflow INFO: [Node] Setting-up "_split0" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/split/mapflow/_split0". 190731-15:17:35,929 nipype.workflow INFO: [Node] Running "_split0" ("nipype.interfaces.fsl.utils.Split"), a CommandLine Interface with command: fslsplit /gs11/users/MBDU/bids/mid_longitudinal_20190717/sub-23649/ses-01/fmap/sub-23649_ses-01_acq-rest_dir-opp_epi.nii.gz -t 190731-15:17:35,931 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_mid_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_opposite_wf.split" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_mid_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/split". 190731-15:17:35,935 nipype.workflow INFO: [Node] Setting-up "_split0" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_mid_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/split/mapflow/_split0". 190731-15:17:35,937 nipype.workflow INFO: [Node] Running "_split0" ("nipype.interfaces.fsl.utils.Split"), a CommandLine Interface with command: fslsplit /gs11/users/MBDU/bids/mid_longitudinal_20190717/sub-23649/ses-02/fmap/sub-23649_ses-02_acq-task_dir-opp_epi.nii.gz -t 190731-15:17:35,969 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_mid_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_matching_wf.split" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_mid_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/split". 190731-15:17:35,973 nipype.workflow INFO: [Node] Setting-up "_split0" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_mid_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/split/mapflow/_split0". 190731-15:17:35,975 nipype.workflow INFO: [Node] Running "_split0" ("nipype.interfaces.fsl.utils.Split"), a CommandLine Interface with command: fslsplit /gs11/users/MBDU/bids/mid_longitudinal_20190717/sub-23649/ses-01/fmap/sub-23649_ses-01_acq-task_dir-match_epi.nii.gz -t 190731-15:17:35,982 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_matching_wf.split" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/split". 190731-15:17:35,986 nipype.workflow INFO: [Node] Setting-up "_split0" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/split/mapflow/_split0". 190731-15:17:35,988 nipype.workflow INFO: [Node] Running "_split0" ("nipype.interfaces.fsl.utils.Split"), a CommandLine Interface with command: fslsplit /gs11/users/MBDU/bids/mid_longitudinal_20190717/sub-23649/ses-02/fmap/sub-23649_ses-02_acq-rest_dir-match_epi.nii.gz -t 190731-15:17:36,0 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_mid_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_matching_wf.split" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_mid_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/split". 190731-15:17:36,6 nipype.workflow INFO: [Node] Setting-up "_split0" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_mid_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/split/mapflow/_split0". 190731-15:17:36,9 nipype.workflow INFO: [Node] Running "_split0" ("nipype.interfaces.fsl.utils.Split"), a CommandLine Interface with command: fslsplit /gs11/users/MBDU/bids/mid_longitudinal_20190717/sub-23649/ses-02/fmap/sub-23649_ses-02_acq-task_dir-match_epi.nii.gz -t 190731-15:17:36,115 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_mid_run_1_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_matching_wf.split" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/split". 190731-15:17:36,119 nipype.workflow INFO: [Node] Setting-up "_split0" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/split/mapflow/_split0". 190731-15:17:36,121 nipype.workflow INFO: [Node] Running "_split0" ("nipype.interfaces.fsl.utils.Split"), a CommandLine Interface with command: fslsplit /gs11/users/MBDU/bids/mid_longitudinal_20190717/sub-23649/ses-03/fmap/sub-23649_ses-03_acq-task_dir-match_epi.nii.gz -t 190731-15:17:36,231 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_mid_run_2_wf.func_derivatives_wf.raw_sources" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_2_wf/func_derivatives_wf/raw_sources". 190731-15:17:36,233 nipype.workflow INFO: [Node] Running "raw_sources" ("nipype.interfaces.utility.wrappers.Function") 190731-15:17:36,238 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_mid_run_2_wf.func_derivatives_wf.raw_sources". 190731-15:17:36,293 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_mid_run_2_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_matching_wf.split" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_2_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/split". 190731-15:17:36,300 nipype.workflow INFO: [Node] Setting-up "_split0" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_2_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/split/mapflow/_split0". 190731-15:17:36,305 nipype.workflow INFO: [Node] Running "_split0" ("nipype.interfaces.fsl.utils.Split"), a CommandLine Interface with command: fslsplit /gs11/users/MBDU/bids/mid_longitudinal_20190717/sub-23649/ses-03/fmap/sub-23649_ses-03_acq-task_dir-match_epi.nii.gz -t 190731-15:17:36,313 nipype.workflow INFO: [Node] Finished "_split0". 190731-15:17:36,315 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_opposite_wf.split". 190731-15:17:36,325 nipype.workflow INFO: [Node] Finished "_split0". 190731-15:17:36,327 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_matching_wf.split". 190731-15:17:36,377 nipype.workflow INFO: [Node] Finished "_split0". 190731-15:17:36,382 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_opposite_wf.split". 190731-15:17:36,427 nipype.workflow INFO: [Node] Finished "_split0". 190731-15:17:36,431 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_matching_wf.split". 190731-15:17:36,477 nipype.workflow INFO: [Node] Finished "_split0". 190731-15:17:36,480 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_mid_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_opposite_wf.split". 190731-15:17:36,542 nipype.workflow INFO: [Node] Finished "_split0". 190731-15:17:36,547 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_mid_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_opposite_wf.split". 190731-15:17:36,585 nipype.workflow INFO: [Node] Finished "_split0". 190731-15:17:36,589 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_mid_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_matching_wf.split". 190731-15:17:36,596 nipype.workflow INFO: [Node] Finished "_split0". 190731-15:17:36,598 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_mid_run_1_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_matching_wf.split". 190731-15:17:36,612 nipype.workflow INFO: [Node] Finished "_split0". 190731-15:17:36,617 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_mid_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_matching_wf.split". 190731-15:17:36,721 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_mid_run_2_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_opposite_wf.split" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_2_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/split". 190731-15:17:36,725 nipype.workflow INFO: [Node] Setting-up "_split0" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_2_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/split/mapflow/_split0". 190731-15:17:36,727 nipype.workflow INFO: [Node] Running "_split0" ("nipype.interfaces.fsl.utils.Split"), a CommandLine Interface with command: fslsplit /gs11/users/MBDU/bids/mid_longitudinal_20190717/sub-23649/ses-03/fmap/sub-23649_ses-03_acq-task_dir-opp_epi.nii.gz -t 190731-15:17:36,799 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_mid_run_1_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_opposite_wf.split" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/split". 190731-15:17:36,803 nipype.workflow INFO: [Node] Setting-up "_split0" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/split/mapflow/_split0". 190731-15:17:36,806 nipype.workflow INFO: [Node] Running "_split0" ("nipype.interfaces.fsl.utils.Split"), a CommandLine Interface with command: fslsplit /gs11/users/MBDU/bids/mid_longitudinal_20190717/sub-23649/ses-03/fmap/sub-23649_ses-03_acq-task_dir-opp_epi.nii.gz -t 190731-15:17:36,827 nipype.workflow INFO: [Node] Finished "_split0". 190731-15:17:36,829 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_mid_run_2_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_matching_wf.split". 190731-15:17:37,200 nipype.workflow INFO: [Node] Finished "_split0". 190731-15:17:37,204 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_mid_run_2_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_opposite_wf.split". 190731-15:17:37,268 nipype.workflow INFO: [Node] Finished "_split0". 190731-15:17:37,271 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_mid_run_1_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_opposite_wf.split". 190731-15:17:38,142 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_rest_echo_1_wf.func_derivatives_wf.raw_sources" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_rest_echo_1_wf/func_derivatives_wf/raw_sources". 190731-15:17:38,143 nipype.workflow INFO: [Node] Running "raw_sources" ("nipype.interfaces.utility.wrappers.Function") 190731-15:17:38,147 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_rest_echo_1_wf.func_derivatives_wf.raw_sources". 190731-15:17:38,478 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_rest_echo_1_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_opposite_wf.split" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/split". 190731-15:17:38,481 nipype.workflow INFO: [Node] Setting-up "_split0" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/split/mapflow/_split0". 190731-15:17:38,484 nipype.workflow INFO: [Node] Running "_split0" ("nipype.interfaces.fsl.utils.Split"), a CommandLine Interface with command: fslsplit /gs11/users/MBDU/bids/mid_longitudinal_20190717/sub-23649/ses-03/fmap/sub-23649_ses-03_acq-rest_dir-opp_epi.nii.gz -t 190731-15:17:38,751 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_rest_echo_1_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_matching_wf.split" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/split". 190731-15:17:38,754 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_04_task_mid_wf.func_derivatives_wf.raw_sources" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_04_task_mid_wf/func_derivatives_wf/raw_sources". 190731-15:17:38,756 nipype.workflow INFO: [Node] Setting-up "_split0" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/split/mapflow/_split0". 190731-15:17:38,757 nipype.workflow INFO: [Node] Running "raw_sources" ("nipype.interfaces.utility.wrappers.Function") 190731-15:17:38,759 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_04_task_mid_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_opposite_wf.split" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_04_task_mid_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/split". 190731-15:17:38,760 nipype.workflow INFO: [Node] Running "_split0" ("nipype.interfaces.fsl.utils.Split"), a CommandLine Interface with command: fslsplit /gs11/users/MBDU/bids/mid_longitudinal_20190717/sub-23649/ses-03/fmap/sub-23649_ses-03_acq-rest_dir-match_epi.nii.gz -t 190731-15:17:38,763 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_04_task_mid_wf.func_derivatives_wf.raw_sources". 190731-15:17:38,764 nipype.workflow INFO: [Node] Setting-up "_split0" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_04_task_mid_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/split/mapflow/_split0". 190731-15:17:38,768 nipype.workflow INFO: [Node] Running "_split0" ("nipype.interfaces.fsl.utils.Split"), a CommandLine Interface with command: fslsplit /gs11/users/MBDU/bids/mid_longitudinal_20190717/sub-23649/ses-04/fmap/sub-23649_ses-04_acq-task_dir-opp_epi.nii.gz -t 190731-15:17:38,870 nipype.workflow INFO: [Node] Finished "_split0". 190731-15:17:38,873 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_rest_echo_1_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_opposite_wf.split". 190731-15:17:39,231 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_04_task_mid_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_matching_wf.split" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_04_task_mid_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/split". 190731-15:17:39,236 nipype.workflow INFO: [Node] Setting-up "_split0" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_04_task_mid_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/split/mapflow/_split0". 190731-15:17:39,239 nipype.workflow INFO: [Node] Running "_split0" ("nipype.interfaces.fsl.utils.Split"), a CommandLine Interface with command: fslsplit /gs11/users/MBDU/bids/mid_longitudinal_20190717/sub-23649/ses-04/fmap/sub-23649_ses-04_acq-task_dir-match_epi.nii.gz -t 190731-15:17:39,248 nipype.workflow INFO: [Node] Finished "_split0". 190731-15:17:39,251 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_rest_echo_1_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_matching_wf.split". 190731-15:17:39,601 nipype.workflow INFO: [Node] Finished "_split0". 190731-15:17:39,604 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_04_task_mid_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_opposite_wf.split". 190731-15:17:39,973 nipype.workflow INFO: [Node] Finished "_split0". 190731-15:17:39,975 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_04_task_mid_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_matching_wf.split". 190731-15:17:40,173 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_mid_wf.bold_reference_wf.validate" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_mid_wf/bold_reference_wf/validate". 190731-15:17:40,175 nipype.workflow INFO: [Node] Running "validate" ("niworkflows.interfaces.images.ValidateImage") 190731-15:17:40,202 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.bold_reference_wf.validate" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/bold_reference_wf/validate". 190731-15:17:40,205 nipype.workflow INFO: [Node] Running "validate" ("niworkflows.interfaces.images.ValidateImage") 190731-15:17:40,303 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_mid_wf.bold_reference_wf.validate". 190731-15:17:40,364 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_mid_wf.bold_reference_wf.validate" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_mid_wf/bold_reference_wf/validate". 190731-15:17:40,367 nipype.workflow INFO: [Node] Running "validate" ("niworkflows.interfaces.images.ValidateImage") 190731-15:17:41,135 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.bold_reference_wf.validate" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/bold_reference_wf/validate". 190731-15:17:41,138 nipype.workflow INFO: [Node] Running "validate" ("niworkflows.interfaces.images.ValidateImage") 190731-15:17:43,183 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_mid_run_1_wf.bold_reference_wf.validate" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_1_wf/bold_reference_wf/validate". 190731-15:17:43,187 nipype.workflow INFO: [Node] Running "validate" ("niworkflows.interfaces.images.ValidateImage") 190731-15:17:43,450 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_mid_wf.bold_reference_wf.gen_ref" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_mid_wf/bold_reference_wf/gen_ref". 190731-15:17:43,452 nipype.workflow INFO: [Node] Running "gen_ref" ("niworkflows.interfaces.registration.EstimateReferenceImage") 190731-15:17:43,577 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_mid_run_2_wf.bold_reference_wf.validate" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_2_wf/bold_reference_wf/validate". 190731-15:17:43,580 nipype.workflow INFO: [Node] Running "validate" ("niworkflows.interfaces.images.ValidateImage") 190731-15:17:44,16 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_mid_wf.bold_reference_wf.gen_ref". 190731-15:17:44,657 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_rest_echo_1_wf.bold_reference_wf.validate" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_rest_echo_1_wf/bold_reference_wf/validate". 190731-15:17:44,659 nipype.workflow INFO: [Node] Running "validate" ("niworkflows.interfaces.images.ValidateImage") 190731-15:17:44,701 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_rest_echo_1_wf.bold_reference_wf.validate". 190731-15:17:44,844 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_mid_wf.bold_hmc_wf.mcflirt" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_mid_wf/bold_hmc_wf/mcflirt". 190731-15:17:44,848 nipype.workflow INFO: [Node] Running "mcflirt" ("nipype.interfaces.fsl.preprocess.MCFLIRT"), a CommandLine Interface with command: mcflirt -in /gs11/users/MBDU/bids/mid_longitudinal_20190717/sub-23649/ses-01/func/sub-23649_ses-01_task-mid_bold.nii.gz -out /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_mid_wf/bold_hmc_wf/mcflirt/sub-23649_ses-01_task-mid_bold_mcf.nii.gz -reffile /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_mid_wf/bold_reference_wf/gen_ref/ref_bold.nii.gz -mats -plots 190731-15:17:45,76 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_mid_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_matching_wf.merge" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_mid_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/merge". 190731-15:17:45,81 nipype.workflow INFO: [Node] Running "merge" ("niworkflows.interfaces.freesurfer.StructuralReference"), a CommandLine Interface with command: mri_robust_template --satit --fixtp --mov /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_mid_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/split/mapflow/_split0/vol0000.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_mid_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/split/mapflow/_split0/vol0001.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_mid_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/split/mapflow/_split0/vol0002.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_mid_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/split/mapflow/_split0/vol0003.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_mid_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/split/mapflow/_split0/vol0004.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_mid_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/split/mapflow/_split0/vol0005.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_mid_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/split/mapflow/_split0/vol0006.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_mid_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/split/mapflow/_split0/vol0007.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_mid_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/split/mapflow/_split0/vol0008.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_mid_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/split/mapflow/_split0/vol0009.nii.gz --inittp 1 --iscale --noit --template template.nii.gz --subsample 200 190731-15:17:45,155 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_mid_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_opposite_wf.merge" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_mid_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/merge". 190731-15:17:45,158 nipype.workflow INFO: [Node] Running "merge" ("niworkflows.interfaces.freesurfer.StructuralReference"), a CommandLine Interface with command: mri_robust_template --satit --fixtp --mov /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_mid_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/split/mapflow/_split0/vol0000.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_mid_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/split/mapflow/_split0/vol0001.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_mid_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/split/mapflow/_split0/vol0002.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_mid_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/split/mapflow/_split0/vol0003.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_mid_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/split/mapflow/_split0/vol0004.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_mid_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/split/mapflow/_split0/vol0005.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_mid_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/split/mapflow/_split0/vol0006.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_mid_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/split/mapflow/_split0/vol0007.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_mid_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/split/mapflow/_split0/vol0008.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_mid_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/split/mapflow/_split0/vol0009.nii.gz --inittp 1 --iscale --noit --template template.nii.gz --subsample 200 190731-15:17:45,211 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_opposite_wf.merge" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/merge". 190731-15:17:45,216 nipype.workflow INFO: [Node] Running "merge" ("niworkflows.interfaces.freesurfer.StructuralReference"), a CommandLine Interface with command: mri_robust_template --satit --fixtp --mov /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/split/mapflow/_split0/vol0000.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/split/mapflow/_split0/vol0001.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/split/mapflow/_split0/vol0002.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/split/mapflow/_split0/vol0003.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/split/mapflow/_split0/vol0004.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/split/mapflow/_split0/vol0005.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/split/mapflow/_split0/vol0006.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/split/mapflow/_split0/vol0007.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/split/mapflow/_split0/vol0008.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/split/mapflow/_split0/vol0009.nii.gz --inittp 1 --iscale --noit --template template.nii.gz --subsample 200 190731-15:17:45,223 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_matching_wf.merge" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/merge". 190731-15:17:45,228 nipype.workflow INFO: [Node] Running "merge" ("niworkflows.interfaces.freesurfer.StructuralReference"), a CommandLine Interface with command: mri_robust_template --satit --fixtp --mov /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/split/mapflow/_split0/vol0000.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/split/mapflow/_split0/vol0001.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/split/mapflow/_split0/vol0002.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/split/mapflow/_split0/vol0003.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/split/mapflow/_split0/vol0004.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/split/mapflow/_split0/vol0005.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/split/mapflow/_split0/vol0006.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/split/mapflow/_split0/vol0007.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/split/mapflow/_split0/vol0008.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/split/mapflow/_split0/vol0009.nii.gz --inittp 1 --iscale --noit --template template.nii.gz --subsample 200 190731-15:17:45,337 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.bold_reference_wf.validate". 190731-15:17:45,338 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_mid_run_2_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_opposite_wf.merge" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_2_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/merge". 190731-15:17:45,343 nipype.workflow INFO: [Node] Running "merge" ("niworkflows.interfaces.freesurfer.StructuralReference"), a CommandLine Interface with command: mri_robust_template --satit --fixtp --mov /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_2_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/split/mapflow/_split0/vol0000.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_2_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/split/mapflow/_split0/vol0001.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_2_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/split/mapflow/_split0/vol0002.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_2_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/split/mapflow/_split0/vol0003.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_2_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/split/mapflow/_split0/vol0004.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_2_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/split/mapflow/_split0/vol0005.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_2_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/split/mapflow/_split0/vol0006.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_2_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/split/mapflow/_split0/vol0007.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_2_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/split/mapflow/_split0/vol0008.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_2_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/split/mapflow/_split0/vol0009.nii.gz --inittp 1 --iscale --noit --template template.nii.gz --subsample 200 190731-15:17:45,408 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_matching_wf.merge" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/merge". 190731-15:17:45,412 nipype.workflow INFO: [Node] Running "merge" ("niworkflows.interfaces.freesurfer.StructuralReference"), a CommandLine Interface with command: mri_robust_template --satit --fixtp --mov /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/split/mapflow/_split0/vol0000.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/split/mapflow/_split0/vol0001.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/split/mapflow/_split0/vol0002.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/split/mapflow/_split0/vol0003.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/split/mapflow/_split0/vol0004.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/split/mapflow/_split0/vol0005.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/split/mapflow/_split0/vol0006.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/split/mapflow/_split0/vol0007.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/split/mapflow/_split0/vol0008.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/split/mapflow/_split0/vol0009.nii.gz --inittp 1 --iscale --noit --template template.nii.gz --subsample 200 190731-15:17:45,427 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_mid_run_1_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_opposite_wf.merge" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/merge". 190731-15:17:45,432 nipype.workflow INFO: [Node] Running "merge" ("niworkflows.interfaces.freesurfer.StructuralReference"), a CommandLine Interface with command: mri_robust_template --satit --fixtp --mov /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/split/mapflow/_split0/vol0000.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/split/mapflow/_split0/vol0001.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/split/mapflow/_split0/vol0002.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/split/mapflow/_split0/vol0003.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/split/mapflow/_split0/vol0004.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/split/mapflow/_split0/vol0005.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/split/mapflow/_split0/vol0006.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/split/mapflow/_split0/vol0007.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/split/mapflow/_split0/vol0008.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/split/mapflow/_split0/vol0009.nii.gz --inittp 1 --iscale --noit --template template.nii.gz --subsample 200 190731-15:17:45,443 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_mid_run_1_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_matching_wf.merge" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/merge". 190731-15:17:45,446 nipype.workflow INFO: [Node] Running "merge" ("niworkflows.interfaces.freesurfer.StructuralReference"), a CommandLine Interface with command: mri_robust_template --satit --fixtp --mov /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/split/mapflow/_split0/vol0000.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/split/mapflow/_split0/vol0001.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/split/mapflow/_split0/vol0002.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/split/mapflow/_split0/vol0003.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/split/mapflow/_split0/vol0004.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/split/mapflow/_split0/vol0005.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/split/mapflow/_split0/vol0006.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/split/mapflow/_split0/vol0007.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/split/mapflow/_split0/vol0008.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/split/mapflow/_split0/vol0009.nii.gz --inittp 1 --iscale --noit --template template.nii.gz --subsample 200 190731-15:17:45,491 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_mid_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_matching_wf.merge" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_mid_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/merge". 190731-15:17:45,496 nipype.workflow INFO: [Node] Running "merge" ("niworkflows.interfaces.freesurfer.StructuralReference"), a CommandLine Interface with command: mri_robust_template --satit --fixtp --mov /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_mid_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/split/mapflow/_split0/vol0000.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_mid_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/split/mapflow/_split0/vol0001.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_mid_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/split/mapflow/_split0/vol0002.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_mid_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/split/mapflow/_split0/vol0003.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_mid_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/split/mapflow/_split0/vol0004.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_mid_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/split/mapflow/_split0/vol0005.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_mid_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/split/mapflow/_split0/vol0006.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_mid_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/split/mapflow/_split0/vol0007.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_mid_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/split/mapflow/_split0/vol0008.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_mid_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/split/mapflow/_split0/vol0009.nii.gz --inittp 1 --iscale --noit --template template.nii.gz --subsample 200 190731-15:17:45,619 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_mid_run_2_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_matching_wf.merge" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_2_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/merge". 190731-15:17:45,624 nipype.workflow INFO: [Node] Running "merge" ("niworkflows.interfaces.freesurfer.StructuralReference"), a CommandLine Interface with command: mri_robust_template --satit --fixtp --mov /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_2_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/split/mapflow/_split0/vol0000.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_2_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/split/mapflow/_split0/vol0001.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_2_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/split/mapflow/_split0/vol0002.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_2_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/split/mapflow/_split0/vol0003.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_2_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/split/mapflow/_split0/vol0004.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_2_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/split/mapflow/_split0/vol0005.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_2_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/split/mapflow/_split0/vol0006.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_2_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/split/mapflow/_split0/vol0007.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_2_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/split/mapflow/_split0/vol0008.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_2_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/split/mapflow/_split0/vol0009.nii.gz --inittp 1 --iscale --noit --template template.nii.gz --subsample 200 190731-15:17:45,740 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.bold_reference_wf.validate". 190731-15:17:46,22 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_mid_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_opposite_wf.merge" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_mid_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/merge". 190731-15:17:46,28 nipype.workflow INFO: [Node] Running "merge" ("niworkflows.interfaces.freesurfer.StructuralReference"), a CommandLine Interface with command: mri_robust_template --satit --fixtp --mov /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_mid_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/split/mapflow/_split0/vol0000.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_mid_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/split/mapflow/_split0/vol0001.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_mid_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/split/mapflow/_split0/vol0002.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_mid_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/split/mapflow/_split0/vol0003.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_mid_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/split/mapflow/_split0/vol0004.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_mid_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/split/mapflow/_split0/vol0005.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_mid_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/split/mapflow/_split0/vol0006.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_mid_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/split/mapflow/_split0/vol0007.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_mid_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/split/mapflow/_split0/vol0008.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_mid_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/split/mapflow/_split0/vol0009.nii.gz --inittp 1 --iscale --noit --template template.nii.gz --subsample 200 190731-15:17:46,692 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_04_task_mid_wf.bold_reference_wf.validate" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_04_task_mid_wf/bold_reference_wf/validate". 190731-15:17:46,695 nipype.workflow INFO: [Node] Running "validate" ("niworkflows.interfaces.images.ValidateImage") 190731-15:17:46,890 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_opposite_wf.merge" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/merge". 190731-15:17:46,895 nipype.workflow INFO: [Node] Running "merge" ("niworkflows.interfaces.freesurfer.StructuralReference"), a CommandLine Interface with command: mri_robust_template --satit --fixtp --mov /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/split/mapflow/_split0/vol0000.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/split/mapflow/_split0/vol0001.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/split/mapflow/_split0/vol0002.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/split/mapflow/_split0/vol0003.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/split/mapflow/_split0/vol0004.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/split/mapflow/_split0/vol0005.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/split/mapflow/_split0/vol0006.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/split/mapflow/_split0/vol0007.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/split/mapflow/_split0/vol0008.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/split/mapflow/_split0/vol0009.nii.gz --inittp 1 --iscale --noit --template template.nii.gz --subsample 200 190731-15:17:48,26 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.bold_reference_wf.gen_ref" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/bold_reference_wf/gen_ref". 190731-15:17:48,28 nipype.workflow INFO: [Node] Running "gen_ref" ("niworkflows.interfaces.registration.EstimateReferenceImage") 190731-15:17:48,39 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_rest_echo_1_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_opposite_wf.merge" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/merge". 190731-15:17:48,71 nipype.workflow INFO: [Node] Running "merge" ("niworkflows.interfaces.freesurfer.StructuralReference"), a CommandLine Interface with command: mri_robust_template --satit --fixtp --mov /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/split/mapflow/_split0/vol0000.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/split/mapflow/_split0/vol0001.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/split/mapflow/_split0/vol0002.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/split/mapflow/_split0/vol0003.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/split/mapflow/_split0/vol0004.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/split/mapflow/_split0/vol0005.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/split/mapflow/_split0/vol0006.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/split/mapflow/_split0/vol0007.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/split/mapflow/_split0/vol0008.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/split/mapflow/_split0/vol0009.nii.gz --inittp 1 --iscale --noit --template template.nii.gz --subsample 200 190731-15:17:48,74 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_04_task_mid_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_matching_wf.merge" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_04_task_mid_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/merge". 190731-15:17:48,94 nipype.workflow INFO: [Node] Running "merge" ("niworkflows.interfaces.freesurfer.StructuralReference"), a CommandLine Interface with command: mri_robust_template --satit --fixtp --mov /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_04_task_mid_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/split/mapflow/_split0/vol0000.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_04_task_mid_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/split/mapflow/_split0/vol0001.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_04_task_mid_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/split/mapflow/_split0/vol0002.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_04_task_mid_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/split/mapflow/_split0/vol0003.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_04_task_mid_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/split/mapflow/_split0/vol0004.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_04_task_mid_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/split/mapflow/_split0/vol0005.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_04_task_mid_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/split/mapflow/_split0/vol0006.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_04_task_mid_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/split/mapflow/_split0/vol0007.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_04_task_mid_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/split/mapflow/_split0/vol0008.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_04_task_mid_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/split/mapflow/_split0/vol0009.nii.gz --inittp 1 --iscale --noit --template template.nii.gz --subsample 200 190731-15:17:48,193 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_rest_echo_1_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_matching_wf.merge" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/merge". 190731-15:17:48,201 nipype.workflow INFO: [Node] Running "merge" ("niworkflows.interfaces.freesurfer.StructuralReference"), a CommandLine Interface with command: mri_robust_template --satit --fixtp --mov /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/split/mapflow/_split0/vol0000.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/split/mapflow/_split0/vol0001.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/split/mapflow/_split0/vol0002.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/split/mapflow/_split0/vol0003.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/split/mapflow/_split0/vol0004.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/split/mapflow/_split0/vol0005.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/split/mapflow/_split0/vol0006.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/split/mapflow/_split0/vol0007.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/split/mapflow/_split0/vol0008.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/split/mapflow/_split0/vol0009.nii.gz --inittp 1 --iscale --noit --template template.nii.gz --subsample 200 190731-15:17:48,478 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.bold_reference_wf.gen_ref". 190731-15:17:48,676 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.bold_reference_wf.gen_ref" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/bold_reference_wf/gen_ref". 190731-15:17:48,678 nipype.workflow INFO: [Node] Running "gen_ref" ("niworkflows.interfaces.registration.EstimateReferenceImage") 190731-15:17:48,851 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_mid_run_1_wf.bold_reference_wf.validate". 190731-15:17:48,959 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_04_task_mid_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_opposite_wf.merge" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_04_task_mid_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/merge". 190731-15:17:48,963 nipype.workflow INFO: [Node] Running "merge" ("niworkflows.interfaces.freesurfer.StructuralReference"), a CommandLine Interface with command: mri_robust_template --satit --fixtp --mov /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_04_task_mid_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/split/mapflow/_split0/vol0000.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_04_task_mid_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/split/mapflow/_split0/vol0001.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_04_task_mid_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/split/mapflow/_split0/vol0002.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_04_task_mid_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/split/mapflow/_split0/vol0003.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_04_task_mid_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/split/mapflow/_split0/vol0004.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_04_task_mid_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/split/mapflow/_split0/vol0005.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_04_task_mid_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/split/mapflow/_split0/vol0006.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_04_task_mid_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/split/mapflow/_split0/vol0007.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_04_task_mid_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/split/mapflow/_split0/vol0008.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_04_task_mid_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/split/mapflow/_split0/vol0009.nii.gz --inittp 1 --iscale --noit --template template.nii.gz --subsample 200 190731-15:17:49,146 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.bold_reference_wf.gen_ref". 190731-15:17:49,342 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_rest_echo_1_wf.bold_reference_wf.gen_ref" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_rest_echo_1_wf/bold_reference_wf/gen_ref". 190731-15:17:49,345 nipype.workflow INFO: [Node] Running "gen_ref" ("niworkflows.interfaces.registration.EstimateReferenceImage") 190731-15:17:49,416 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_mid_wf.bold_reference_wf.validate". 190731-15:17:49,797 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_rest_echo_1_wf.bold_reference_wf.gen_ref". 190731-15:17:50,78 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_mid_wf.bold_stc_wf.slice_timing_correction" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_mid_wf/bold_stc_wf/slice_timing_correction". 190731-15:17:50,82 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.bold_hmc_wf.mcflirt" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/bold_hmc_wf/mcflirt". 190731-15:17:50,84 nipype.workflow INFO: [Node] Running "slice_timing_correction" ("nipype.interfaces.afni.preprocess.TShift"), a CommandLine Interface with command: 3dTshift -ignore 4 -prefix sub-23649_ses-01_task-mid_bold_tshift.nii.gz -tpattern @slice_timing.1D -TR 2s /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_mid_wf/bold_stc_wf/slice_timing_correction/sub-23649_ses-01_task-mid_bold.nii.gz 190731-15:17:50,86 nipype.workflow INFO: [Node] Running "mcflirt" ("nipype.interfaces.fsl.preprocess.MCFLIRT"), a CommandLine Interface with command: mcflirt -in /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/bold_reference_wf/validate/sub-23649_ses-01_task-rest_echo-1_bold_valid.nii.gz -out /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/bold_hmc_wf/mcflirt/sub-23649_ses-01_task-rest_echo-1_bold_valid_mcf.nii.gz -reffile /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/bold_reference_wf/gen_ref/ref_bold.nii.gz -mats -plots 190731-15:17:50,317 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_mid_run_2_wf.bold_reference_wf.validate". 190731-15:17:50,696 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.bold_hmc_wf.mcflirt" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/bold_hmc_wf/mcflirt". 190731-15:17:50,700 nipype.workflow INFO: [Node] Running "mcflirt" ("nipype.interfaces.fsl.preprocess.MCFLIRT"), a CommandLine Interface with command: mcflirt -in /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/bold_reference_wf/validate/sub-23649_ses-02_task-rest_echo-1_bold_valid.nii.gz -out /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/bold_hmc_wf/mcflirt/sub-23649_ses-02_task-rest_echo-1_bold_valid_mcf.nii.gz -reffile /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/bold_reference_wf/gen_ref/ref_bold.nii.gz -mats -plots 190731-15:17:52,38 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.bold_stc_wf.slice_timing_correction" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/bold_stc_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-01..func..sub-23649_ses-01_task-rest_echo-4_bold.nii.gz/slice_timing_correction". 190731-15:17:52,44 nipype.workflow INFO: [Node] Running "slice_timing_correction" ("nipype.interfaces.afni.preprocess.TShift"), a CommandLine Interface with command: 3dTshift -ignore 4 -prefix sub-23649_ses-01_task-rest_echo-4_bold_tshift.nii.gz -tpattern @slice_timing.1D -TR 2.5s /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/bold_stc_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-01..func..sub-23649_ses-01_task-rest_echo-4_bold.nii.gz/slice_timing_correction/sub-23649_ses-01_task-rest_echo-4_bold.nii.gz 190731-15:17:52,47 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.bold_stc_wf.slice_timing_correction" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/bold_stc_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-01..func..sub-23649_ses-01_task-rest_echo-3_bold.nii.gz/slice_timing_correction". 190731-15:17:52,48 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.bold_stc_wf.slice_timing_correction" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/bold_stc_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-01..func..sub-23649_ses-01_task-rest_echo-2_bold.nii.gz/slice_timing_correction". 190731-15:17:52,53 nipype.workflow INFO: [Node] Running "slice_timing_correction" ("nipype.interfaces.afni.preprocess.TShift"), a CommandLine Interface with command: 3dTshift -ignore 4 -prefix sub-23649_ses-01_task-rest_echo-2_bold_tshift.nii.gz -tpattern @slice_timing.1D -TR 2.5s /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/bold_stc_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-01..func..sub-23649_ses-01_task-rest_echo-2_bold.nii.gz/slice_timing_correction/sub-23649_ses-01_task-rest_echo-2_bold.nii.gz 190731-15:17:52,53 nipype.workflow INFO: [Node] Running "slice_timing_correction" ("nipype.interfaces.afni.preprocess.TShift"), a CommandLine Interface with command: 3dTshift -ignore 4 -prefix sub-23649_ses-01_task-rest_echo-3_bold_tshift.nii.gz -tpattern @slice_timing.1D -TR 2.5s /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/bold_stc_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-01..func..sub-23649_ses-01_task-rest_echo-3_bold.nii.gz/slice_timing_correction/sub-23649_ses-01_task-rest_echo-3_bold.nii.gz 190731-15:17:54,59 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_04_task_mid_wf.bold_reference_wf.validate". 190731-15:17:56,34 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.bold_stc_wf.slice_timing_correction" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/bold_stc_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-01..func..sub-23649_ses-01_task-rest_echo-1_bold.nii.gz/slice_timing_correction". 190731-15:17:56,40 nipype.workflow INFO: [Node] Running "slice_timing_correction" ("nipype.interfaces.afni.preprocess.TShift"), a CommandLine Interface with command: 3dTshift -ignore 4 -prefix sub-23649_ses-01_task-rest_echo-1_bold_tshift.nii.gz -tpattern @slice_timing.1D -TR 2.5s /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/bold_stc_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-01..func..sub-23649_ses-01_task-rest_echo-1_bold.nii.gz/slice_timing_correction/sub-23649_ses-01_task-rest_echo-1_bold.nii.gz 190731-15:18:06,503 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.bold_stc_wf.slice_timing_correction". 190731-15:18:08,54 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.bold_stc_wf.copy_xform" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/bold_stc_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-01..func..sub-23649_ses-01_task-rest_echo-3_bold.nii.gz/copy_xform". 190731-15:18:08,57 nipype.workflow INFO: [Node] Running "copy_xform" ("niworkflows.interfaces.utils.CopyXForm") 190731-15:18:09,678 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.bold_stc_wf.slice_timing_correction". 190731-15:18:11,181 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.bold_stc_wf.copy_xform". 190731-15:18:12,74 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.bold_split" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-01..func..sub-23649_ses-01_task-rest_echo-3_bold.nii.gz/bold_split". 190731-15:18:12,77 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.bold_stc_wf.copy_xform" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/bold_stc_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-01..func..sub-23649_ses-01_task-rest_echo-1_bold.nii.gz/copy_xform". 190731-15:18:12,77 nipype.workflow INFO: [Node] Running "bold_split" ("nipype.interfaces.fsl.utils.Split"), a CommandLine Interface with command: fslsplit /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/bold_stc_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-01..func..sub-23649_ses-01_task-rest_echo-3_bold.nii.gz/copy_xform/sub-23649_ses-01_task-rest_echo-3_bold_tshift_xform.nii.gz -t 190731-15:18:12,80 nipype.workflow INFO: [Node] Running "copy_xform" ("niworkflows.interfaces.utils.CopyXForm") 190731-15:18:12,659 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.bold_stc_wf.slice_timing_correction". 190731-15:18:12,885 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.bold_stc_wf.slice_timing_correction". 190731-15:18:14,52 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.bold_stc_wf.copy_xform" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/bold_stc_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-01..func..sub-23649_ses-01_task-rest_echo-4_bold.nii.gz/copy_xform". 190731-15:18:14,54 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.bold_stc_wf.copy_xform" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/bold_stc_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-01..func..sub-23649_ses-01_task-rest_echo-2_bold.nii.gz/copy_xform". 190731-15:18:14,55 nipype.workflow INFO: [Node] Running "copy_xform" ("niworkflows.interfaces.utils.CopyXForm") 190731-15:18:14,57 nipype.workflow INFO: [Node] Running "copy_xform" ("niworkflows.interfaces.utils.CopyXForm") 190731-15:18:15,525 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.bold_stc_wf.copy_xform". 190731-15:18:17,209 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.bold_stc_wf.copy_xform". 190731-15:18:17,245 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.bold_stc_wf.copy_xform". 190731-15:18:18,58 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.bold_split" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-01..func..sub-23649_ses-01_task-rest_echo-4_bold.nii.gz/bold_split". 190731-15:18:18,61 nipype.workflow INFO: [Node] Running "bold_split" ("nipype.interfaces.fsl.utils.Split"), a CommandLine Interface with command: fslsplit /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/bold_stc_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-01..func..sub-23649_ses-01_task-rest_echo-4_bold.nii.gz/copy_xform/sub-23649_ses-01_task-rest_echo-4_bold_tshift_xform.nii.gz -t 190731-15:18:18,64 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.bold_split" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-01..func..sub-23649_ses-01_task-rest_echo-1_bold.nii.gz/bold_split". 190731-15:18:18,65 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.bold_split" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-01..func..sub-23649_ses-01_task-rest_echo-2_bold.nii.gz/bold_split". 190731-15:18:18,67 nipype.workflow INFO: [Node] Running "bold_split" ("nipype.interfaces.fsl.utils.Split"), a CommandLine Interface with command: fslsplit /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/bold_stc_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-01..func..sub-23649_ses-01_task-rest_echo-1_bold.nii.gz/copy_xform/sub-23649_ses-01_task-rest_echo-1_bold_tshift_xform.nii.gz -t 190731-15:18:18,70 nipype.workflow INFO: [Node] Running "bold_split" ("nipype.interfaces.fsl.utils.Split"), a CommandLine Interface with command: fslsplit /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/bold_stc_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-01..func..sub-23649_ses-01_task-rest_echo-2_bold.nii.gz/copy_xform/sub-23649_ses-01_task-rest_echo-2_bold_tshift_xform.nii.gz -t 190731-15:18:18,495 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_mid_wf.bold_stc_wf.slice_timing_correction". 190731-15:18:20,84 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_mid_wf.bold_stc_wf.copy_xform" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_mid_wf/bold_stc_wf/copy_xform". 190731-15:18:20,87 nipype.workflow INFO: [Node] Running "copy_xform" ("niworkflows.interfaces.utils.CopyXForm") 190731-15:18:20,876 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.bold_split". 190731-15:18:22,826 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_mid_wf.bold_reference_wf.gen_ref" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_mid_wf/bold_reference_wf/gen_ref". 190731-15:18:22,829 nipype.workflow INFO: [Node] Running "gen_ref" ("niworkflows.interfaces.registration.EstimateReferenceImage") 190731-15:18:23,667 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_mid_wf.bold_reference_wf.gen_ref". 190731-15:18:26,107 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_mid_wf.bold_hmc_wf.mcflirt" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_mid_wf/bold_hmc_wf/mcflirt". 190731-15:18:26,111 nipype.workflow INFO: [Node] Running "mcflirt" ("nipype.interfaces.fsl.preprocess.MCFLIRT"), a CommandLine Interface with command: mcflirt -in /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_mid_wf/bold_reference_wf/validate/sub-23649_ses-02_task-mid_bold_valid.nii.gz -out /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_mid_wf/bold_hmc_wf/mcflirt/sub-23649_ses-02_task-mid_bold_valid_mcf.nii.gz -reffile /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_mid_wf/bold_reference_wf/gen_ref/ref_bold.nii.gz -mats -plots 190731-15:18:26,556 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.bold_split". 190731-15:18:27,629 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.bold_split". 190731-15:18:28,11 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_mid_wf.bold_stc_wf.copy_xform". 190731-15:18:28,257 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.bold_split". 190731-15:18:30,201 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_mid_run_1_wf.bold_reference_wf.gen_ref" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_1_wf/bold_reference_wf/gen_ref". 190731-15:18:30,203 nipype.workflow INFO: [Node] Running "gen_ref" ("niworkflows.interfaces.registration.EstimateReferenceImage") 190731-15:18:30,642 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_mid_run_1_wf.bold_reference_wf.gen_ref". 190731-15:18:30,914 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_mid_wf.bold_split" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_mid_wf/bold_split". 190731-15:18:30,918 nipype.workflow INFO: [Node] Running "bold_split" ("nipype.interfaces.fsl.utils.Split"), a CommandLine Interface with command: fslsplit /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_mid_wf/bold_stc_wf/copy_xform/sub-23649_ses-01_task-mid_bold_tshift_xform.nii.gz -t 190731-15:18:30,919 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_mid_wf.bold_stc_wf.slice_timing_correction" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_mid_wf/bold_stc_wf/slice_timing_correction". 190731-15:18:30,926 nipype.workflow INFO: [Node] Running "slice_timing_correction" ("nipype.interfaces.afni.preprocess.TShift"), a CommandLine Interface with command: 3dTshift -ignore 4 -prefix sub-23649_ses-02_task-mid_bold_valid_tshift.nii.gz -tpattern @slice_timing.1D -TR 2s /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_mid_wf/bold_stc_wf/slice_timing_correction/sub-23649_ses-02_task-mid_bold_valid.nii.gz 190731-15:18:30,930 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.bold_stc_wf.slice_timing_correction" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/bold_stc_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-02..func..sub-23649_ses-02_task-rest_echo-4_bold.nii.gz/slice_timing_correction". 190731-15:18:30,934 nipype.workflow INFO: [Node] Running "slice_timing_correction" ("nipype.interfaces.afni.preprocess.TShift"), a CommandLine Interface with command: 3dTshift -ignore 4 -prefix sub-23649_ses-02_task-rest_echo-4_bold_tshift.nii.gz -tpattern @slice_timing.1D -TR 2.5s /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/bold_stc_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-02..func..sub-23649_ses-02_task-rest_echo-4_bold.nii.gz/slice_timing_correction/sub-23649_ses-02_task-rest_echo-4_bold.nii.gz 190731-15:18:32,920 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.bold_stc_wf.slice_timing_correction" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/bold_stc_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-02..func..sub-23649_ses-02_task-rest_echo-3_bold.nii.gz/slice_timing_correction". 190731-15:18:32,926 nipype.workflow INFO: [Node] Running "slice_timing_correction" ("nipype.interfaces.afni.preprocess.TShift"), a CommandLine Interface with command: 3dTshift -ignore 4 -prefix sub-23649_ses-02_task-rest_echo-3_bold_tshift.nii.gz -tpattern @slice_timing.1D -TR 2.5s /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/bold_stc_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-02..func..sub-23649_ses-02_task-rest_echo-3_bold.nii.gz/slice_timing_correction/sub-23649_ses-02_task-rest_echo-3_bold.nii.gz 190731-15:18:45,206 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.bold_stc_wf.slice_timing_correction". 190731-15:18:46,918 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.bold_stc_wf.copy_xform" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/bold_stc_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-02..func..sub-23649_ses-02_task-rest_echo-4_bold.nii.gz/copy_xform". 190731-15:18:46,920 nipype.workflow INFO: [Node] Running "copy_xform" ("niworkflows.interfaces.utils.CopyXForm") 190731-15:18:49,814 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.bold_stc_wf.copy_xform". 190731-15:18:50,141 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_mid_wf.bold_split". 190731-15:18:50,920 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.bold_split" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-02..func..sub-23649_ses-02_task-rest_echo-4_bold.nii.gz/bold_split". 190731-15:18:50,923 nipype.workflow INFO: [Node] Running "bold_split" ("nipype.interfaces.fsl.utils.Split"), a CommandLine Interface with command: fslsplit /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/bold_stc_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-02..func..sub-23649_ses-02_task-rest_echo-4_bold.nii.gz/copy_xform/sub-23649_ses-02_task-rest_echo-4_bold_tshift_xform.nii.gz -t 190731-15:18:50,936 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.bold_stc_wf.slice_timing_correction" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/bold_stc_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-02..func..sub-23649_ses-02_task-rest_echo-2_bold.nii.gz/slice_timing_correction". 190731-15:18:50,942 nipype.workflow INFO: [Node] Running "slice_timing_correction" ("nipype.interfaces.afni.preprocess.TShift"), a CommandLine Interface with command: 3dTshift -ignore 4 -prefix sub-23649_ses-02_task-rest_echo-2_bold_tshift.nii.gz -tpattern @slice_timing.1D -TR 2.5s /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/bold_stc_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-02..func..sub-23649_ses-02_task-rest_echo-2_bold.nii.gz/slice_timing_correction/sub-23649_ses-02_task-rest_echo-2_bold.nii.gz 190731-15:18:51,872 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_matching_wf.merge". 190731-15:18:52,915 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.bold_stc_wf.slice_timing_correction" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/bold_stc_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-02..func..sub-23649_ses-02_task-rest_echo-1_bold.nii.gz/slice_timing_correction". 190731-15:18:52,920 nipype.workflow INFO: [Node] Running "slice_timing_correction" ("nipype.interfaces.afni.preprocess.TShift"), a CommandLine Interface with command: 3dTshift -ignore 4 -prefix sub-23649_ses-02_task-rest_echo-1_bold_tshift.nii.gz -tpattern @slice_timing.1D -TR 2.5s /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/bold_stc_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-02..func..sub-23649_ses-02_task-rest_echo-1_bold.nii.gz/slice_timing_correction/sub-23649_ses-02_task-rest_echo-1_bold.nii.gz 190731-15:18:53,703 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.bold_stc_wf.slice_timing_correction". 190731-15:18:54,910 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_rest_echo_1_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_opposite_wf.merge". 190731-15:18:54,926 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.bold_stc_wf.copy_xform" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/bold_stc_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-02..func..sub-23649_ses-02_task-rest_echo-3_bold.nii.gz/copy_xform". 190731-15:18:54,929 nipype.workflow INFO: [Node] Running "copy_xform" ("niworkflows.interfaces.utils.CopyXForm") 190731-15:18:55,144 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_rest_echo_1_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_matching_wf.merge". 190731-15:18:56,918 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_mid_run_1_wf.bold_hmc_wf.mcflirt" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_1_wf/bold_hmc_wf/mcflirt". 190731-15:18:56,922 nipype.workflow INFO: [Node] Running "mcflirt" ("nipype.interfaces.fsl.preprocess.MCFLIRT"), a CommandLine Interface with command: mcflirt -in /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_1_wf/bold_reference_wf/validate/sub-23649_ses-03_task-mid_run-1_bold_valid.nii.gz -out /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_1_wf/bold_hmc_wf/mcflirt/sub-23649_ses-03_task-mid_run-1_bold_valid_mcf.nii.gz -reffile /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_1_wf/bold_reference_wf/gen_ref/ref_bold.nii.gz -mats -plots 190731-15:18:57,927 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.bold_stc_wf.copy_xform". 190731-15:18:58,256 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_mid_run_2_wf.bold_reference_wf.gen_ref" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_2_wf/bold_reference_wf/gen_ref". 190731-15:18:58,258 nipype.workflow INFO: [Node] Running "gen_ref" ("niworkflows.interfaces.registration.EstimateReferenceImage") 190731-15:18:58,786 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_mid_run_2_wf.bold_reference_wf.gen_ref". 190731-15:18:58,956 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.bold_split" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-02..func..sub-23649_ses-02_task-rest_echo-3_bold.nii.gz/bold_split". 190731-15:18:58,959 nipype.workflow INFO: [Node] Running "bold_split" ("nipype.interfaces.fsl.utils.Split"), a CommandLine Interface with command: fslsplit /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/bold_stc_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-02..func..sub-23649_ses-02_task-rest_echo-3_bold.nii.gz/copy_xform/sub-23649_ses-02_task-rest_echo-3_bold_tshift_xform.nii.gz -t 190731-15:19:00,384 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.bold_split". 190731-15:19:00,992 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_mid_run_1_wf.bold_stc_wf.slice_timing_correction" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_1_wf/bold_stc_wf/slice_timing_correction". 190731-15:19:00,998 nipype.workflow INFO: [Node] Running "slice_timing_correction" ("nipype.interfaces.afni.preprocess.TShift"), a CommandLine Interface with command: 3dTshift -ignore 4 -prefix sub-23649_ses-03_task-mid_run-1_bold_valid_tshift.nii.gz -tpattern @slice_timing.1D -TR 2s /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_1_wf/bold_stc_wf/slice_timing_correction/sub-23649_ses-03_task-mid_run-1_bold_valid.nii.gz 190731-15:19:02,249 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_opposite_wf.merge". 190731-15:19:02,950 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_mid_run_2_wf.bold_hmc_wf.mcflirt" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_2_wf/bold_hmc_wf/mcflirt". 190731-15:19:02,953 nipype.workflow INFO: [Node] Running "mcflirt" ("nipype.interfaces.fsl.preprocess.MCFLIRT"), a CommandLine Interface with command: mcflirt -in /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_2_wf/bold_reference_wf/validate/sub-23649_ses-03_task-mid_run-2_bold_valid.nii.gz -out /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_2_wf/bold_hmc_wf/mcflirt/sub-23649_ses-03_task-mid_run-2_bold_valid_mcf.nii.gz -reffile /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_2_wf/bold_reference_wf/gen_ref/ref_bold.nii.gz -mats -plots 190731-15:19:03,577 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_rest_echo_1_wf.bold_hmc_wf.mcflirt" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_rest_echo_1_wf/bold_hmc_wf/mcflirt". 190731-15:19:03,579 nipype.workflow INFO: [Node] Running "mcflirt" ("nipype.interfaces.fsl.preprocess.MCFLIRT"), a CommandLine Interface with command: mcflirt -in /gs11/users/MBDU/bids/mid_longitudinal_20190717/sub-23649/ses-03/func/sub-23649_ses-03_task-rest_echo-1_bold.nii.gz -out /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_rest_echo_1_wf/bold_hmc_wf/mcflirt/sub-23649_ses-03_task-rest_echo-1_bold_mcf.nii.gz -reffile /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_rest_echo_1_wf/bold_reference_wf/gen_ref/ref_bold.nii.gz -mats -plots 190731-15:19:04,941 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_matching_wf.merge". 190731-15:19:06,650 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.bold_stc_wf.slice_timing_correction". 190731-15:19:06,940 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_mid_run_2_wf.bold_stc_wf.slice_timing_correction" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_2_wf/bold_stc_wf/slice_timing_correction". 190731-15:19:06,946 nipype.workflow INFO: [Node] Running "slice_timing_correction" ("nipype.interfaces.afni.preprocess.TShift"), a CommandLine Interface with command: 3dTshift -ignore 4 -prefix sub-23649_ses-03_task-mid_run-2_bold_valid_tshift.nii.gz -tpattern @slice_timing.1D -TR 2s /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_2_wf/bold_stc_wf/slice_timing_correction/sub-23649_ses-03_task-mid_run-2_bold_valid.nii.gz 190731-15:19:07,82 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_mid_wf.bold_stc_wf.slice_timing_correction". 190731-15:19:07,817 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.bold_stc_wf.slice_timing_correction". 190731-15:19:08,653 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.bold_split". 190731-15:19:09,1 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_mid_wf.bold_stc_wf.copy_xform" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_mid_wf/bold_stc_wf/copy_xform". 190731-15:19:09,1 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.bold_stc_wf.copy_xform" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/bold_stc_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-02..func..sub-23649_ses-02_task-rest_echo-2_bold.nii.gz/copy_xform". 190731-15:19:09,1 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.bold_stc_wf.copy_xform" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/bold_stc_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-02..func..sub-23649_ses-02_task-rest_echo-1_bold.nii.gz/copy_xform". 190731-15:19:09,4 nipype.workflow INFO: [Node] Running "copy_xform" ("niworkflows.interfaces.utils.CopyXForm") 190731-15:19:09,4 nipype.workflow INFO: [Node] Running "copy_xform" ("niworkflows.interfaces.utils.CopyXForm") 190731-15:19:09,4 nipype.workflow INFO: [Node] Running "copy_xform" ("niworkflows.interfaces.utils.CopyXForm") 190731-15:19:12,207 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_04_task_mid_wf.bold_reference_wf.gen_ref" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_04_task_mid_wf/bold_reference_wf/gen_ref". 190731-15:19:12,210 nipype.workflow INFO: [Node] Running "gen_ref" ("niworkflows.interfaces.registration.EstimateReferenceImage") 190731-15:19:12,669 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_opposite_wf.merge". 190731-15:19:12,970 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_04_task_mid_wf.bold_reference_wf.gen_ref". 190731-15:19:13,669 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.bold_stc_wf.copy_xform". 190731-15:19:14,357 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.bold_stc_wf.copy_xform". 190731-15:19:14,982 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.bold_split" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-02..func..sub-23649_ses-02_task-rest_echo-2_bold.nii.gz/bold_split". 190731-15:19:14,985 nipype.workflow INFO: [Node] Running "bold_split" ("nipype.interfaces.fsl.utils.Split"), a CommandLine Interface with command: fslsplit /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/bold_stc_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-02..func..sub-23649_ses-02_task-rest_echo-2_bold.nii.gz/copy_xform/sub-23649_ses-02_task-rest_echo-2_bold_tshift_xform.nii.gz -t 190731-15:19:14,986 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_rest_echo_1_wf.bold_stc_wf.slice_timing_correction" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_rest_echo_1_wf/bold_stc_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-03..func..sub-23649_ses-03_task-rest_echo-4_bold.nii.gz/slice_timing_correction". 190731-15:19:14,990 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_rest_echo_1_wf.bold_stc_wf.slice_timing_correction" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_rest_echo_1_wf/bold_stc_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-03..func..sub-23649_ses-03_task-rest_echo-3_bold.nii.gz/slice_timing_correction". 190731-15:19:14,992 nipype.workflow INFO: [Node] Running "slice_timing_correction" ("nipype.interfaces.afni.preprocess.TShift"), a CommandLine Interface with command: 3dTshift -ignore 4 -prefix sub-23649_ses-03_task-rest_echo-4_bold_tshift.nii.gz -tpattern @slice_timing.1D -TR 2.5s /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_rest_echo_1_wf/bold_stc_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-03..func..sub-23649_ses-03_task-rest_echo-4_bold.nii.gz/slice_timing_correction/sub-23649_ses-03_task-rest_echo-4_bold.nii.gz 190731-15:19:14,995 nipype.workflow INFO: [Node] Running "slice_timing_correction" ("nipype.interfaces.afni.preprocess.TShift"), a CommandLine Interface with command: 3dTshift -ignore 4 -prefix sub-23649_ses-03_task-rest_echo-3_bold_tshift.nii.gz -tpattern @slice_timing.1D -TR 2.5s /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_rest_echo_1_wf/bold_stc_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-03..func..sub-23649_ses-03_task-rest_echo-3_bold.nii.gz/slice_timing_correction/sub-23649_ses-03_task-rest_echo-3_bold.nii.gz 190731-15:19:16,408 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_mid_wf.bold_stc_wf.copy_xform". 190731-15:19:16,932 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.bold_split" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-02..func..sub-23649_ses-02_task-rest_echo-1_bold.nii.gz/bold_split". 190731-15:19:16,936 nipype.workflow INFO: [Node] Running "bold_split" ("nipype.interfaces.fsl.utils.Split"), a CommandLine Interface with command: fslsplit /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/bold_stc_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-02..func..sub-23649_ses-02_task-rest_echo-1_bold.nii.gz/copy_xform/sub-23649_ses-02_task-rest_echo-1_bold_tshift_xform.nii.gz -t 190731-15:19:17,159 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.bold_hmc_wf.mcflirt". 190731-15:19:18,585 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.bold_hmc_wf.mcflirt". 190731-15:19:18,982 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_mid_wf.bold_split" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_mid_wf/bold_split". 190731-15:19:18,986 nipype.workflow INFO: [Node] Running "bold_split" ("nipype.interfaces.fsl.utils.Split"), a CommandLine Interface with command: fslsplit /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_mid_wf/bold_stc_wf/copy_xform/sub-23649_ses-02_task-mid_bold_valid_tshift_xform.nii.gz -t 190731-15:19:19,0 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.bold_hmc_wf.normalize_motion" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/bold_hmc_wf/normalize_motion". 190731-15:19:19,3 nipype.workflow INFO: [Node] Running "normalize_motion" ("niworkflows.interfaces.utils.NormalizeMotionParams") 190731-15:19:19,17 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.bold_hmc_wf.normalize_motion". 190731-15:19:19,382 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_mid_run_1_wf.bold_stc_wf.slice_timing_correction". 190731-15:19:20,963 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.bold_hmc_wf.normalize_motion" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/bold_hmc_wf/normalize_motion". 190731-15:19:20,966 nipype.workflow INFO: [Node] Running "normalize_motion" ("niworkflows.interfaces.utils.NormalizeMotionParams") 190731-15:19:20,979 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.bold_hmc_wf.normalize_motion". 190731-15:19:21,618 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.bold_confounds_wf.fdisp" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/bold_confounds_wf/fdisp". 190731-15:19:21,621 nipype.workflow INFO: [Node] Running "fdisp" ("nipype.algorithms.confounds.FramewiseDisplacement") 190731-15:19:21,631 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_mid_run_1_wf.bold_stc_wf.copy_xform" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_1_wf/bold_stc_wf/copy_xform". 190731-15:19:21,633 nipype.workflow INFO: [Node] Running "copy_xform" ("niworkflows.interfaces.utils.CopyXForm") 190731-15:19:21,634 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.bold_confounds_wf.fdisp". 190731-15:19:23,643 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.bold_confounds_wf.fdisp" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/bold_confounds_wf/fdisp". 190731-15:19:23,646 nipype.workflow INFO: [Node] Running "fdisp" ("nipype.algorithms.confounds.FramewiseDisplacement") 190731-15:19:23,649 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_rest_echo_1_wf.bold_stc_wf.slice_timing_correction" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_rest_echo_1_wf/bold_stc_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-03..func..sub-23649_ses-03_task-rest_echo-2_bold.nii.gz/slice_timing_correction". 190731-15:19:23,655 nipype.workflow INFO: [Node] Running "slice_timing_correction" ("nipype.interfaces.afni.preprocess.TShift"), a CommandLine Interface with command: 3dTshift -ignore 4 -prefix sub-23649_ses-03_task-rest_echo-2_bold_tshift.nii.gz -tpattern @slice_timing.1D -TR 2.5s /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_rest_echo_1_wf/bold_stc_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-03..func..sub-23649_ses-03_task-rest_echo-2_bold.nii.gz/slice_timing_correction/sub-23649_ses-03_task-rest_echo-2_bold.nii.gz 190731-15:19:23,658 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.bold_confounds_wf.fdisp". 190731-15:19:23,871 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.bold_split". 190731-15:19:24,984 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_rest_echo_1_wf.bold_stc_wf.slice_timing_correction" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_rest_echo_1_wf/bold_stc_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-03..func..sub-23649_ses-03_task-rest_echo-1_bold.nii.gz/slice_timing_correction". 190731-15:19:24,989 nipype.workflow INFO: [Node] Running "slice_timing_correction" ("nipype.interfaces.afni.preprocess.TShift"), a CommandLine Interface with command: 3dTshift -ignore 4 -prefix sub-23649_ses-03_task-rest_echo-1_bold_tshift.nii.gz -tpattern @slice_timing.1D -TR 2.5s /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_rest_echo_1_wf/bold_stc_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-03..func..sub-23649_ses-03_task-rest_echo-1_bold.nii.gz/slice_timing_correction/sub-23649_ses-03_task-rest_echo-1_bold.nii.gz 190731-15:19:24,995 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_04_task_mid_wf.bold_hmc_wf.mcflirt" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_04_task_mid_wf/bold_hmc_wf/mcflirt". 190731-15:19:25,0 nipype.workflow INFO: [Node] Running "mcflirt" ("nipype.interfaces.fsl.preprocess.MCFLIRT"), a CommandLine Interface with command: mcflirt -in /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_04_task_mid_wf/bold_reference_wf/validate/sub-23649_ses-04_task-mid_bold_valid.nii.gz -out /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_04_task_mid_wf/bold_hmc_wf/mcflirt/sub-23649_ses-04_task-mid_bold_valid_mcf.nii.gz -reffile /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_04_task_mid_wf/bold_reference_wf/gen_ref/ref_bold.nii.gz -mats -plots 190731-15:19:25,334 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.bold_split". 190731-15:19:25,556 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_mid_run_1_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_opposite_wf.merge". 190731-15:19:25,907 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_mid_run_1_wf.bold_stc_wf.copy_xform". 190731-15:19:26,495 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_mid_run_2_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_opposite_wf.merge". 190731-15:19:26,948 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_mid_run_1_wf.bold_split" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_1_wf/bold_split". 190731-15:19:26,951 nipype.workflow INFO: [Node] Running "bold_split" ("nipype.interfaces.fsl.utils.Split"), a CommandLine Interface with command: fslsplit /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_1_wf/bold_stc_wf/copy_xform/sub-23649_ses-03_task-mid_run-1_bold_valid_tshift_xform.nii.gz -t 190731-15:19:27,525 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_04_task_rest_echo_1_wf.func_derivatives_wf.raw_sources" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_04_task_rest_echo_1_wf/func_derivatives_wf/raw_sources". 190731-15:19:27,528 nipype.workflow INFO: [Node] Running "raw_sources" ("nipype.interfaces.utility.wrappers.Function") 190731-15:19:27,530 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_04_task_rest_echo_1_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_opposite_wf.split" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_04_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/split". 190731-15:19:27,534 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_04_task_rest_echo_1_wf.func_derivatives_wf.raw_sources". 190731-15:19:27,535 nipype.workflow INFO: [Node] Setting-up "_split0" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_04_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/split/mapflow/_split0". 190731-15:19:27,538 nipype.workflow INFO: [Node] Running "_split0" ("nipype.interfaces.fsl.utils.Split"), a CommandLine Interface with command: fslsplit /gs11/users/MBDU/bids/mid_longitudinal_20190717/sub-23649/ses-04/fmap/sub-23649_ses-04_acq-rest_dir-opp_epi.nii.gz -t 190731-15:19:28,66 nipype.workflow INFO: [Node] Finished "_split0". 190731-15:19:28,70 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_04_task_rest_echo_1_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_opposite_wf.split". 190731-15:19:28,285 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_rest_echo_1_wf.bold_stc_wf.slice_timing_correction". 190731-15:19:28,930 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_rest_echo_1_wf.bold_stc_wf.copy_xform" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_rest_echo_1_wf/bold_stc_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-03..func..sub-23649_ses-03_task-rest_echo-3_bold.nii.gz/copy_xform". 190731-15:19:28,933 nipype.workflow INFO: [Node] Running "copy_xform" ("niworkflows.interfaces.utils.CopyXForm") 190731-15:19:28,935 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_04_task_mid_wf.bold_stc_wf.slice_timing_correction" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_04_task_mid_wf/bold_stc_wf/slice_timing_correction". 190731-15:19:28,940 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_04_task_rest_echo_1_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_opposite_wf.merge" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_04_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/merge". 190731-15:19:28,940 nipype.workflow INFO: [Node] Running "slice_timing_correction" ("nipype.interfaces.afni.preprocess.TShift"), a CommandLine Interface with command: 3dTshift -ignore 4 -prefix sub-23649_ses-04_task-mid_bold_valid_tshift.nii.gz -tpattern @slice_timing.1D -TR 2s /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_04_task_mid_wf/bold_stc_wf/slice_timing_correction/sub-23649_ses-04_task-mid_bold_valid.nii.gz 190731-15:19:28,944 nipype.workflow INFO: [Node] Running "merge" ("niworkflows.interfaces.freesurfer.StructuralReference"), a CommandLine Interface with command: mri_robust_template --satit --fixtp --mov /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_04_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/split/mapflow/_split0/vol0000.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_04_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/split/mapflow/_split0/vol0001.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_04_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/split/mapflow/_split0/vol0002.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_04_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/split/mapflow/_split0/vol0003.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_04_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/split/mapflow/_split0/vol0004.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_04_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/split/mapflow/_split0/vol0005.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_04_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/split/mapflow/_split0/vol0006.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_04_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/split/mapflow/_split0/vol0007.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_04_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/split/mapflow/_split0/vol0008.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_04_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/split/mapflow/_split0/vol0009.nii.gz --inittp 1 --iscale --noit --template template.nii.gz --subsample 200 190731-15:19:28,944 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_04_task_rest_echo_1_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_matching_wf.split" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_04_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/split". 190731-15:19:28,950 nipype.workflow INFO: [Node] Setting-up "_split0" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_04_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/split/mapflow/_split0". 190731-15:19:28,953 nipype.workflow INFO: [Node] Running "_split0" ("nipype.interfaces.fsl.utils.Split"), a CommandLine Interface with command: fslsplit /gs11/users/MBDU/bids/mid_longitudinal_20190717/sub-23649/ses-04/fmap/sub-23649_ses-04_acq-rest_dir-match_epi.nii.gz -t 190731-15:19:29,87 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_rest_echo_1_wf.bold_stc_wf.slice_timing_correction". 190731-15:19:29,579 nipype.workflow INFO: [Node] Finished "_split0". 190731-15:19:29,582 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_04_task_rest_echo_1_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_matching_wf.split". 190731-15:19:30,947 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_rest_echo_1_wf.bold_stc_wf.copy_xform" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_rest_echo_1_wf/bold_stc_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-03..func..sub-23649_ses-03_task-rest_echo-4_bold.nii.gz/copy_xform". 190731-15:19:30,950 nipype.workflow INFO: [Node] Running "copy_xform" ("niworkflows.interfaces.utils.CopyXForm") 190731-15:19:31,594 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_04_task_rest_echo_1_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_matching_wf.merge" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_04_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/merge". 190731-15:19:31,599 nipype.workflow INFO: [Node] Running "merge" ("niworkflows.interfaces.freesurfer.StructuralReference"), a CommandLine Interface with command: mri_robust_template --satit --fixtp --mov /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_04_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/split/mapflow/_split0/vol0000.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_04_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/split/mapflow/_split0/vol0001.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_04_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/split/mapflow/_split0/vol0002.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_04_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/split/mapflow/_split0/vol0003.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_04_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/split/mapflow/_split0/vol0004.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_04_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/split/mapflow/_split0/vol0005.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_04_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/split/mapflow/_split0/vol0006.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_04_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/split/mapflow/_split0/vol0007.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_04_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/split/mapflow/_split0/vol0008.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_04_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/split/mapflow/_split0/vol0009.nii.gz --inittp 1 --iscale --noit --template template.nii.gz --subsample 200 190731-15:19:32,3 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_rest_echo_1_wf.bold_stc_wf.copy_xform". 190731-15:19:32,934 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_rest_echo_1_wf.bold_split" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_rest_echo_1_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-03..func..sub-23649_ses-03_task-rest_echo-3_bold.nii.gz/bold_split". 190731-15:19:32,937 nipype.workflow INFO: [Node] Running "bold_split" ("nipype.interfaces.fsl.utils.Split"), a CommandLine Interface with command: fslsplit /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_rest_echo_1_wf/bold_stc_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-03..func..sub-23649_ses-03_task-rest_echo-3_bold.nii.gz/copy_xform/sub-23649_ses-03_task-rest_echo-3_bold_tshift_xform.nii.gz -t 190731-15:19:33,719 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_mid_run_2_wf.bold_stc_wf.slice_timing_correction". 190731-15:19:34,977 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_mid_run_2_wf.bold_stc_wf.copy_xform" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_2_wf/bold_stc_wf/copy_xform". 190731-15:19:34,979 nipype.workflow INFO: [Node] Running "copy_xform" ("niworkflows.interfaces.utils.CopyXForm") 190731-15:19:35,324 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_rest_echo_1_wf.bold_stc_wf.copy_xform". 190731-15:19:36,622 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_rest_echo_1_wf.bold_stc_wf.slice_timing_correction". 190731-15:19:36,948 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_rest_echo_1_wf.bold_split" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_rest_echo_1_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-03..func..sub-23649_ses-03_task-rest_echo-4_bold.nii.gz/bold_split". 190731-15:19:36,953 nipype.workflow INFO: [Node] Running "bold_split" ("nipype.interfaces.fsl.utils.Split"), a CommandLine Interface with command: fslsplit /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_rest_echo_1_wf/bold_stc_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-03..func..sub-23649_ses-03_task-rest_echo-4_bold.nii.gz/copy_xform/sub-23649_ses-03_task-rest_echo-4_bold_tshift_xform.nii.gz -t 190731-15:19:38,877 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_rest_echo_1_wf.bold_stc_wf.slice_timing_correction". 190731-15:19:38,983 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_mid_run_1_wf.bold_split". 190731-15:19:38,991 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_rest_echo_1_wf.bold_stc_wf.copy_xform" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_rest_echo_1_wf/bold_stc_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-03..func..sub-23649_ses-03_task-rest_echo-2_bold.nii.gz/copy_xform". 190731-15:19:38,994 nipype.workflow INFO: [Node] Running "copy_xform" ("niworkflows.interfaces.utils.CopyXForm") 190731-15:19:39,751 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_04_task_mid_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_opposite_wf.merge". 190731-15:19:40,61 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_mid_wf.bold_split". 190731-15:19:40,969 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_rest_echo_1_wf.bold_stc_wf.copy_xform" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_rest_echo_1_wf/bold_stc_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-03..func..sub-23649_ses-03_task-rest_echo-1_bold.nii.gz/copy_xform". 190731-15:19:40,971 nipype.workflow INFO: [Node] Running "copy_xform" ("niworkflows.interfaces.utils.CopyXForm") 190731-15:19:40,987 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_04_task_rest_echo_1_wf.bold_reference_wf.validate" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_04_task_rest_echo_1_wf/bold_reference_wf/validate". 190731-15:19:40,990 nipype.workflow INFO: [Node] Running "validate" ("niworkflows.interfaces.images.ValidateImage") 190731-15:19:40,991 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.anat_preproc_wf.brain_extraction_wf.res_tmpl" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/anat_preproc_wf/brain_extraction_wf/res_tmpl". 190731-15:19:40,992 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.anat_preproc_wf.brain_extraction_wf.lap_tmpl" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/anat_preproc_wf/brain_extraction_wf/lap_tmpl". 190731-15:19:40,994 nipype.workflow INFO: [Node] Running "res_tmpl" ("niworkflows.interfaces.ants.ResampleImageBySpacing"), a CommandLine Interface with command: ResampleImageBySpacing 3 /home/sahad3/.cache/templateflow/tpl-OASIS30ANTs/tpl-OASIS30ANTs_res-01_T1w.nii.gz tpl-OASIS30ANTs_res-01_T1w_resampled.nii.gz 4 4 4 1 190731-15:19:40,995 nipype.workflow INFO: [Node] Running "lap_tmpl" ("niworkflows.interfaces.ants.ImageMath"), a CommandLine Interface with command: ImageMath 3 tpl-OASIS30ANTs_res-01_T1w_maths.nii.gz Laplacian /home/sahad3/.cache/templateflow/tpl-OASIS30ANTs/tpl-OASIS30ANTs_res-01_T1w.nii.gz 1.5 1 190731-15:19:41,642 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_mid_run_2_wf.bold_stc_wf.copy_xform". 190731-15:19:41,916 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_rest_echo_1_wf.bold_stc_wf.copy_xform". 190731-15:19:42,923 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_mid_run_2_wf.bold_split" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_2_wf/bold_split". 190731-15:19:42,924 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_rest_echo_1_wf.bold_split" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_rest_echo_1_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-03..func..sub-23649_ses-03_task-rest_echo-2_bold.nii.gz/bold_split". 190731-15:19:42,926 nipype.workflow INFO: [Node] Running "bold_split" ("nipype.interfaces.fsl.utils.Split"), a CommandLine Interface with command: fslsplit /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_rest_echo_1_wf/bold_stc_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-03..func..sub-23649_ses-03_task-rest_echo-2_bold.nii.gz/copy_xform/sub-23649_ses-03_task-rest_echo-2_bold_tshift_xform.nii.gz -t 190731-15:19:42,926 nipype.workflow INFO: [Node] Running "bold_split" ("nipype.interfaces.fsl.utils.Split"), a CommandLine Interface with command: fslsplit /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_2_wf/bold_stc_wf/copy_xform/sub-23649_ses-03_task-mid_run-2_bold_valid_tshift_xform.nii.gz -t 190731-15:19:44,112 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_04_task_rest_echo_1_wf.bold_reference_wf.validate". 190731-15:19:44,205 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_rest_echo_1_wf.bold_stc_wf.copy_xform". 190731-15:19:44,808 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_rest_echo_1_wf.bold_split". 190731-15:19:44,945 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_rest_echo_1_wf.bold_split" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_rest_echo_1_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-03..func..sub-23649_ses-03_task-rest_echo-1_bold.nii.gz/bold_split". 190731-15:19:44,948 nipype.workflow INFO: [Node] Running "bold_split" ("nipype.interfaces.fsl.utils.Split"), a CommandLine Interface with command: fslsplit /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_rest_echo_1_wf/bold_stc_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-03..func..sub-23649_ses-03_task-rest_echo-1_bold.nii.gz/copy_xform/sub-23649_ses-03_task-rest_echo-1_bold_tshift_xform.nii.gz -t 190731-15:19:45,573 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_04_task_rest_echo_1_wf.bold_reference_wf.gen_ref" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_04_task_rest_echo_1_wf/bold_reference_wf/gen_ref". 190731-15:19:45,577 nipype.workflow INFO: [Node] Running "gen_ref" ("niworkflows.interfaces.registration.EstimateReferenceImage") 190731-15:19:45,623 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_rest_echo_1_wf.bold_split". 190731-15:19:45,650 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.anat_preproc_wf.brain_extraction_wf.res_tmpl". 190731-15:19:45,961 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_04_task_rest_echo_1_wf.bold_reference_wf.gen_ref". 190731-15:19:46,961 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_04_task_rest_echo_1_wf.bold_hmc_wf.mcflirt" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_04_task_rest_echo_1_wf/bold_hmc_wf/mcflirt". 190731-15:19:46,965 nipype.workflow INFO: [Node] Running "mcflirt" ("nipype.interfaces.fsl.preprocess.MCFLIRT"), a CommandLine Interface with command: mcflirt -in /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_04_task_rest_echo_1_wf/bold_reference_wf/validate/sub-23649_ses-04_task-rest_echo-1_bold_valid.nii.gz -out /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_04_task_rest_echo_1_wf/bold_hmc_wf/mcflirt/sub-23649_ses-04_task-rest_echo-1_bold_valid_mcf.nii.gz -reffile /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_04_task_rest_echo_1_wf/bold_reference_wf/gen_ref/ref_bold.nii.gz -mats -plots 190731-15:19:48,269 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.bidssrc" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/bidssrc". 190731-15:19:48,273 nipype.workflow INFO: [Node] Running "bidssrc" ("niworkflows.interfaces.bids.BIDSDataGrabber") 190731-15:19:48,274 nipype.interface WARNING: No "flair" images found for sub- 190731-15:19:48,274 nipype.interface WARNING: No "sbref" images found for sub- 190731-15:19:48,274 nipype.interface WARNING: No "roi" images found for sub- 190731-15:19:48,288 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.bidssrc". 190731-15:19:50,217 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_mid_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_matching_wf.merge". 190731-15:19:52,231 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_rest_echo_1_wf.bold_split". 190731-15:19:52,778 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_rest_echo_1_wf.bold_split". 190731-15:19:55,468 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_04_task_mid_wf.bold_stc_wf.slice_timing_correction". 190731-15:19:56,88 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.anat_preproc_wf.brain_extraction_wf.lap_tmpl". 190731-15:19:56,404 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_04_task_mid_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_matching_wf.merge". 190731-15:19:57,613 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_mid_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.init_aff" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_mid_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/init_aff". 190731-15:19:57,615 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_04_task_mid_wf.bold_stc_wf.copy_xform" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_04_task_mid_wf/bold_stc_wf/copy_xform". 190731-15:19:57,617 nipype.workflow INFO: [Node] Running "copy_xform" ("niworkflows.interfaces.utils.CopyXForm") 190731-15:19:57,617 nipype.workflow INFO: [Node] Running "init_aff" ("niworkflows.interfaces.ants.AI"), a CommandLine Interface with command: antsAI -c [10,0.000001,10] -d 3 -x /home/sahad3/.cache/templateflow/tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_res-02_desc-brain_mask.nii.gz -m Mattes[/home/sahad3/.cache/templateflow/tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_res-02_desc-fMRIPrep_boldref.nii.gz,/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_mid_wf/bold_reference_wf/gen_ref/ref_bold.nii.gz,32,Regular,0.200000] -o initialization.mat -p 0 -s [20.000000,0.120000] -t Affine[0.100000] -v 1 190731-15:20:00,329 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_mid_run_2_wf.bold_split". 190731-15:20:01,634 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_04_task_rest_echo_1_wf.bold_stc_wf.slice_timing_correction" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_04_task_rest_echo_1_wf/bold_stc_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-04..func..sub-23649_ses-04_task-rest_echo-4_bold.nii.gz/slice_timing_correction". 190731-15:20:01,637 nipype.workflow INFO: [Node] Running "slice_timing_correction" ("nipype.interfaces.afni.preprocess.TShift"), a CommandLine Interface with command: 3dTshift -ignore 4 -prefix sub-23649_ses-04_task-rest_echo-4_bold_tshift.nii.gz -tpattern @slice_timing.1D -TR 2.5s /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_04_task_rest_echo_1_wf/bold_stc_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-04..func..sub-23649_ses-04_task-rest_echo-4_bold.nii.gz/slice_timing_correction/sub-23649_ses-04_task-rest_echo-4_bold.nii.gz 190731-15:20:04,453 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_04_task_mid_wf.bold_stc_wf.copy_xform". 190731-15:20:05,674 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_04_task_mid_wf.bold_split" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_04_task_mid_wf/bold_split". 190731-15:20:05,676 nipype.workflow INFO: [Node] Running "bold_split" ("nipype.interfaces.fsl.utils.Split"), a CommandLine Interface with command: fslsplit /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_04_task_mid_wf/bold_stc_wf/copy_xform/sub-23649_ses-04_task-mid_bold_valid_tshift_xform.nii.gz -t 190731-15:20:09,743 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_mid_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_opposite_wf.merge". 190731-15:20:10,35 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_mid_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.init_aff". 190731-15:20:11,671 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_mid_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.norm" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_mid_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/norm". 190731-15:20:11,674 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_04_task_rest_echo_1_wf.bold_stc_wf.slice_timing_correction" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_04_task_rest_echo_1_wf/bold_stc_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-04..func..sub-23649_ses-04_task-rest_echo-3_bold.nii.gz/slice_timing_correction". 190731-15:20:11,676 nipype.workflow INFO: [Node] Running "norm" ("niworkflows.interfaces.fixes.FixHeaderRegistration"), a CommandLine Interface with command: antsRegistration --collapse-output-transforms 1 --dimensionality 3 --float 1 --initial-moving-transform [ /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_mid_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/init_aff/initialization.mat, 0 ] --initialize-transforms-per-stage 0 --interpolation Linear --output transform --transform Affine[ 0.1 ] --metric Mattes[ /home/sahad3/.cache/templateflow/tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_res-02_desc-fMRIPrep_boldref.nii.gz, /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_mid_wf/bold_reference_wf/gen_ref/ref_bold.nii.gz, 1, 64, Random, 0.2 ] --convergence [ 200, 1e-09, 10 ] --smoothing-sigmas 2.0mm --shrink-factors 2 --use-estimate-learning-rate-once 1 --use-histogram-matching 1 --winsorize-image-intensities [ 0.05, 0.98 ] --write-composite-transform 0 190731-15:20:11,679 nipype.workflow INFO: [Node] Running "slice_timing_correction" ("nipype.interfaces.afni.preprocess.TShift"), a CommandLine Interface with command: 3dTshift -ignore 4 -prefix sub-23649_ses-04_task-rest_echo-3_bold_tshift.nii.gz -tpattern @slice_timing.1D -TR 2.5s /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_04_task_rest_echo_1_wf/bold_stc_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-04..func..sub-23649_ses-04_task-rest_echo-3_bold.nii.gz/slice_timing_correction/sub-23649_ses-04_task-rest_echo-3_bold.nii.gz 190731-15:20:13,151 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_04_task_rest_echo_1_wf.bold_stc_wf.slice_timing_correction". 190731-15:20:13,900 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_mid_run_2_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_matching_wf.merge". 190731-15:20:14,920 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_mid_run_1_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_matching_wf.merge". 190731-15:20:15,423 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_mid_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.norm". 190731-15:20:15,619 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_04_task_rest_echo_1_wf.bold_stc_wf.copy_xform" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_04_task_rest_echo_1_wf/bold_stc_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-04..func..sub-23649_ses-04_task-rest_echo-4_bold.nii.gz/copy_xform". 190731-15:20:15,622 nipype.workflow INFO: [Node] Running "copy_xform" ("niworkflows.interfaces.utils.CopyXForm") 190731-15:20:15,623 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_04_task_rest_echo_1_wf.bold_stc_wf.slice_timing_correction" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_04_task_rest_echo_1_wf/bold_stc_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-04..func..sub-23649_ses-04_task-rest_echo-2_bold.nii.gz/slice_timing_correction". 190731-15:20:15,628 nipype.workflow INFO: [Node] Running "slice_timing_correction" ("nipype.interfaces.afni.preprocess.TShift"), a CommandLine Interface with command: 3dTshift -ignore 4 -prefix sub-23649_ses-04_task-rest_echo-2_bold_tshift.nii.gz -tpattern @slice_timing.1D -TR 2.5s /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_04_task_rest_echo_1_wf/bold_stc_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-04..func..sub-23649_ses-04_task-rest_echo-2_bold.nii.gz/slice_timing_correction/sub-23649_ses-04_task-rest_echo-2_bold.nii.gz 190731-15:20:15,635 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_04_task_rest_echo_1_wf.bold_stc_wf.slice_timing_correction" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_04_task_rest_echo_1_wf/bold_stc_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-04..func..sub-23649_ses-04_task-rest_echo-1_bold.nii.gz/slice_timing_correction". 190731-15:20:15,641 nipype.workflow INFO: [Node] Running "slice_timing_correction" ("nipype.interfaces.afni.preprocess.TShift"), a CommandLine Interface with command: 3dTshift -ignore 4 -prefix sub-23649_ses-04_task-rest_echo-1_bold_tshift.nii.gz -tpattern @slice_timing.1D -TR 2.5s /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_04_task_rest_echo_1_wf/bold_stc_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-04..func..sub-23649_ses-04_task-rest_echo-1_bold.nii.gz/slice_timing_correction/sub-23649_ses-04_task-rest_echo-1_bold.nii.gz 190731-15:20:17,583 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_mid_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.map_brainmask" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_mid_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/map_brainmask". 190731-15:20:17,586 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.anat_preproc_wf.brain_extraction_wf.mrg_tmpl" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/anat_preproc_wf/brain_extraction_wf/mrg_tmpl". 190731-15:20:17,586 nipype.workflow INFO: [Node] Running "map_brainmask" ("niworkflows.interfaces.fixes.FixHeaderApplyTransforms"), a CommandLine Interface with command: antsApplyTransforms --default-value 0 --float 1 --input /home/sahad3/.cache/templateflow/tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_res-02_desc-brain_mask.nii.gz --interpolation MultiLabel --output tpl-MNI152NLin2009cAsym_res-02_desc-brain_mask_trans.nii.gz --reference-image /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_mid_wf/bold_reference_wf/gen_ref/ref_bold.nii.gz --transform [ /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_mid_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/norm/transform0GenericAffine.mat, 1 ] 190731-15:20:17,589 nipype.workflow INFO: [Node] Running "mrg_tmpl" ("nipype.interfaces.utility.base.Merge") 190731-15:20:17,595 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.anat_preproc_wf.brain_extraction_wf.mrg_tmpl". 190731-15:20:17,605 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.anat_preproc_wf.anat_template_wf.t1_template_dimensions" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/anat_preproc_wf/anat_template_wf/t1_template_dimensions". 190731-15:20:17,608 nipype.workflow INFO: [Node] Running "t1_template_dimensions" ("niworkflows.interfaces.images.TemplateDimensions") 190731-15:20:17,689 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_04_task_rest_echo_1_wf.bold_stc_wf.copy_xform". 190731-15:20:17,997 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.anat_preproc_wf.anat_template_wf.t1_template_dimensions". 190731-15:20:18,159 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.bids_info" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/bids_info". 190731-15:20:18,161 nipype.workflow INFO: [Node] Running "bids_info" ("niworkflows.interfaces.bids.BIDSInfo") 190731-15:20:19,671 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_04_task_rest_echo_1_wf.bold_split" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_04_task_rest_echo_1_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-04..func..sub-23649_ses-04_task-rest_echo-4_bold.nii.gz/bold_split". 190731-15:20:19,675 nipype.workflow INFO: [Node] Running "bold_split" ("nipype.interfaces.fsl.utils.Split"), a CommandLine Interface with command: fslsplit /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_04_task_rest_echo_1_wf/bold_stc_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-04..func..sub-23649_ses-04_task-rest_echo-4_bold.nii.gz/copy_xform/sub-23649_ses-04_task-rest_echo-4_bold_tshift_xform.nii.gz -t 190731-15:20:20,279 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.anat_preproc_wf.anat_derivatives_wf.raw_sources" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/anat_preproc_wf/anat_derivatives_wf/raw_sources". 190731-15:20:20,281 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.anat_preproc_wf.anat_derivatives_wf.t1_name" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/anat_preproc_wf/anat_derivatives_wf/t1_name". 190731-15:20:20,282 nipype.workflow INFO: [Node] Running "raw_sources" ("nipype.interfaces.utility.wrappers.Function") 190731-15:20:20,283 nipype.workflow INFO: [Node] Running "t1_name" ("nipype.interfaces.utility.wrappers.Function") 190731-15:20:20,286 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.anat_preproc_wf.anat_derivatives_wf.t1_name". 190731-15:20:20,287 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.anat_preproc_wf.anat_derivatives_wf.raw_sources". 190731-15:20:20,769 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_mid_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.map_brainmask". 190731-15:20:21,613 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_mid_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.pre_mask_dilate" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_mid_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/pre_mask_dilate". 190731-15:20:21,618 nipype.workflow INFO: [Node] Running "pre_mask_dilate" ("nipype.interfaces.fsl.maths.DilateImage"), a CommandLine Interface with command: fslmaths -dt char /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_mid_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/map_brainmask/tpl-MNI152NLin2009cAsym_res-02_desc-brain_mask_trans.nii.gz -kernel sphere 3.0000 -dilF /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_mid_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/pre_mask_dilate/tpl-MNI152NLin2009cAsym_res-02_desc-brain_mask_trans_dil.nii.gz 190731-15:20:21,620 nipype.workflow INFO: [Node] Setting-up "_t1_conform0" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/anat_preproc_wf/anat_template_wf/t1_conform/mapflow/_t1_conform0". 190731-15:20:21,623 nipype.workflow INFO: [Node] Running "_t1_conform0" ("niworkflows.interfaces.images.Conform") 190731-15:20:21,637 nipype.workflow INFO: [Node] Setting-up "_t1_conform2" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/anat_preproc_wf/anat_template_wf/t1_conform/mapflow/_t1_conform2". 190731-15:20:21,639 nipype.workflow INFO: [Node] Running "_t1_conform2" ("niworkflows.interfaces.images.Conform") 190731-15:20:21,643 nipype.workflow INFO: [Node] Setting-up "_t1_conform1" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/anat_preproc_wf/anat_template_wf/t1_conform/mapflow/_t1_conform1". 190731-15:20:21,646 nipype.workflow INFO: [Node] Running "_t1_conform1" ("niworkflows.interfaces.images.Conform") 190731-15:20:21,663 nipype.workflow INFO: [Node] Setting-up "_t1_conform3" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/anat_preproc_wf/anat_template_wf/t1_conform/mapflow/_t1_conform3". 190731-15:20:21,665 nipype.workflow INFO: [Node] Running "_t1_conform3" ("niworkflows.interfaces.images.Conform") 190731-15:20:21,695 nipype.workflow INFO: [Node] Finished "_t1_conform1". 190731-15:20:21,703 nipype.workflow INFO: [Node] Finished "_t1_conform0". 190731-15:20:21,726 nipype.workflow INFO: [Node] Finished "_t1_conform3". 190731-15:20:21,950 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_mid_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.pre_mask_dilate". 190731-15:20:22,609 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_04_task_rest_echo_1_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_matching_wf.merge". 190731-15:20:23,141 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_04_task_rest_echo_1_wf.bold_stc_wf.slice_timing_correction". 190731-15:20:23,278 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_mid_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_opposite_wf.merge". 190731-15:20:23,398 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_04_task_mid_wf.bold_split". 190731-15:20:23,851 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_rest_echo_1_wf.bold_hmc_wf.mcflirt". 190731-15:20:24,860 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_mid_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_matching_wf.merge". 190731-15:20:25,520 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_mid_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.n4_correct" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_mid_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/n4_correct". 190731-15:20:25,523 nipype.workflow INFO: [Node] Running "n4_correct" ("nipype.interfaces.ants.segmentation.N4BiasFieldCorrection"), a CommandLine Interface with command: N4BiasFieldCorrection --bspline-fitting [ 200 ] -d 3 --input-image /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_mid_wf/bold_reference_wf/gen_ref/ref_bold.nii.gz --mask-image /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_mid_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/check_hdr/tpl-MNI152NLin2009cAsym_res-02_desc-brain_mask_trans_dil_hdr.nii.gz --output ref_bold_corrected.nii.gz 190731-15:20:25,523 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_rest_echo_1_wf.bold_hmc_wf.normalize_motion" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_rest_echo_1_wf/bold_hmc_wf/normalize_motion". 190731-15:20:25,525 nipype.workflow INFO: [Node] Running "normalize_motion" ("niworkflows.interfaces.utils.NormalizeMotionParams") 190731-15:20:25,529 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_mid_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_opposite_wf.enhance_and_skullstrip_bold_wf.init_aff" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_mid_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/enhance_and_skullstrip_bold_wf/init_aff". 190731-15:20:25,531 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_04_task_rest_echo_1_wf.bold_stc_wf.copy_xform" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_04_task_rest_echo_1_wf/bold_stc_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-04..func..sub-23649_ses-04_task-rest_echo-3_bold.nii.gz/copy_xform". 190731-15:20:25,532 nipype.workflow INFO: [Node] Running "init_aff" ("niworkflows.interfaces.ants.AI"), a CommandLine Interface with command: antsAI -c [10,0.000001,10] -d 3 -x /home/sahad3/.cache/templateflow/tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_res-02_desc-brain_mask.nii.gz -m Mattes[/home/sahad3/.cache/templateflow/tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_res-02_desc-fMRIPrep_boldref.nii.gz,/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_mid_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/merge/template.nii.gz,32,Regular,0.200000] -o initialization.mat -p 0 -s [20.000000,0.120000] -t Affine[0.100000] -v 1 190731-15:20:25,534 nipype.workflow INFO: [Node] Running "copy_xform" ("niworkflows.interfaces.utils.CopyXForm") 190731-15:20:25,539 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_rest_echo_1_wf.bold_hmc_wf.normalize_motion". 190731-15:20:26,655 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_04_task_rest_echo_1_wf.bold_stc_wf.slice_timing_correction". 190731-15:20:27,486 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_mid_wf.bold_hmc_wf.mcflirt". 190731-15:20:27,932 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_04_task_rest_echo_1_wf.bold_stc_wf.copy_xform". 190731-15:20:28,101 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_rest_echo_1_wf.bold_confounds_wf.fdisp" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_rest_echo_1_wf/bold_confounds_wf/fdisp". 190731-15:20:28,103 nipype.workflow INFO: [Node] Running "fdisp" ("nipype.algorithms.confounds.FramewiseDisplacement") 190731-15:20:28,109 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_04_task_rest_echo_1_wf.bold_stc_wf.copy_xform" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_04_task_rest_echo_1_wf/bold_stc_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-04..func..sub-23649_ses-04_task-rest_echo-1_bold.nii.gz/copy_xform". 190731-15:20:28,111 nipype.workflow INFO: [Node] Running "copy_xform" ("niworkflows.interfaces.utils.CopyXForm") 190731-15:20:28,115 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_rest_echo_1_wf.bold_confounds_wf.fdisp". 190731-15:20:28,489 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_mid_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.n4_correct". 190731-15:20:28,560 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_04_task_rest_echo_1_wf.bold_split". 190731-15:20:29,465 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_04_task_rest_echo_1_wf.bold_stc_wf.slice_timing_correction". 190731-15:20:29,532 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_mid_wf.bold_hmc_wf.normalize_motion" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_mid_wf/bold_hmc_wf/normalize_motion". 190731-15:20:29,534 nipype.workflow INFO: [Node] Running "normalize_motion" ("niworkflows.interfaces.utils.NormalizeMotionParams") 190731-15:20:29,534 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_mid_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_pass" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_mid_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_pass". 190731-15:20:29,536 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_04_task_rest_echo_1_wf.bold_split" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_04_task_rest_echo_1_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-04..func..sub-23649_ses-04_task-rest_echo-3_bold.nii.gz/bold_split". 190731-15:20:29,538 nipype.workflow INFO: [Node] Running "bold_split" ("nipype.interfaces.fsl.utils.Split"), a CommandLine Interface with command: fslsplit /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_04_task_rest_echo_1_wf/bold_stc_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-04..func..sub-23649_ses-04_task-rest_echo-3_bold.nii.gz/copy_xform/sub-23649_ses-04_task-rest_echo-3_bold_tshift_xform.nii.gz -t 190731-15:20:29,538 nipype.workflow INFO: [Node] Running "skullstrip_first_pass" ("nipype.interfaces.fsl.preprocess.BET"), a CommandLine Interface with command: bet /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_mid_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/n4_correct/ref_bold_corrected.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_mid_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_pass/ref_bold_corrected_brain.nii.gz -f 0.20 -m 190731-15:20:29,555 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_mid_wf.bold_hmc_wf.normalize_motion". 190731-15:20:29,910 nipype.workflow INFO: [Node] Finished "_t1_conform2". 190731-15:20:30,829 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_04_task_rest_echo_1_wf.bold_stc_wf.copy_xform". 190731-15:20:31,613 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_mid_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_pass". 190731-15:20:31,987 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_mid_wf.bold_confounds_wf.fdisp" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_mid_wf/bold_confounds_wf/fdisp". 190731-15:20:31,989 nipype.workflow INFO: [Node] Running "fdisp" ("nipype.algorithms.confounds.FramewiseDisplacement") 190731-15:20:31,995 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_04_task_rest_echo_1_wf.bold_stc_wf.copy_xform" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_04_task_rest_echo_1_wf/bold_stc_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-04..func..sub-23649_ses-04_task-rest_echo-2_bold.nii.gz/copy_xform". 190731-15:20:31,998 nipype.workflow INFO: [Node] Running "copy_xform" ("niworkflows.interfaces.utils.CopyXForm") 190731-15:20:31,998 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_04_task_rest_echo_1_wf.bold_split" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_04_task_rest_echo_1_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-04..func..sub-23649_ses-04_task-rest_echo-1_bold.nii.gz/bold_split". 190731-15:20:32,1 nipype.workflow INFO: [Node] Running "bold_split" ("nipype.interfaces.fsl.utils.Split"), a CommandLine Interface with command: fslsplit /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_04_task_rest_echo_1_wf/bold_stc_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-04..func..sub-23649_ses-04_task-rest_echo-1_bold.nii.gz/copy_xform/sub-23649_ses-04_task-rest_echo-1_bold_tshift_xform.nii.gz -t 190731-15:20:32,2 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_mid_wf.bold_confounds_wf.fdisp". 190731-15:20:32,10 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.anat_preproc_wf.anat_template_wf.t1_conform" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/anat_preproc_wf/anat_template_wf/t1_conform". 190731-15:20:32,14 nipype.workflow INFO: [Node] Setting-up "_t1_conform0" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/anat_preproc_wf/anat_template_wf/t1_conform/mapflow/_t1_conform0". 190731-15:20:32,15 nipype.workflow INFO: [Node] Cached "_t1_conform0" - collecting precomputed outputs 190731-15:20:32,15 nipype.workflow INFO: [Node] "_t1_conform0" found cached. 190731-15:20:32,17 nipype.workflow INFO: [Node] Setting-up "_t1_conform1" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/anat_preproc_wf/anat_template_wf/t1_conform/mapflow/_t1_conform1". 190731-15:20:32,18 nipype.workflow INFO: [Node] Cached "_t1_conform1" - collecting precomputed outputs 190731-15:20:32,18 nipype.workflow INFO: [Node] "_t1_conform1" found cached. 190731-15:20:32,20 nipype.workflow INFO: [Node] Setting-up "_t1_conform2" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/anat_preproc_wf/anat_template_wf/t1_conform/mapflow/_t1_conform2". 190731-15:20:32,21 nipype.workflow INFO: [Node] Cached "_t1_conform2" - collecting precomputed outputs 190731-15:20:32,21 nipype.workflow INFO: [Node] "_t1_conform2" found cached. 190731-15:20:32,23 nipype.workflow INFO: [Node] Setting-up "_t1_conform3" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/anat_preproc_wf/anat_template_wf/t1_conform/mapflow/_t1_conform3". 190731-15:20:32,24 nipype.workflow INFO: [Node] Cached "_t1_conform3" - collecting precomputed outputs 190731-15:20:32,24 nipype.workflow INFO: [Node] "_t1_conform3" found cached. 190731-15:20:32,28 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.anat_preproc_wf.anat_template_wf.t1_conform". 190731-15:20:32,706 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.bids_info". 190731-15:20:32,738 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_04_task_rest_echo_1_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_opposite_wf.merge". 190731-15:20:32,824 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_mid_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_opposite_wf.enhance_and_skullstrip_bold_wf.init_aff". 190731-15:20:33,517 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_mid_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_opposite_wf.enhance_and_skullstrip_bold_wf.norm" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_mid_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/enhance_and_skullstrip_bold_wf/norm". 190731-15:20:33,522 nipype.workflow INFO: [Node] Running "norm" ("niworkflows.interfaces.fixes.FixHeaderRegistration"), a CommandLine Interface with command: antsRegistration --collapse-output-transforms 1 --dimensionality 3 --float 1 --initial-moving-transform [ /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_mid_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/enhance_and_skullstrip_bold_wf/init_aff/initialization.mat, 0 ] --initialize-transforms-per-stage 0 --interpolation Linear --output transform --transform Affine[ 0.1 ] --metric Mattes[ /home/sahad3/.cache/templateflow/tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_res-02_desc-fMRIPrep_boldref.nii.gz, /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_mid_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/merge/template.nii.gz, 1, 64, Random, 0.2 ] --convergence [ 200, 1e-09, 10 ] --smoothing-sigmas 2.0mm --shrink-factors 2 --use-estimate-learning-rate-once 1 --use-histogram-matching 1 --winsorize-image-intensities [ 0.05, 0.98 ] --write-composite-transform 0 190731-15:20:33,535 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_mid_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_matching_wf.enhance_and_skullstrip_bold_wf.init_aff" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_mid_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/enhance_and_skullstrip_bold_wf/init_aff". 190731-15:20:33,539 nipype.workflow INFO: [Node] Running "init_aff" ("niworkflows.interfaces.ants.AI"), a CommandLine Interface with command: antsAI -c [10,0.000001,10] -d 3 -x /home/sahad3/.cache/templateflow/tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_res-02_desc-brain_mask.nii.gz -m Mattes[/home/sahad3/.cache/templateflow/tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_res-02_desc-fMRIPrep_boldref.nii.gz,/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_mid_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/merge/template.nii.gz,32,Regular,0.200000] -o initialization.mat -p 0 -s [20.000000,0.120000] -t Affine[0.100000] -v 1 190731-15:20:34,319 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_04_task_rest_echo_1_wf.bold_stc_wf.copy_xform". 190731-15:20:35,113 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_mid_run_1_wf.bold_hmc_wf.mcflirt". 190731-15:20:35,576 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_mid_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_dilate" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_mid_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_dilate". 190731-15:20:35,580 nipype.workflow INFO: [Node] Running "skullstrip_first_dilate" ("nipype.interfaces.fsl.maths.DilateImage"), a CommandLine Interface with command: fslmaths -dt char /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_mid_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_pass/ref_bold_corrected_brain_mask.nii.gz -kernel sphere 6.0000 -dilF /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_mid_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_dilate/ref_bold_corrected_brain_mask_dil.nii.gz 190731-15:20:35,887 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_mid_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_opposite_wf.enhance_and_skullstrip_bold_wf.norm". 190731-15:20:36,98 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_04_task_rest_echo_1_wf.bold_split". 190731-15:20:36,195 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_mid_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_dilate". 190731-15:20:37,514 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_mid_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_opposite_wf.enhance_and_skullstrip_bold_wf.map_brainmask" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_mid_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/enhance_and_skullstrip_bold_wf/map_brainmask". 190731-15:20:37,518 nipype.workflow INFO: [Node] Running "map_brainmask" ("niworkflows.interfaces.fixes.FixHeaderApplyTransforms"), a CommandLine Interface with command: antsApplyTransforms --default-value 0 --float 1 --input /home/sahad3/.cache/templateflow/tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_res-02_desc-brain_mask.nii.gz --interpolation MultiLabel --output tpl-MNI152NLin2009cAsym_res-02_desc-brain_mask_trans.nii.gz --reference-image /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_mid_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/merge/template.nii.gz --transform [ /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_mid_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/enhance_and_skullstrip_bold_wf/norm/transform0GenericAffine.mat, 1 ] 190731-15:20:37,542 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_mid_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_mask" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_mid_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_mask". 190731-15:20:37,545 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_mid_run_1_wf.bold_hmc_wf.normalize_motion" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_1_wf/bold_hmc_wf/normalize_motion". 190731-15:20:37,546 nipype.workflow INFO: [Node] Running "skullstrip_first_mask" ("nipype.interfaces.fsl.maths.ApplyMask"), a CommandLine Interface with command: fslmaths /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_mid_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_pass/ref_bold_corrected_brain.nii.gz -mas /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_mid_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_dilate/ref_bold_corrected_brain_mask_dil.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_mid_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_mask/ref_bold_corrected_brain_masked.nii.gz 190731-15:20:37,546 nipype.workflow INFO: [Node] Running "normalize_motion" ("niworkflows.interfaces.utils.NormalizeMotionParams") 190731-15:20:37,550 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_mid_wf.bold_hmc_wf.fsl2itk" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_mid_wf/bold_hmc_wf/fsl2itk". 190731-15:20:37,555 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_mid_run_1_wf.bold_hmc_wf.normalize_motion". 190731-15:20:37,564 nipype.workflow INFO: [Node] Running "fsl2itk" ("niworkflows.interfaces.itk.MCFLIRT2ITK") 190731-15:20:37,679 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_mid_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_mask". 190731-15:20:38,112 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_04_task_rest_echo_1_wf.bold_split". 190731-15:20:39,68 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_mid_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_matching_wf.enhance_and_skullstrip_bold_wf.init_aff". 190731-15:20:39,534 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_mid_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.unifize" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_mid_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/unifize". 190731-15:20:39,536 nipype.workflow INFO: [Node] Running "unifize" ("nipype.interfaces.afni.utils.Unifize"), a CommandLine Interface with command: 3dUnifize -clfrac 0.2 -rbt 18.3 65.0 90.0 -prefix uni.nii.gz -T2 -input /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_mid_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/unifize/ref_bold_corrected_brain_masked.nii.gz 190731-15:20:39,960 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_mid_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_opposite_wf.enhance_and_skullstrip_bold_wf.map_brainmask". 190731-15:20:40,14 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_mid_run_1_wf.bold_confounds_wf.fdisp" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_1_wf/bold_confounds_wf/fdisp". 190731-15:20:40,15 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_04_task_rest_echo_1_wf.bold_split" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_04_task_rest_echo_1_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-04..func..sub-23649_ses-04_task-rest_echo-2_bold.nii.gz/bold_split". 190731-15:20:40,16 nipype.workflow INFO: [Node] Running "fdisp" ("nipype.algorithms.confounds.FramewiseDisplacement") 190731-15:20:40,18 nipype.workflow INFO: [Node] Running "bold_split" ("nipype.interfaces.fsl.utils.Split"), a CommandLine Interface with command: fslsplit /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_04_task_rest_echo_1_wf/bold_stc_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-04..func..sub-23649_ses-04_task-rest_echo-2_bold.nii.gz/copy_xform/sub-23649_ses-04_task-rest_echo-2_bold_tshift_xform.nii.gz -t 190731-15:20:40,24 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_mid_run_1_wf.bold_confounds_wf.fdisp". 190731-15:20:40,959 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_mid_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.unifize". 190731-15:20:41,525 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_mid_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_opposite_wf.enhance_and_skullstrip_bold_wf.pre_mask_dilate" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_mid_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/enhance_and_skullstrip_bold_wf/pre_mask_dilate". 190731-15:20:41,527 nipype.workflow INFO: [Node] Running "pre_mask_dilate" ("nipype.interfaces.fsl.maths.DilateImage"), a CommandLine Interface with command: fslmaths -dt char /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_mid_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/enhance_and_skullstrip_bold_wf/map_brainmask/tpl-MNI152NLin2009cAsym_res-02_desc-brain_mask_trans.nii.gz -kernel sphere 3.0000 -dilF /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_mid_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/enhance_and_skullstrip_bold_wf/pre_mask_dilate/tpl-MNI152NLin2009cAsym_res-02_desc-brain_mask_trans_dil.nii.gz 190731-15:20:41,530 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_mid_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_matching_wf.enhance_and_skullstrip_bold_wf.norm" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_mid_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/enhance_and_skullstrip_bold_wf/norm". 190731-15:20:41,531 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_mid_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.fixhdr_unifize" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_mid_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/fixhdr_unifize". 190731-15:20:41,533 nipype.workflow INFO: [Node] Running "fixhdr_unifize" ("niworkflows.interfaces.utils.CopyXForm") 190731-15:20:41,534 nipype.workflow INFO: [Node] Running "norm" ("niworkflows.interfaces.fixes.FixHeaderRegistration"), a CommandLine Interface with command: antsRegistration --collapse-output-transforms 1 --dimensionality 3 --float 1 --initial-moving-transform [ /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_mid_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/enhance_and_skullstrip_bold_wf/init_aff/initialization.mat, 0 ] --initialize-transforms-per-stage 0 --interpolation Linear --output transform --transform Affine[ 0.1 ] --metric Mattes[ /home/sahad3/.cache/templateflow/tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_res-02_desc-fMRIPrep_boldref.nii.gz, /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_mid_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/merge/template.nii.gz, 1, 64, Random, 0.2 ] --convergence [ 200, 1e-09, 10 ] --smoothing-sigmas 2.0mm --shrink-factors 2 --use-estimate-learning-rate-once 1 --use-histogram-matching 1 --winsorize-image-intensities [ 0.05, 0.98 ] --write-composite-transform 0 190731-15:20:41,569 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_mid_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.fixhdr_unifize". 190731-15:20:41,721 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_mid_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_opposite_wf.enhance_and_skullstrip_bold_wf.pre_mask_dilate". 190731-15:20:42,145 nipype.workflow INFO: [Node] Setting-up "_n4_correct0" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/anat_preproc_wf/anat_template_wf/n4_correct/mapflow/_n4_correct0". 190731-15:20:42,149 nipype.workflow INFO: [Node] Running "_n4_correct0" ("nipype.interfaces.ants.segmentation.N4BiasFieldCorrection"), a CommandLine Interface with command: N4BiasFieldCorrection -d 3 --input-image /gs11/users/MBDU/bids/mid_longitudinal_20190717/sub-23649/ses-01/anat/sub-23649_ses-01_acq-mprage_rec-ORIG_T1w.nii.gz --output sub-23649_ses-01_acq-mprage_rec-ORIG_T1w_corrected.nii.gz 190731-15:20:42,647 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_mid_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_matching_wf.enhance_and_skullstrip_bold_wf.norm". 190731-15:20:44,124 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_mid_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_matching_wf.enhance_and_skullstrip_bold_wf.map_brainmask" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_mid_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/enhance_and_skullstrip_bold_wf/map_brainmask". 190731-15:20:44,125 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_mid_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.skullstrip_second_pass" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_mid_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_second_pass". 190731-15:20:44,127 nipype.workflow INFO: [Node] Running "map_brainmask" ("niworkflows.interfaces.fixes.FixHeaderApplyTransforms"), a CommandLine Interface with command: antsApplyTransforms --default-value 0 --float 1 --input /home/sahad3/.cache/templateflow/tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_res-02_desc-brain_mask.nii.gz --interpolation MultiLabel --output tpl-MNI152NLin2009cAsym_res-02_desc-brain_mask_trans.nii.gz --reference-image /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_mid_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/merge/template.nii.gz --transform [ /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_mid_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/enhance_and_skullstrip_bold_wf/norm/transform0GenericAffine.mat, 1 ] 190731-15:20:44,128 nipype.workflow INFO: [Node] Running "skullstrip_second_pass" ("nipype.interfaces.afni.preprocess.Automask"), a CommandLine Interface with command: 3dAutomask -apply_prefix uni_xform_masked.nii.gz -dilate 1 -prefix uni_xform_mask.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_mid_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_second_pass/uni_xform.nii.gz 190731-15:20:44,138 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_opposite_wf.enhance_and_skullstrip_bold_wf.init_aff" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/enhance_and_skullstrip_bold_wf/init_aff". 190731-15:20:44,141 nipype.workflow INFO: [Node] Running "init_aff" ("niworkflows.interfaces.ants.AI"), a CommandLine Interface with command: antsAI -c [10,0.000001,10] -d 3 -x /home/sahad3/.cache/templateflow/tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_res-02_desc-brain_mask.nii.gz -m Mattes[/home/sahad3/.cache/templateflow/tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_res-02_desc-fMRIPrep_boldref.nii.gz,/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/merge/template.nii.gz,32,Regular,0.200000] -o initialization.mat -p 0 -s [20.000000,0.120000] -t Affine[0.100000] -v 1 190731-15:20:44,355 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_mid_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.skullstrip_second_pass". 190731-15:20:45,531 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_mid_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_opposite_wf.enhance_and_skullstrip_bold_wf.n4_correct" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_mid_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/enhance_and_skullstrip_bold_wf/n4_correct". 190731-15:20:45,534 nipype.workflow INFO: [Node] Running "n4_correct" ("nipype.interfaces.ants.segmentation.N4BiasFieldCorrection"), a CommandLine Interface with command: N4BiasFieldCorrection --bspline-fitting [ 200 ] -d 3 --input-image /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_mid_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/merge/template.nii.gz --mask-image /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_mid_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/enhance_and_skullstrip_bold_wf/check_hdr/tpl-MNI152NLin2009cAsym_res-02_desc-brain_mask_trans_dil_hdr.nii.gz --output template_corrected.nii.gz 190731-15:20:46,468 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_04_task_rest_echo_1_wf.bold_split". 190731-15:20:46,492 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_mid_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_matching_wf.enhance_and_skullstrip_bold_wf.map_brainmask". 190731-15:20:47,517 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_mid_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_matching_wf.enhance_and_skullstrip_bold_wf.pre_mask_dilate" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_mid_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/enhance_and_skullstrip_bold_wf/pre_mask_dilate". 190731-15:20:47,518 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_mid_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.fixhdr_skullstrip2" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_mid_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/fixhdr_skullstrip2". 190731-15:20:47,520 nipype.workflow INFO: [Node] Running "fixhdr_skullstrip2" ("niworkflows.interfaces.utils.CopyXForm") 190731-15:20:47,520 nipype.workflow INFO: [Node] Running "pre_mask_dilate" ("nipype.interfaces.fsl.maths.DilateImage"), a CommandLine Interface with command: fslmaths -dt char /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_mid_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/enhance_and_skullstrip_bold_wf/map_brainmask/tpl-MNI152NLin2009cAsym_res-02_desc-brain_mask_trans.nii.gz -kernel sphere 3.0000 -dilF /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_mid_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/enhance_and_skullstrip_bold_wf/pre_mask_dilate/tpl-MNI152NLin2009cAsym_res-02_desc-brain_mask_trans_dil.nii.gz 190731-15:20:47,544 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_mid_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.fixhdr_skullstrip2". 190731-15:20:47,739 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_mid_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_matching_wf.enhance_and_skullstrip_bold_wf.pre_mask_dilate". 190731-15:20:48,275 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_mid_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_opposite_wf.enhance_and_skullstrip_bold_wf.n4_correct". 190731-15:20:49,548 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_mid_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_opposite_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_pass" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_mid_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_pass". 190731-15:20:49,551 nipype.workflow INFO: [Node] Running "skullstrip_first_pass" ("nipype.interfaces.fsl.preprocess.BET"), a CommandLine Interface with command: bet /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_mid_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/enhance_and_skullstrip_bold_wf/n4_correct/template_corrected.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_mid_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_pass/template_corrected_brain.nii.gz -f 0.20 -m 190731-15:20:49,821 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_opposite_wf.enhance_and_skullstrip_bold_wf.init_aff". 190731-15:20:50,84 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_mid_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.combine_masks" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_mid_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/combine_masks". 190731-15:20:50,86 nipype.workflow INFO: [Node] Running "combine_masks" ("nipype.interfaces.fsl.maths.BinaryMaths"), a CommandLine Interface with command: fslmaths /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_mid_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_pass/ref_bold_corrected_brain_mask.nii.gz -mul /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_mid_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/fixhdr_skullstrip2/uni_xform_mask_xform.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_mid_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/combine_masks/ref_bold_corrected_brain_mask_maths.nii.gz 190731-15:20:50,209 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_mid_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.combine_masks". 190731-15:20:50,587 nipype.workflow INFO: [Node] Setting-up "_n4_correct1" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/anat_preproc_wf/anat_template_wf/n4_correct/mapflow/_n4_correct1". 190731-15:20:50,591 nipype.workflow INFO: [Node] Running "_n4_correct1" ("nipype.interfaces.ants.segmentation.N4BiasFieldCorrection"), a CommandLine Interface with command: N4BiasFieldCorrection -d 3 --input-image /gs11/users/MBDU/bids/mid_longitudinal_20190717/sub-23649/ses-02/anat/sub-23649_ses-02_acq-mprage_rec-ORIG_T1w.nii.gz --output sub-23649_ses-02_acq-mprage_rec-ORIG_T1w_corrected.nii.gz 190731-15:20:50,671 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_04_task_rest_echo_1_wf.bold_hmc_wf.mcflirt". 190731-15:20:51,529 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_mid_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_matching_wf.enhance_and_skullstrip_bold_wf.n4_correct" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_mid_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/enhance_and_skullstrip_bold_wf/n4_correct". 190731-15:20:51,531 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_mid_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.apply_mask" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_mid_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/apply_mask". 190731-15:20:51,531 nipype.workflow INFO: [Node] Running "n4_correct" ("nipype.interfaces.ants.segmentation.N4BiasFieldCorrection"), a CommandLine Interface with command: N4BiasFieldCorrection --bspline-fitting [ 200 ] -d 3 --input-image /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_mid_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/merge/template.nii.gz --mask-image /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_mid_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/enhance_and_skullstrip_bold_wf/check_hdr/tpl-MNI152NLin2009cAsym_res-02_desc-brain_mask_trans_dil_hdr.nii.gz --output template_corrected.nii.gz 190731-15:20:51,533 nipype.workflow INFO: [Node] Running "apply_mask" ("nipype.interfaces.fsl.maths.ApplyMask"), a CommandLine Interface with command: fslmaths /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_mid_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/fixhdr_unifize/uni_xform.nii.gz -mas /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_mid_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/combine_masks/ref_bold_corrected_brain_mask_maths.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_mid_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/apply_mask/uni_xform_masked.nii.gz 190731-15:20:51,536 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_opposite_wf.enhance_and_skullstrip_bold_wf.norm" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/enhance_and_skullstrip_bold_wf/norm". 190731-15:20:51,540 nipype.workflow INFO: [Node] Running "norm" ("niworkflows.interfaces.fixes.FixHeaderRegistration"), a CommandLine Interface with command: antsRegistration --collapse-output-transforms 1 --dimensionality 3 --float 1 --initial-moving-transform [ /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/enhance_and_skullstrip_bold_wf/init_aff/initialization.mat, 0 ] --initialize-transforms-per-stage 0 --interpolation Linear --output transform --transform Affine[ 0.1 ] --metric Mattes[ /home/sahad3/.cache/templateflow/tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_res-02_desc-fMRIPrep_boldref.nii.gz, /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/merge/template.nii.gz, 1, 64, Random, 0.2 ] --convergence [ 200, 1e-09, 10 ] --smoothing-sigmas 2.0mm --shrink-factors 2 --use-estimate-learning-rate-once 1 --use-histogram-matching 1 --winsorize-image-intensities [ 0.05, 0.98 ] --write-composite-transform 0 190731-15:20:51,650 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_mid_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.apply_mask". 190731-15:20:51,783 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_mid_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_opposite_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_pass". 190731-15:20:52,907 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_opposite_wf.enhance_and_skullstrip_bold_wf.norm". 190731-15:20:53,525 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_mid_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_opposite_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_dilate" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_mid_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_dilate". 190731-15:20:53,528 nipype.workflow INFO: [Node] Running "skullstrip_first_dilate" ("nipype.interfaces.fsl.maths.DilateImage"), a CommandLine Interface with command: fslmaths -dt char /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_mid_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_pass/template_corrected_brain_mask.nii.gz -kernel sphere 6.0000 -dilF /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_mid_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_dilate/template_corrected_brain_mask_dil.nii.gz 190731-15:20:53,529 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_opposite_wf.enhance_and_skullstrip_bold_wf.map_brainmask" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/enhance_and_skullstrip_bold_wf/map_brainmask". 190731-15:20:53,532 nipype.workflow INFO: [Node] Running "map_brainmask" ("niworkflows.interfaces.fixes.FixHeaderApplyTransforms"), a CommandLine Interface with command: antsApplyTransforms --default-value 0 --float 1 --input /home/sahad3/.cache/templateflow/tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_res-02_desc-brain_mask.nii.gz --interpolation MultiLabel --output tpl-MNI152NLin2009cAsym_res-02_desc-brain_mask_trans.nii.gz --reference-image /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/merge/template.nii.gz --transform [ /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/enhance_and_skullstrip_bold_wf/norm/transform0GenericAffine.mat, 1 ] 190731-15:20:53,539 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_matching_wf.enhance_and_skullstrip_bold_wf.init_aff" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/enhance_and_skullstrip_bold_wf/init_aff". 190731-15:20:53,542 nipype.workflow INFO: [Node] Running "init_aff" ("niworkflows.interfaces.ants.AI"), a CommandLine Interface with command: antsAI -c [10,0.000001,10] -d 3 -x /home/sahad3/.cache/templateflow/tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_res-02_desc-brain_mask.nii.gz -m Mattes[/home/sahad3/.cache/templateflow/tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_res-02_desc-fMRIPrep_boldref.nii.gz,/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/merge/template.nii.gz,32,Regular,0.200000] -o initialization.mat -p 0 -s [20.000000,0.120000] -t Affine[0.100000] -v 1 190731-15:20:53,976 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_mid_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_opposite_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_dilate". 190731-15:20:54,167 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_mid_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_matching_wf.enhance_and_skullstrip_bold_wf.n4_correct". 190731-15:20:55,572 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_mid_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_opposite_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_mask" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_mid_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_mask". 190731-15:20:55,575 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_mid_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_matching_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_pass" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_mid_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_pass". 190731-15:20:55,575 nipype.workflow INFO: [Node] Running "skullstrip_first_mask" ("nipype.interfaces.fsl.maths.ApplyMask"), a CommandLine Interface with command: fslmaths /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_mid_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_pass/template_corrected_brain.nii.gz -mas /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_mid_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_dilate/template_corrected_brain_mask_dil.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_mid_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_mask/template_corrected_brain_masked.nii.gz 190731-15:20:55,577 nipype.workflow INFO: [Node] Running "skullstrip_first_pass" ("nipype.interfaces.fsl.preprocess.BET"), a CommandLine Interface with command: bet /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_mid_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/enhance_and_skullstrip_bold_wf/n4_correct/template_corrected.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_mid_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_pass/template_corrected_brain.nii.gz -f 0.20 -m 190731-15:20:55,705 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_mid_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_opposite_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_mask". 190731-15:20:55,754 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_opposite_wf.enhance_and_skullstrip_bold_wf.map_brainmask". 190731-15:20:57,573 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_mid_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_opposite_wf.enhance_and_skullstrip_bold_wf.unifize" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_mid_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/enhance_and_skullstrip_bold_wf/unifize". 190731-15:20:57,576 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_opposite_wf.enhance_and_skullstrip_bold_wf.pre_mask_dilate" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/enhance_and_skullstrip_bold_wf/pre_mask_dilate". 190731-15:20:57,577 nipype.workflow INFO: [Node] Running "unifize" ("nipype.interfaces.afni.utils.Unifize"), a CommandLine Interface with command: 3dUnifize -clfrac 0.2 -rbt 18.3 65.0 90.0 -prefix uni.nii.gz -T2 -input /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_mid_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/enhance_and_skullstrip_bold_wf/unifize/template_corrected_brain_masked.nii.gz 190731-15:20:57,579 nipype.workflow INFO: [Node] Running "pre_mask_dilate" ("nipype.interfaces.fsl.maths.DilateImage"), a CommandLine Interface with command: fslmaths -dt char /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/enhance_and_skullstrip_bold_wf/map_brainmask/tpl-MNI152NLin2009cAsym_res-02_desc-brain_mask_trans.nii.gz -kernel sphere 3.0000 -dilF /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/enhance_and_skullstrip_bold_wf/pre_mask_dilate/tpl-MNI152NLin2009cAsym_res-02_desc-brain_mask_trans_dil.nii.gz 190731-15:20:57,676 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_mid_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_matching_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_pass". 190731-15:20:57,756 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_opposite_wf.enhance_and_skullstrip_bold_wf.pre_mask_dilate". 190731-15:20:58,926 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_mid_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_opposite_wf.enhance_and_skullstrip_bold_wf.unifize". 190731-15:20:58,934 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_matching_wf.enhance_and_skullstrip_bold_wf.init_aff". 190731-15:20:59,529 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_mid_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_opposite_wf.enhance_and_skullstrip_bold_wf.fixhdr_unifize" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_mid_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/enhance_and_skullstrip_bold_wf/fixhdr_unifize". 190731-15:20:59,531 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_mid_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_matching_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_dilate" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_mid_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_dilate". 190731-15:20:59,531 nipype.workflow INFO: [Node] Running "fixhdr_unifize" ("niworkflows.interfaces.utils.CopyXForm") 190731-15:20:59,534 nipype.workflow INFO: [Node] Running "skullstrip_first_dilate" ("nipype.interfaces.fsl.maths.DilateImage"), a CommandLine Interface with command: fslmaths -dt char /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_mid_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_pass/template_corrected_brain_mask.nii.gz -kernel sphere 6.0000 -dilF /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_mid_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_dilate/template_corrected_brain_mask_dil.nii.gz 190731-15:20:59,548 nipype.interface WARNING: q-forms of reference and mask are substantially different 190731-15:20:59,574 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_mid_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_opposite_wf.enhance_and_skullstrip_bold_wf.fixhdr_unifize". 190731-15:20:59,999 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_mid_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_matching_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_dilate". 190731-15:21:00,34 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_matching_wf.enhance_and_skullstrip_bold_wf.norm" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/enhance_and_skullstrip_bold_wf/norm". 190731-15:21:00,36 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_04_task_rest_echo_1_wf.bold_hmc_wf.normalize_motion" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_04_task_rest_echo_1_wf/bold_hmc_wf/normalize_motion". 190731-15:21:00,38 nipype.workflow INFO: [Node] Running "normalize_motion" ("niworkflows.interfaces.utils.NormalizeMotionParams") 190731-15:21:00,38 nipype.workflow INFO: [Node] Running "norm" ("niworkflows.interfaces.fixes.FixHeaderRegistration"), a CommandLine Interface with command: antsRegistration --collapse-output-transforms 1 --dimensionality 3 --float 1 --initial-moving-transform [ /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/enhance_and_skullstrip_bold_wf/init_aff/initialization.mat, 0 ] --initialize-transforms-per-stage 0 --interpolation Linear --output transform --transform Affine[ 0.1 ] --metric Mattes[ /home/sahad3/.cache/templateflow/tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_res-02_desc-fMRIPrep_boldref.nii.gz, /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/merge/template.nii.gz, 1, 64, Random, 0.2 ] --convergence [ 200, 1e-09, 10 ] --smoothing-sigmas 2.0mm --shrink-factors 2 --use-estimate-learning-rate-once 1 --use-histogram-matching 1 --winsorize-image-intensities [ 0.05, 0.98 ] --write-composite-transform 0 190731-15:21:00,46 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_04_task_rest_echo_1_wf.bold_hmc_wf.normalize_motion". 190731-15:21:01,60 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_matching_wf.enhance_and_skullstrip_bold_wf.norm". 190731-15:21:01,528 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_mid_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_opposite_wf.enhance_and_skullstrip_bold_wf.skullstrip_second_pass" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_mid_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/enhance_and_skullstrip_bold_wf/skullstrip_second_pass". 190731-15:21:01,530 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_mid_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_matching_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_mask" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_mid_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_mask". 190731-15:21:01,531 nipype.workflow INFO: [Node] Running "skullstrip_second_pass" ("nipype.interfaces.afni.preprocess.Automask"), a CommandLine Interface with command: 3dAutomask -apply_prefix uni_xform_masked.nii.gz -dilate 1 -prefix uni_xform_mask.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_mid_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/enhance_and_skullstrip_bold_wf/skullstrip_second_pass/uni_xform.nii.gz 190731-15:21:01,532 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_opposite_wf.enhance_and_skullstrip_bold_wf.n4_correct" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/enhance_and_skullstrip_bold_wf/n4_correct". 190731-15:21:01,533 nipype.workflow INFO: [Node] Running "skullstrip_first_mask" ("nipype.interfaces.fsl.maths.ApplyMask"), a CommandLine Interface with command: fslmaths /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_mid_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_pass/template_corrected_brain.nii.gz -mas /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_mid_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_dilate/template_corrected_brain_mask_dil.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_mid_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_mask/template_corrected_brain_masked.nii.gz 190731-15:21:01,535 nipype.workflow INFO: [Node] Running "n4_correct" ("nipype.interfaces.ants.segmentation.N4BiasFieldCorrection"), a CommandLine Interface with command: N4BiasFieldCorrection --bspline-fitting [ 200 ] -d 3 --input-image /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/merge/template.nii.gz --mask-image /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/enhance_and_skullstrip_bold_wf/check_hdr/tpl-MNI152NLin2009cAsym_res-02_desc-brain_mask_trans_dil_hdr.nii.gz --output template_corrected.nii.gz 190731-15:21:01,656 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_mid_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_matching_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_mask". 190731-15:21:01,701 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_mid_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_opposite_wf.enhance_and_skullstrip_bold_wf.skullstrip_second_pass". 190731-15:21:03,525 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_mid_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_opposite_wf.enhance_and_skullstrip_bold_wf.fixhdr_skullstrip2" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_mid_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/enhance_and_skullstrip_bold_wf/fixhdr_skullstrip2". 190731-15:21:03,526 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_mid_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_matching_wf.enhance_and_skullstrip_bold_wf.unifize" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_mid_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/enhance_and_skullstrip_bold_wf/unifize". 190731-15:21:03,527 nipype.workflow INFO: [Node] Running "fixhdr_skullstrip2" ("niworkflows.interfaces.utils.CopyXForm") 190731-15:21:03,529 nipype.workflow INFO: [Node] Running "unifize" ("nipype.interfaces.afni.utils.Unifize"), a CommandLine Interface with command: 3dUnifize -clfrac 0.2 -rbt 18.3 65.0 90.0 -prefix uni.nii.gz -T2 -input /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_mid_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/enhance_and_skullstrip_bold_wf/unifize/template_corrected_brain_masked.nii.gz 190731-15:21:03,529 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_matching_wf.enhance_and_skullstrip_bold_wf.map_brainmask" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/enhance_and_skullstrip_bold_wf/map_brainmask". 190731-15:21:03,532 nipype.workflow INFO: [Node] Running "map_brainmask" ("niworkflows.interfaces.fixes.FixHeaderApplyTransforms"), a CommandLine Interface with command: antsApplyTransforms --default-value 0 --float 1 --input /home/sahad3/.cache/templateflow/tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_res-02_desc-brain_mask.nii.gz --interpolation MultiLabel --output tpl-MNI152NLin2009cAsym_res-02_desc-brain_mask_trans.nii.gz --reference-image /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/merge/template.nii.gz --transform [ /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/enhance_and_skullstrip_bold_wf/norm/transform0GenericAffine.mat, 1 ] 190731-15:21:03,605 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_mid_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_opposite_wf.enhance_and_skullstrip_bold_wf.fixhdr_skullstrip2". 190731-15:21:03,868 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_opposite_wf.enhance_and_skullstrip_bold_wf.n4_correct". 190731-15:21:04,37 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_04_task_rest_echo_1_wf.bold_confounds_wf.fdisp" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_04_task_rest_echo_1_wf/bold_confounds_wf/fdisp". 190731-15:21:04,38 nipype.workflow INFO: [Node] Setting-up "_n4_correct2" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/anat_preproc_wf/anat_template_wf/n4_correct/mapflow/_n4_correct2". 190731-15:21:04,39 nipype.workflow INFO: [Node] Running "fdisp" ("nipype.algorithms.confounds.FramewiseDisplacement") 190731-15:21:04,40 nipype.workflow INFO: [Node] Setting-up "_n4_correct3" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/anat_preproc_wf/anat_template_wf/n4_correct/mapflow/_n4_correct3". 190731-15:21:04,41 nipype.workflow INFO: [Node] Setting-up "_t1_conform_xfm0" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/anat_preproc_wf/anat_template_wf/t1_conform_xfm/mapflow/_t1_conform_xfm0". 190731-15:21:04,41 nipype.workflow INFO: [Node] Running "_n4_correct2" ("nipype.interfaces.ants.segmentation.N4BiasFieldCorrection"), a CommandLine Interface with command: N4BiasFieldCorrection -d 3 --input-image /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/anat_preproc_wf/anat_template_wf/t1_conform/mapflow/_t1_conform2/sub-23649_ses-03_acq-mprage_rec-ORIG_T1w_ras.nii.gz --output sub-23649_ses-03_acq-mprage_rec-ORIG_T1w_ras_corrected.nii.gz 190731-15:21:04,43 nipype.workflow INFO: [Node] Setting-up "_t1_conform_xfm1" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/anat_preproc_wf/anat_template_wf/t1_conform_xfm/mapflow/_t1_conform_xfm1". 190731-15:21:04,43 nipype.workflow INFO: [Node] Running "_n4_correct3" ("nipype.interfaces.ants.segmentation.N4BiasFieldCorrection"), a CommandLine Interface with command: N4BiasFieldCorrection -d 3 --input-image /gs11/users/MBDU/bids/mid_longitudinal_20190717/sub-23649/ses-04/anat/sub-23649_ses-04_acq-mprage_rec-ORIG_T1w.nii.gz --output sub-23649_ses-04_acq-mprage_rec-ORIG_T1w_corrected.nii.gz 190731-15:21:04,45 nipype.workflow INFO: [Node] Running "_t1_conform_xfm0" ("niworkflows.interfaces.freesurfer.PatchedLTAConvert"), a CommandLine Interface with command: lta_convert --inlta identity.nofile --outlta /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/anat_preproc_wf/anat_template_wf/t1_conform_xfm/mapflow/_t1_conform_xfm0/out.lta --src /gs11/users/MBDU/bids/mid_longitudinal_20190717/sub-23649/ses-01/anat/sub-23649_ses-01_acq-mprage_rec-ORIG_T1w.nii.gz --trg /gs11/users/MBDU/bids/mid_longitudinal_20190717/sub-23649/ses-01/anat/sub-23649_ses-01_acq-mprage_rec-ORIG_T1w.nii.gz 190731-15:21:04,45 nipype.workflow INFO: [Node] Setting-up "_t1_conform_xfm3" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/anat_preproc_wf/anat_template_wf/t1_conform_xfm/mapflow/_t1_conform_xfm3". 190731-15:21:04,46 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_04_task_rest_echo_1_wf.bold_confounds_wf.fdisp". 190731-15:21:04,46 nipype.workflow INFO: [Node] Running "_t1_conform_xfm1" ("niworkflows.interfaces.freesurfer.PatchedLTAConvert"), a CommandLine Interface with command: lta_convert --inlta identity.nofile --outlta /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/anat_preproc_wf/anat_template_wf/t1_conform_xfm/mapflow/_t1_conform_xfm1/out.lta --src /gs11/users/MBDU/bids/mid_longitudinal_20190717/sub-23649/ses-02/anat/sub-23649_ses-02_acq-mprage_rec-ORIG_T1w.nii.gz --trg /gs11/users/MBDU/bids/mid_longitudinal_20190717/sub-23649/ses-02/anat/sub-23649_ses-02_acq-mprage_rec-ORIG_T1w.nii.gz 190731-15:21:04,49 nipype.workflow INFO: [Node] Running "_t1_conform_xfm3" ("niworkflows.interfaces.freesurfer.PatchedLTAConvert"), a CommandLine Interface with command: lta_convert --inlta identity.nofile --outlta /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/anat_preproc_wf/anat_template_wf/t1_conform_xfm/mapflow/_t1_conform_xfm3/out.lta --src /gs11/users/MBDU/bids/mid_longitudinal_20190717/sub-23649/ses-04/anat/sub-23649_ses-04_acq-mprage_rec-ORIG_T1w.nii.gz --trg /gs11/users/MBDU/bids/mid_longitudinal_20190717/sub-23649/ses-04/anat/sub-23649_ses-04_acq-mprage_rec-ORIG_T1w.nii.gz 190731-15:21:04,290 nipype.workflow INFO: [Node] Finished "_t1_conform_xfm3". 190731-15:21:04,294 nipype.workflow INFO: [Node] Finished "_t1_conform_xfm0". 190731-15:21:04,295 nipype.workflow INFO: [Node] Finished "_t1_conform_xfm1". 190731-15:21:04,380 nipype.workflow INFO: [Node] Setting-up "_t1_conform_xfm2" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/anat_preproc_wf/anat_template_wf/t1_conform_xfm/mapflow/_t1_conform_xfm2". 190731-15:21:04,383 nipype.workflow INFO: [Node] Running "_t1_conform_xfm2" ("niworkflows.interfaces.freesurfer.PatchedLTAConvert"), a CommandLine Interface with command: lta_convert --inlta identity.nofile --outlta /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/anat_preproc_wf/anat_template_wf/t1_conform_xfm/mapflow/_t1_conform_xfm2/out.lta --src /gs11/users/MBDU/bids/mid_longitudinal_20190717/sub-23649/ses-03/anat/sub-23649_ses-03_acq-mprage_rec-ORIG_T1w.nii.gz --trg /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/anat_preproc_wf/anat_template_wf/t1_conform/mapflow/_t1_conform2/sub-23649_ses-03_acq-mprage_rec-ORIG_T1w_ras.nii.gz 190731-15:21:04,517 nipype.workflow INFO: [Node] Finished "_t1_conform_xfm2". 190731-15:21:04,829 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_mid_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_matching_wf.enhance_and_skullstrip_bold_wf.unifize". 190731-15:21:05,367 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_matching_wf.enhance_and_skullstrip_bold_wf.map_brainmask". 190731-15:21:05,557 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_mid_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_opposite_wf.enhance_and_skullstrip_bold_wf.combine_masks" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_mid_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/enhance_and_skullstrip_bold_wf/combine_masks". 190731-15:21:05,559 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_mid_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_matching_wf.enhance_and_skullstrip_bold_wf.fixhdr_unifize" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_mid_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/enhance_and_skullstrip_bold_wf/fixhdr_unifize". 190731-15:21:05,560 nipype.workflow INFO: [Node] Running "combine_masks" ("nipype.interfaces.fsl.maths.BinaryMaths"), a CommandLine Interface with command: fslmaths /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_mid_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_pass/template_corrected_brain_mask.nii.gz -mul /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_mid_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/enhance_and_skullstrip_bold_wf/fixhdr_skullstrip2/uni_xform_mask_xform.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_mid_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/enhance_and_skullstrip_bold_wf/combine_masks/template_corrected_brain_mask_maths.nii.gz 190731-15:21:05,561 nipype.workflow INFO: [Node] Running "fixhdr_unifize" ("niworkflows.interfaces.utils.CopyXForm") 190731-15:21:05,562 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_opposite_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_pass" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_pass". 190731-15:21:05,564 nipype.workflow INFO: [Node] Running "skullstrip_first_pass" ("nipype.interfaces.fsl.preprocess.BET"), a CommandLine Interface with command: bet /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/enhance_and_skullstrip_bold_wf/n4_correct/template_corrected.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_pass/template_corrected_brain.nii.gz -f 0.20 -m 190731-15:21:05,566 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.anat_preproc_wf.anat_template_wf.t1_conform_xfm" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/anat_preproc_wf/anat_template_wf/t1_conform_xfm". 190731-15:21:05,570 nipype.workflow INFO: [Node] Setting-up "_t1_conform_xfm0" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/anat_preproc_wf/anat_template_wf/t1_conform_xfm/mapflow/_t1_conform_xfm0". 190731-15:21:05,571 nipype.workflow INFO: [Node] Cached "_t1_conform_xfm0" - collecting precomputed outputs 190731-15:21:05,571 nipype.workflow INFO: [Node] "_t1_conform_xfm0" found cached. 190731-15:21:05,572 nipype.workflow INFO: [Node] Setting-up "_t1_conform_xfm1" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/anat_preproc_wf/anat_template_wf/t1_conform_xfm/mapflow/_t1_conform_xfm1". 190731-15:21:05,573 nipype.workflow INFO: [Node] Cached "_t1_conform_xfm1" - collecting precomputed outputs 190731-15:21:05,573 nipype.workflow INFO: [Node] "_t1_conform_xfm1" found cached. 190731-15:21:05,575 nipype.workflow INFO: [Node] Setting-up "_t1_conform_xfm2" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/anat_preproc_wf/anat_template_wf/t1_conform_xfm/mapflow/_t1_conform_xfm2". 190731-15:21:05,576 nipype.workflow INFO: [Node] Cached "_t1_conform_xfm2" - collecting precomputed outputs 190731-15:21:05,576 nipype.workflow INFO: [Node] "_t1_conform_xfm2" found cached. 190731-15:21:05,577 nipype.workflow INFO: [Node] Setting-up "_t1_conform_xfm3" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/anat_preproc_wf/anat_template_wf/t1_conform_xfm/mapflow/_t1_conform_xfm3". 190731-15:21:05,578 nipype.workflow INFO: [Node] Cached "_t1_conform_xfm3" - collecting precomputed outputs 190731-15:21:05,578 nipype.workflow INFO: [Node] "_t1_conform_xfm3" found cached. 190731-15:21:05,580 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.anat_preproc_wf.anat_template_wf.t1_conform_xfm". 190731-15:21:05,604 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_mid_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_matching_wf.enhance_and_skullstrip_bold_wf.fixhdr_unifize". 190731-15:21:05,672 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_mid_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_opposite_wf.enhance_and_skullstrip_bold_wf.combine_masks". 190731-15:21:07,561 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_mid_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_opposite_wf.enhance_and_skullstrip_bold_wf.apply_mask" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_mid_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/enhance_and_skullstrip_bold_wf/apply_mask". 190731-15:21:07,563 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_mid_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_matching_wf.enhance_and_skullstrip_bold_wf.skullstrip_second_pass" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_mid_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/enhance_and_skullstrip_bold_wf/skullstrip_second_pass". 190731-15:21:07,565 nipype.workflow INFO: [Node] Running "apply_mask" ("nipype.interfaces.fsl.maths.ApplyMask"), a CommandLine Interface with command: fslmaths /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_mid_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/enhance_and_skullstrip_bold_wf/fixhdr_unifize/uni_xform.nii.gz -mas /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_mid_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/enhance_and_skullstrip_bold_wf/combine_masks/template_corrected_brain_mask_maths.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_mid_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/enhance_and_skullstrip_bold_wf/apply_mask/uni_xform_masked.nii.gz 190731-15:21:07,566 nipype.workflow INFO: [Node] Running "skullstrip_second_pass" ("nipype.interfaces.afni.preprocess.Automask"), a CommandLine Interface with command: 3dAutomask -apply_prefix uni_xform_masked.nii.gz -dilate 1 -prefix uni_xform_mask.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_mid_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/enhance_and_skullstrip_bold_wf/skullstrip_second_pass/uni_xform.nii.gz 190731-15:21:07,565 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_matching_wf.enhance_and_skullstrip_bold_wf.pre_mask_dilate" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/enhance_and_skullstrip_bold_wf/pre_mask_dilate". 190731-15:21:07,568 nipype.workflow INFO: [Node] Running "pre_mask_dilate" ("nipype.interfaces.fsl.maths.DilateImage"), a CommandLine Interface with command: fslmaths -dt char /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/enhance_and_skullstrip_bold_wf/map_brainmask/tpl-MNI152NLin2009cAsym_res-02_desc-brain_mask_trans.nii.gz -kernel sphere 3.0000 -dilF /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/enhance_and_skullstrip_bold_wf/pre_mask_dilate/tpl-MNI152NLin2009cAsym_res-02_desc-brain_mask_trans_dil.nii.gz 190731-15:21:07,684 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_mid_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_opposite_wf.enhance_and_skullstrip_bold_wf.apply_mask". 190731-15:21:07,739 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_matching_wf.enhance_and_skullstrip_bold_wf.pre_mask_dilate". 190731-15:21:07,750 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_mid_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_matching_wf.enhance_and_skullstrip_bold_wf.skullstrip_second_pass". 190731-15:21:08,217 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_opposite_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_pass". 190731-15:21:08,849 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_mid_wf.bold_hmc_wf.fsl2itk". 190731-15:21:09,528 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_mid_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_matching_wf.enhance_and_skullstrip_bold_wf.fixhdr_skullstrip2" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_mid_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/enhance_and_skullstrip_bold_wf/fixhdr_skullstrip2". 190731-15:21:09,530 nipype.workflow INFO: [Node] Running "fixhdr_skullstrip2" ("niworkflows.interfaces.utils.CopyXForm") 190731-15:21:09,533 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_mid_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_opposite_wf.fmap2ref_reg" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_mid_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/fmap2ref_reg". 190731-15:21:09,534 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_opposite_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_dilate" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_dilate". 190731-15:21:09,537 nipype.workflow INFO: [Node] Running "skullstrip_first_dilate" ("nipype.interfaces.fsl.maths.DilateImage"), a CommandLine Interface with command: fslmaths -dt char /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_pass/template_corrected_brain_mask.nii.gz -kernel sphere 6.0000 -dilF /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_dilate/template_corrected_brain_mask_dil.nii.gz 190731-15:21:09,538 nipype.workflow INFO: [Node] Running "fmap2ref_reg" ("nipype.interfaces.ants.registration.Registration"), a CommandLine Interface with command: antsRegistration --collapse-output-transforms 1 --dimensionality 3 --float 1 --initialize-transforms-per-stage 0 --interpolation LanczosWindowedSinc --output [ transform, transform_Warped.nii.gz ] --transform Translation[ 0.05 ] --metric Mattes[ /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_mid_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/apply_mask/uni_xform_masked.nii.gz, /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_mid_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/enhance_and_skullstrip_bold_wf/apply_mask/uni_xform_masked.nii.gz, 1, 64, Random, 0.5 ] --convergence [ 500, 1e-07, 200 ] --smoothing-sigmas 8.0mm --shrink-factors 2 --use-estimate-learning-rate-once 1 --use-histogram-matching 1 --transform Rigid[ 0.01 ] --metric Mattes[ /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_mid_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/apply_mask/uni_xform_masked.nii.gz, /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_mid_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/enhance_and_skullstrip_bold_wf/apply_mask/uni_xform_masked.nii.gz, 1, 64, Random, 0.5 ] --convergence [ 200, 1e-08, 100 ] --smoothing-sigmas 2.0mm --shrink-factors 1 --use-estimate-learning-rate-once 1 --use-histogram-matching 1 --winsorize-image-intensities [ 0.005, 0.998 ] --write-composite-transform 1 190731-15:21:09,551 nipype.interface WARNING: q-forms of reference and mask are substantially different 190731-15:21:09,556 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_mid_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_matching_wf.enhance_and_skullstrip_bold_wf.fixhdr_skullstrip2". 190731-15:21:09,889 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_opposite_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_dilate". 190731-15:21:11,55 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_mid_wf.bold_hmc_wf.mcflirt". 190731-15:21:11,526 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_mid_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_matching_wf.enhance_and_skullstrip_bold_wf.combine_masks" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_mid_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/enhance_and_skullstrip_bold_wf/combine_masks". 190731-15:21:11,526 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_matching_wf.enhance_and_skullstrip_bold_wf.n4_correct" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/enhance_and_skullstrip_bold_wf/n4_correct". 190731-15:21:11,526 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_opposite_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_mask" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_mask". 190731-15:21:11,528 nipype.workflow INFO: [Node] Running "n4_correct" ("nipype.interfaces.ants.segmentation.N4BiasFieldCorrection"), a CommandLine Interface with command: N4BiasFieldCorrection --bspline-fitting [ 200 ] -d 3 --input-image /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/merge/template.nii.gz --mask-image /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/enhance_and_skullstrip_bold_wf/check_hdr/tpl-MNI152NLin2009cAsym_res-02_desc-brain_mask_trans_dil_hdr.nii.gz --output template_corrected.nii.gz 190731-15:21:11,529 nipype.workflow INFO: [Node] Running "combine_masks" ("nipype.interfaces.fsl.maths.BinaryMaths"), a CommandLine Interface with command: fslmaths /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_mid_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_pass/template_corrected_brain_mask.nii.gz -mul /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_mid_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/enhance_and_skullstrip_bold_wf/fixhdr_skullstrip2/uni_xform_mask_xform.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_mid_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/enhance_and_skullstrip_bold_wf/combine_masks/template_corrected_brain_mask_maths.nii.gz 190731-15:21:11,530 nipype.workflow INFO: [Node] Running "skullstrip_first_mask" ("nipype.interfaces.fsl.maths.ApplyMask"), a CommandLine Interface with command: fslmaths /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_pass/template_corrected_brain.nii.gz -mas /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_dilate/template_corrected_brain_mask_dil.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_mask/template_corrected_brain_masked.nii.gz 190731-15:21:11,663 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_mid_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_matching_wf.enhance_and_skullstrip_bold_wf.combine_masks". 190731-15:21:11,678 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_opposite_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_mask". 190731-15:21:13,531 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_mid_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_matching_wf.enhance_and_skullstrip_bold_wf.apply_mask" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_mid_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/enhance_and_skullstrip_bold_wf/apply_mask". 190731-15:21:13,532 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_opposite_wf.enhance_and_skullstrip_bold_wf.unifize" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/enhance_and_skullstrip_bold_wf/unifize". 190731-15:21:13,533 nipype.workflow INFO: [Node] Running "apply_mask" ("nipype.interfaces.fsl.maths.ApplyMask"), a CommandLine Interface with command: fslmaths /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_mid_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/enhance_and_skullstrip_bold_wf/fixhdr_unifize/uni_xform.nii.gz -mas /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_mid_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/enhance_and_skullstrip_bold_wf/combine_masks/template_corrected_brain_mask_maths.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_mid_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/enhance_and_skullstrip_bold_wf/apply_mask/uni_xform_masked.nii.gz 190731-15:21:13,534 nipype.workflow INFO: [Node] Running "unifize" ("nipype.interfaces.afni.utils.Unifize"), a CommandLine Interface with command: 3dUnifize -clfrac 0.2 -rbt 18.3 65.0 90.0 -prefix uni.nii.gz -T2 -input /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/enhance_and_skullstrip_bold_wf/unifize/template_corrected_brain_masked.nii.gz 190731-15:21:13,536 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_mid_wf.bold_hmc_wf.normalize_motion" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_mid_wf/bold_hmc_wf/normalize_motion". 190731-15:21:13,538 nipype.workflow INFO: [Node] Running "normalize_motion" ("niworkflows.interfaces.utils.NormalizeMotionParams") 190731-15:21:13,552 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_mid_wf.bold_hmc_wf.normalize_motion". 190731-15:21:13,641 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_mid_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_matching_wf.enhance_and_skullstrip_bold_wf.apply_mask". 190731-15:21:13,682 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_matching_wf.enhance_and_skullstrip_bold_wf.n4_correct". 190731-15:21:14,617 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_opposite_wf.enhance_and_skullstrip_bold_wf.unifize". 190731-15:21:15,533 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_mid_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_matching_wf.fmap2ref_reg" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_mid_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/fmap2ref_reg". 190731-15:21:15,535 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_opposite_wf.enhance_and_skullstrip_bold_wf.fixhdr_unifize" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/enhance_and_skullstrip_bold_wf/fixhdr_unifize". 190731-15:21:15,537 nipype.workflow INFO: [Node] Running "fixhdr_unifize" ("niworkflows.interfaces.utils.CopyXForm") 190731-15:21:15,537 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_matching_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_pass" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_pass". 190731-15:21:15,539 nipype.workflow INFO: [Node] Running "fmap2ref_reg" ("nipype.interfaces.ants.registration.Registration"), a CommandLine Interface with command: antsRegistration --collapse-output-transforms 1 --dimensionality 3 --float 1 --initialize-transforms-per-stage 0 --interpolation LanczosWindowedSinc --output [ transform, transform_Warped.nii.gz ] --transform Translation[ 0.05 ] --metric Mattes[ /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_mid_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/apply_mask/uni_xform_masked.nii.gz, /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_mid_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/enhance_and_skullstrip_bold_wf/apply_mask/uni_xform_masked.nii.gz, 1, 64, Random, 0.5 ] --convergence [ 500, 1e-07, 200 ] --smoothing-sigmas 8.0mm --shrink-factors 2 --use-estimate-learning-rate-once 1 --use-histogram-matching 1 --transform Rigid[ 0.01 ] --metric Mattes[ /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_mid_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/apply_mask/uni_xform_masked.nii.gz, /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_mid_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/enhance_and_skullstrip_bold_wf/apply_mask/uni_xform_masked.nii.gz, 1, 64, Random, 0.5 ] --convergence [ 200, 1e-08, 100 ] --smoothing-sigmas 2.0mm --shrink-factors 1 --use-estimate-learning-rate-once 1 --use-histogram-matching 1 --winsorize-image-intensities [ 0.005, 0.998 ] --write-composite-transform 1 190731-15:21:15,541 nipype.workflow INFO: [Node] Running "skullstrip_first_pass" ("nipype.interfaces.fsl.preprocess.BET"), a CommandLine Interface with command: bet /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/enhance_and_skullstrip_bold_wf/n4_correct/template_corrected.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_pass/template_corrected_brain.nii.gz -f 0.20 -m 190731-15:21:15,583 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_opposite_wf.enhance_and_skullstrip_bold_wf.fixhdr_unifize". 190731-15:21:17,591 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_opposite_wf.enhance_and_skullstrip_bold_wf.skullstrip_second_pass" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/enhance_and_skullstrip_bold_wf/skullstrip_second_pass". 190731-15:21:17,595 nipype.workflow INFO: [Node] Running "skullstrip_second_pass" ("nipype.interfaces.afni.preprocess.Automask"), a CommandLine Interface with command: 3dAutomask -apply_prefix uni_xform_masked.nii.gz -dilate 1 -prefix uni_xform_mask.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/enhance_and_skullstrip_bold_wf/skullstrip_second_pass/uni_xform.nii.gz 190731-15:21:17,777 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_opposite_wf.enhance_and_skullstrip_bold_wf.skullstrip_second_pass". 190731-15:21:17,779 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_matching_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_pass". 190731-15:21:19,586 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_opposite_wf.enhance_and_skullstrip_bold_wf.fixhdr_skullstrip2" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/enhance_and_skullstrip_bold_wf/fixhdr_skullstrip2". 190731-15:21:19,588 nipype.workflow INFO: [Node] Running "fixhdr_skullstrip2" ("niworkflows.interfaces.utils.CopyXForm") 190731-15:21:19,588 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_matching_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_dilate" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_dilate". 190731-15:21:19,591 nipype.workflow INFO: [Node] Running "skullstrip_first_dilate" ("nipype.interfaces.fsl.maths.DilateImage"), a CommandLine Interface with command: fslmaths -dt char /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_pass/template_corrected_brain_mask.nii.gz -kernel sphere 6.0000 -dilF /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_dilate/template_corrected_brain_mask_dil.nii.gz 190731-15:21:19,614 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_opposite_wf.enhance_and_skullstrip_bold_wf.fixhdr_skullstrip2". 190731-15:21:19,967 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_matching_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_dilate". 190731-15:21:21,616 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_opposite_wf.enhance_and_skullstrip_bold_wf.combine_masks" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/enhance_and_skullstrip_bold_wf/combine_masks". 190731-15:21:21,618 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_matching_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_mask" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_mask". 190731-15:21:21,619 nipype.workflow INFO: [Node] Running "combine_masks" ("nipype.interfaces.fsl.maths.BinaryMaths"), a CommandLine Interface with command: fslmaths /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_pass/template_corrected_brain_mask.nii.gz -mul /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/enhance_and_skullstrip_bold_wf/fixhdr_skullstrip2/uni_xform_mask_xform.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/enhance_and_skullstrip_bold_wf/combine_masks/template_corrected_brain_mask_maths.nii.gz 190731-15:21:21,621 nipype.workflow INFO: [Node] Running "skullstrip_first_mask" ("nipype.interfaces.fsl.maths.ApplyMask"), a CommandLine Interface with command: fslmaths /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_pass/template_corrected_brain.nii.gz -mas /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_dilate/template_corrected_brain_mask_dil.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_mask/template_corrected_brain_masked.nii.gz 190731-15:21:21,741 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_opposite_wf.enhance_and_skullstrip_bold_wf.combine_masks". 190731-15:21:21,744 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_matching_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_mask". 190731-15:21:23,635 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_opposite_wf.enhance_and_skullstrip_bold_wf.apply_mask" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/enhance_and_skullstrip_bold_wf/apply_mask". 190731-15:21:23,636 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_matching_wf.enhance_and_skullstrip_bold_wf.unifize" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/enhance_and_skullstrip_bold_wf/unifize". 190731-15:21:23,637 nipype.workflow INFO: [Node] Running "apply_mask" ("nipype.interfaces.fsl.maths.ApplyMask"), a CommandLine Interface with command: fslmaths /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/enhance_and_skullstrip_bold_wf/fixhdr_unifize/uni_xform.nii.gz -mas /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/enhance_and_skullstrip_bold_wf/combine_masks/template_corrected_brain_mask_maths.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/enhance_and_skullstrip_bold_wf/apply_mask/uni_xform_masked.nii.gz 190731-15:21:23,640 nipype.workflow INFO: [Node] Running "unifize" ("nipype.interfaces.afni.utils.Unifize"), a CommandLine Interface with command: 3dUnifize -clfrac 0.2 -rbt 18.3 65.0 90.0 -prefix uni.nii.gz -T2 -input /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/enhance_and_skullstrip_bold_wf/unifize/template_corrected_brain_masked.nii.gz 190731-15:21:23,848 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_opposite_wf.enhance_and_skullstrip_bold_wf.apply_mask". 190731-15:21:24,833 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_matching_wf.enhance_and_skullstrip_bold_wf.unifize". 190731-15:21:25,623 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_matching_wf.enhance_and_skullstrip_bold_wf.fixhdr_unifize" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/enhance_and_skullstrip_bold_wf/fixhdr_unifize". 190731-15:21:25,626 nipype.workflow INFO: [Node] Running "fixhdr_unifize" ("niworkflows.interfaces.utils.CopyXForm") 190731-15:21:25,676 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_matching_wf.enhance_and_skullstrip_bold_wf.fixhdr_unifize". 190731-15:21:26,142 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_mid_wf.bold_confounds_wf.fdisp" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_mid_wf/bold_confounds_wf/fdisp". 190731-15:21:26,144 nipype.workflow INFO: [Node] Running "fdisp" ("nipype.algorithms.confounds.FramewiseDisplacement") 190731-15:21:26,161 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_mid_wf.bold_confounds_wf.fdisp". 190731-15:21:27,646 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_matching_wf.enhance_and_skullstrip_bold_wf.skullstrip_second_pass" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/enhance_and_skullstrip_bold_wf/skullstrip_second_pass". 190731-15:21:27,650 nipype.workflow INFO: [Node] Running "skullstrip_second_pass" ("nipype.interfaces.afni.preprocess.Automask"), a CommandLine Interface with command: 3dAutomask -apply_prefix uni_xform_masked.nii.gz -dilate 1 -prefix uni_xform_mask.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/enhance_and_skullstrip_bold_wf/skullstrip_second_pass/uni_xform.nii.gz 190731-15:21:27,840 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_matching_wf.enhance_and_skullstrip_bold_wf.skullstrip_second_pass". 190731-15:21:29,612 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_matching_wf.enhance_and_skullstrip_bold_wf.fixhdr_skullstrip2" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/enhance_and_skullstrip_bold_wf/fixhdr_skullstrip2". 190731-15:21:29,614 nipype.workflow INFO: [Node] Running "fixhdr_skullstrip2" ("niworkflows.interfaces.utils.CopyXForm") 190731-15:21:29,638 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_matching_wf.enhance_and_skullstrip_bold_wf.fixhdr_skullstrip2". 190731-15:21:30,322 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_mid_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_opposite_wf.fmap2ref_reg". 190731-15:21:31,593 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_matching_wf.enhance_and_skullstrip_bold_wf.combine_masks" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/enhance_and_skullstrip_bold_wf/combine_masks". 190731-15:21:31,597 nipype.workflow INFO: [Node] Running "combine_masks" ("nipype.interfaces.fsl.maths.BinaryMaths"), a CommandLine Interface with command: fslmaths /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_pass/template_corrected_brain_mask.nii.gz -mul /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/enhance_and_skullstrip_bold_wf/fixhdr_skullstrip2/uni_xform_mask_xform.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/enhance_and_skullstrip_bold_wf/combine_masks/template_corrected_brain_mask_maths.nii.gz 190731-15:21:31,622 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.bold_hmc_wf.fsl2itk" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/bold_hmc_wf/fsl2itk". 190731-15:21:31,630 nipype.workflow INFO: [Node] Running "fsl2itk" ("niworkflows.interfaces.itk.MCFLIRT2ITK") 190731-15:21:31,716 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_matching_wf.enhance_and_skullstrip_bold_wf.combine_masks". 190731-15:21:33,608 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_matching_wf.enhance_and_skullstrip_bold_wf.apply_mask" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/enhance_and_skullstrip_bold_wf/apply_mask". 190731-15:21:33,610 nipype.workflow INFO: [Node] Running "apply_mask" ("nipype.interfaces.fsl.maths.ApplyMask"), a CommandLine Interface with command: fslmaths /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/enhance_and_skullstrip_bold_wf/fixhdr_unifize/uni_xform.nii.gz -mas /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/enhance_and_skullstrip_bold_wf/combine_masks/template_corrected_brain_mask_maths.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/enhance_and_skullstrip_bold_wf/apply_mask/uni_xform_masked.nii.gz 190731-15:21:33,732 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_matching_wf.enhance_and_skullstrip_bold_wf.apply_mask". 190731-15:21:35,878 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_04_task_mid_wf.bold_hmc_wf.mcflirt". 190731-15:21:36,331 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_mid_run_2_wf.bold_hmc_wf.mcflirt". 190731-15:21:37,40 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_mid_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_matching_wf.fmap2ref_reg". 190731-15:21:37,566 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_mid_wf.sdc_wf.pepolar_unwarp_wf.qwarp" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_mid_wf/sdc_wf/pepolar_unwarp_wf/qwarp". 190731-15:21:37,570 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_mid_run_2_wf.bold_hmc_wf.normalize_motion" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_2_wf/bold_hmc_wf/normalize_motion". 190731-15:21:37,571 nipype.workflow INFO: [Node] Running "qwarp" ("nipype.interfaces.afni.preprocess.QwarpPlusMinus"), a CommandLine Interface with command: 3dQwarp -prefix Qwarp.nii.gz -plusminus -noXdis -noZdis -base /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_mid_wf/sdc_wf/pepolar_unwarp_wf/qwarp/transform_Warped.nii.gz -blur -1.0 -1.0 -source /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_mid_wf/sdc_wf/pepolar_unwarp_wf/qwarp/transform_Warped_c0000.nii.gz -minpatch 9 -nopadWARP -noweight -pblur 0.05 0.05 190731-15:21:37,571 nipype.workflow INFO: [Node] Running "normalize_motion" ("niworkflows.interfaces.utils.NormalizeMotionParams") 190731-15:21:37,574 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_04_task_mid_wf.bold_hmc_wf.normalize_motion" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_04_task_mid_wf/bold_hmc_wf/normalize_motion". 190731-15:21:37,575 nipype.workflow INFO: [Node] Running "normalize_motion" ("niworkflows.interfaces.utils.NormalizeMotionParams") 190731-15:21:37,584 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_mid_run_2_wf.bold_hmc_wf.normalize_motion". 190731-15:21:37,587 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_04_task_mid_wf.bold_hmc_wf.normalize_motion". 190731-15:21:40,154 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_mid_run_2_wf.bold_confounds_wf.fdisp" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_2_wf/bold_confounds_wf/fdisp". 190731-15:21:40,156 nipype.workflow INFO: [Node] Running "fdisp" ("nipype.algorithms.confounds.FramewiseDisplacement") 190731-15:21:40,166 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_mid_run_2_wf.bold_confounds_wf.fdisp". 190731-15:21:40,664 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_04_task_mid_wf.bold_confounds_wf.fdisp" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_04_task_mid_wf/bold_confounds_wf/fdisp". 190731-15:21:40,667 nipype.workflow INFO: [Node] Running "fdisp" ("nipype.algorithms.confounds.FramewiseDisplacement") 190731-15:21:40,684 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_04_task_mid_wf.bold_confounds_wf.fdisp". 190731-15:21:50,149 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.bold_hmc_wf.fsl2itk". 190731-15:21:51,602 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.init_aff" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/init_aff". 190731-15:21:51,605 nipype.workflow INFO: [Node] Running "init_aff" ("niworkflows.interfaces.ants.AI"), a CommandLine Interface with command: antsAI -c [10,0.000001,10] -d 3 -x /home/sahad3/.cache/templateflow/tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_res-02_desc-brain_mask.nii.gz -m Mattes[/home/sahad3/.cache/templateflow/tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_res-02_desc-fMRIPrep_boldref.nii.gz,/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/bold_reference_wf/gen_ref/ref_bold.nii.gz,32,Regular,0.200000] -o initialization.mat -p 0 -s [20.000000,0.120000] -t Affine[0.100000] -v 1 190731-15:21:57,697 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.init_aff". 190731-15:21:59,598 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.norm" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/norm". 190731-15:21:59,602 nipype.workflow INFO: [Node] Running "norm" ("niworkflows.interfaces.fixes.FixHeaderRegistration"), a CommandLine Interface with command: antsRegistration --collapse-output-transforms 1 --dimensionality 3 --float 1 --initial-moving-transform [ /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/init_aff/initialization.mat, 0 ] --initialize-transforms-per-stage 0 --interpolation Linear --output transform --transform Affine[ 0.1 ] --metric Mattes[ /home/sahad3/.cache/templateflow/tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_res-02_desc-fMRIPrep_boldref.nii.gz, /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/bold_reference_wf/gen_ref/ref_bold.nii.gz, 1, 64, Random, 0.2 ] --convergence [ 200, 1e-09, 10 ] --smoothing-sigmas 2.0mm --shrink-factors 2 --use-estimate-learning-rate-once 1 --use-histogram-matching 1 --winsorize-image-intensities [ 0.05, 0.98 ] --write-composite-transform 0 190731-15:22:01,897 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.norm". 190731-15:22:03,704 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.map_brainmask" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/map_brainmask". 190731-15:22:03,707 nipype.workflow INFO: [Node] Running "map_brainmask" ("niworkflows.interfaces.fixes.FixHeaderApplyTransforms"), a CommandLine Interface with command: antsApplyTransforms --default-value 0 --float 1 --input /home/sahad3/.cache/templateflow/tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_res-02_desc-brain_mask.nii.gz --interpolation MultiLabel --output tpl-MNI152NLin2009cAsym_res-02_desc-brain_mask_trans.nii.gz --reference-image /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/bold_reference_wf/gen_ref/ref_bold.nii.gz --transform [ /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/norm/transform0GenericAffine.mat, 1 ] 190731-15:22:03,721 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_mid_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_opposite_wf.enhance_and_skullstrip_bold_wf.init_aff" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_mid_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/enhance_and_skullstrip_bold_wf/init_aff". 190731-15:22:03,725 nipype.workflow INFO: [Node] Running "init_aff" ("niworkflows.interfaces.ants.AI"), a CommandLine Interface with command: antsAI -c [10,0.000001,10] -d 3 -x /home/sahad3/.cache/templateflow/tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_res-02_desc-brain_mask.nii.gz -m Mattes[/home/sahad3/.cache/templateflow/tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_res-02_desc-fMRIPrep_boldref.nii.gz,/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_mid_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/merge/template.nii.gz,32,Regular,0.200000] -o initialization.mat -p 0 -s [20.000000,0.120000] -t Affine[0.100000] -v 1 190731-15:22:05,879 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.map_brainmask". 190731-15:22:07,631 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.pre_mask_dilate" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/pre_mask_dilate". 190731-15:22:07,635 nipype.workflow INFO: [Node] Running "pre_mask_dilate" ("nipype.interfaces.fsl.maths.DilateImage"), a CommandLine Interface with command: fslmaths -dt char /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/map_brainmask/tpl-MNI152NLin2009cAsym_res-02_desc-brain_mask_trans.nii.gz -kernel sphere 3.0000 -dilF /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/pre_mask_dilate/tpl-MNI152NLin2009cAsym_res-02_desc-brain_mask_trans_dil.nii.gz 190731-15:22:07,883 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.pre_mask_dilate". 190731-15:22:09,634 nipype.interface WARNING: q-forms of reference and mask are substantially different 190731-15:22:11,573 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_mid_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_opposite_wf.enhance_and_skullstrip_bold_wf.init_aff". 190731-15:22:11,651 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.n4_correct" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/n4_correct". 190731-15:22:11,655 nipype.workflow INFO: [Node] Running "n4_correct" ("nipype.interfaces.ants.segmentation.N4BiasFieldCorrection"), a CommandLine Interface with command: N4BiasFieldCorrection --bspline-fitting [ 200 ] -d 3 --input-image /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/bold_reference_wf/gen_ref/ref_bold.nii.gz --mask-image /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/check_hdr/tpl-MNI152NLin2009cAsym_res-02_desc-brain_mask_trans_dil_hdr.nii.gz --output ref_bold_corrected.nii.gz 190731-15:22:13,693 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_mid_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_opposite_wf.enhance_and_skullstrip_bold_wf.norm" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_mid_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/enhance_and_skullstrip_bold_wf/norm". 190731-15:22:13,700 nipype.workflow INFO: [Node] Running "norm" ("niworkflows.interfaces.fixes.FixHeaderRegistration"), a CommandLine Interface with command: antsRegistration --collapse-output-transforms 1 --dimensionality 3 --float 1 --initial-moving-transform [ /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_mid_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/enhance_and_skullstrip_bold_wf/init_aff/initialization.mat, 0 ] --initialize-transforms-per-stage 0 --interpolation Linear --output transform --transform Affine[ 0.1 ] --metric Mattes[ /home/sahad3/.cache/templateflow/tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_res-02_desc-fMRIPrep_boldref.nii.gz, /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_mid_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/merge/template.nii.gz, 1, 64, Random, 0.2 ] --convergence [ 200, 1e-09, 10 ] --smoothing-sigmas 2.0mm --shrink-factors 2 --use-estimate-learning-rate-once 1 --use-histogram-matching 1 --winsorize-image-intensities [ 0.05, 0.98 ] --write-composite-transform 0 190731-15:22:13,909 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.n4_correct". 190731-15:22:15,651 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_pass" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_pass". 190731-15:22:15,654 nipype.workflow INFO: [Node] Running "skullstrip_first_pass" ("nipype.interfaces.fsl.preprocess.BET"), a CommandLine Interface with command: bet /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/n4_correct/ref_bold_corrected.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_pass/ref_bold_corrected_brain.nii.gz -f 0.20 -m 190731-15:22:17,507 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_mid_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_opposite_wf.enhance_and_skullstrip_bold_wf.norm". 190731-15:22:18,98 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_pass". 190731-15:22:19,661 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_dilate" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_dilate". 190731-15:22:19,664 nipype.workflow INFO: [Node] Running "skullstrip_first_dilate" ("nipype.interfaces.fsl.maths.DilateImage"), a CommandLine Interface with command: fslmaths -dt char /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_pass/ref_bold_corrected_brain_mask.nii.gz -kernel sphere 6.0000 -dilF /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_dilate/ref_bold_corrected_brain_mask_dil.nii.gz 190731-15:22:19,664 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_mid_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_opposite_wf.enhance_and_skullstrip_bold_wf.map_brainmask" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_mid_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/enhance_and_skullstrip_bold_wf/map_brainmask". 190731-15:22:19,668 nipype.workflow INFO: [Node] Running "map_brainmask" ("niworkflows.interfaces.fixes.FixHeaderApplyTransforms"), a CommandLine Interface with command: antsApplyTransforms --default-value 0 --float 1 --input /home/sahad3/.cache/templateflow/tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_res-02_desc-brain_mask.nii.gz --interpolation MultiLabel --output tpl-MNI152NLin2009cAsym_res-02_desc-brain_mask_trans.nii.gz --reference-image /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_mid_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/merge/template.nii.gz --transform [ /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_mid_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/enhance_and_skullstrip_bold_wf/norm/transform0GenericAffine.mat, 1 ] 190731-15:22:19,681 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_mid_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_matching_wf.enhance_and_skullstrip_bold_wf.init_aff" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_mid_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/enhance_and_skullstrip_bold_wf/init_aff". 190731-15:22:19,684 nipype.workflow INFO: [Node] Running "init_aff" ("niworkflows.interfaces.ants.AI"), a CommandLine Interface with command: antsAI -c [10,0.000001,10] -d 3 -x /home/sahad3/.cache/templateflow/tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_res-02_desc-brain_mask.nii.gz -m Mattes[/home/sahad3/.cache/templateflow/tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_res-02_desc-fMRIPrep_boldref.nii.gz,/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_mid_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/merge/template.nii.gz,32,Regular,0.200000] -o initialization.mat -p 0 -s [20.000000,0.120000] -t Affine[0.100000] -v 1 190731-15:22:20,153 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_dilate". 190731-15:22:21,610 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_mask" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_mask". 190731-15:22:21,614 nipype.workflow INFO: [Node] Running "skullstrip_first_mask" ("nipype.interfaces.fsl.maths.ApplyMask"), a CommandLine Interface with command: fslmaths /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_pass/ref_bold_corrected_brain.nii.gz -mas /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_dilate/ref_bold_corrected_brain_mask_dil.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_mask/ref_bold_corrected_brain_masked.nii.gz 190731-15:22:21,771 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_mask". 190731-15:22:22,280 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_mid_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_opposite_wf.enhance_and_skullstrip_bold_wf.map_brainmask". 190731-15:22:23,617 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.unifize" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/unifize". 190731-15:22:23,620 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_mid_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_opposite_wf.enhance_and_skullstrip_bold_wf.pre_mask_dilate" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_mid_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/enhance_and_skullstrip_bold_wf/pre_mask_dilate". 190731-15:22:23,622 nipype.workflow INFO: [Node] Running "unifize" ("nipype.interfaces.afni.utils.Unifize"), a CommandLine Interface with command: 3dUnifize -clfrac 0.2 -rbt 18.3 65.0 90.0 -prefix uni.nii.gz -T2 -input /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/unifize/ref_bold_corrected_brain_masked.nii.gz 190731-15:22:23,623 nipype.workflow INFO: [Node] Running "pre_mask_dilate" ("nipype.interfaces.fsl.maths.DilateImage"), a CommandLine Interface with command: fslmaths -dt char /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_mid_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/enhance_and_skullstrip_bold_wf/map_brainmask/tpl-MNI152NLin2009cAsym_res-02_desc-brain_mask_trans.nii.gz -kernel sphere 3.0000 -dilF /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_mid_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/enhance_and_skullstrip_bold_wf/pre_mask_dilate/tpl-MNI152NLin2009cAsym_res-02_desc-brain_mask_trans_dil.nii.gz 190731-15:22:23,971 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_mid_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_opposite_wf.enhance_and_skullstrip_bold_wf.pre_mask_dilate". 190731-15:22:24,810 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.unifize". 190731-15:22:25,641 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.fixhdr_unifize" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/fixhdr_unifize". 190731-15:22:25,643 nipype.workflow INFO: [Node] Running "fixhdr_unifize" ("niworkflows.interfaces.utils.CopyXForm") 190731-15:22:25,690 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.fixhdr_unifize". 190731-15:22:27,646 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.skullstrip_second_pass" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_second_pass". 190731-15:22:27,648 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_mid_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_opposite_wf.enhance_and_skullstrip_bold_wf.n4_correct" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_mid_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/enhance_and_skullstrip_bold_wf/n4_correct". 190731-15:22:27,649 nipype.workflow INFO: [Node] Running "skullstrip_second_pass" ("nipype.interfaces.afni.preprocess.Automask"), a CommandLine Interface with command: 3dAutomask -apply_prefix uni_xform_masked.nii.gz -dilate 1 -prefix uni_xform_mask.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_second_pass/uni_xform.nii.gz 190731-15:22:27,650 nipype.workflow INFO: [Node] Running "n4_correct" ("nipype.interfaces.ants.segmentation.N4BiasFieldCorrection"), a CommandLine Interface with command: N4BiasFieldCorrection --bspline-fitting [ 200 ] -d 3 --input-image /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_mid_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/merge/template.nii.gz --mask-image /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_mid_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/enhance_and_skullstrip_bold_wf/check_hdr/tpl-MNI152NLin2009cAsym_res-02_desc-brain_mask_trans_dil_hdr.nii.gz --output template_corrected.nii.gz 190731-15:22:27,687 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_mid_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_matching_wf.enhance_and_skullstrip_bold_wf.init_aff". 190731-15:22:27,841 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.skullstrip_second_pass". 190731-15:22:29,668 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.fixhdr_skullstrip2" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/fixhdr_skullstrip2". 190731-15:22:29,670 nipype.workflow INFO: [Node] Running "fixhdr_skullstrip2" ("niworkflows.interfaces.utils.CopyXForm") 190731-15:22:29,676 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_mid_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_matching_wf.enhance_and_skullstrip_bold_wf.norm" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_mid_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/enhance_and_skullstrip_bold_wf/norm". 190731-15:22:29,682 nipype.workflow INFO: [Node] Running "norm" ("niworkflows.interfaces.fixes.FixHeaderRegistration"), a CommandLine Interface with command: antsRegistration --collapse-output-transforms 1 --dimensionality 3 --float 1 --initial-moving-transform [ /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_mid_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/enhance_and_skullstrip_bold_wf/init_aff/initialization.mat, 0 ] --initialize-transforms-per-stage 0 --interpolation Linear --output transform --transform Affine[ 0.1 ] --metric Mattes[ /home/sahad3/.cache/templateflow/tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_res-02_desc-fMRIPrep_boldref.nii.gz, /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_mid_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/merge/template.nii.gz, 1, 64, Random, 0.2 ] --convergence [ 200, 1e-09, 10 ] --smoothing-sigmas 2.0mm --shrink-factors 2 --use-estimate-learning-rate-once 1 --use-histogram-matching 1 --winsorize-image-intensities [ 0.05, 0.98 ] --write-composite-transform 0 190731-15:22:29,698 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.fixhdr_skullstrip2". 190731-15:22:30,380 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_mid_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_opposite_wf.enhance_and_skullstrip_bold_wf.n4_correct". 190731-15:22:31,673 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.combine_masks" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/combine_masks". 190731-15:22:31,674 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_mid_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_opposite_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_pass" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_mid_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_pass". 190731-15:22:31,676 nipype.workflow INFO: [Node] Running "combine_masks" ("nipype.interfaces.fsl.maths.BinaryMaths"), a CommandLine Interface with command: fslmaths /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_pass/ref_bold_corrected_brain_mask.nii.gz -mul /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/fixhdr_skullstrip2/uni_xform_mask_xform.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/combine_masks/ref_bold_corrected_brain_mask_maths.nii.gz 190731-15:22:31,678 nipype.workflow INFO: [Node] Running "skullstrip_first_pass" ("nipype.interfaces.fsl.preprocess.BET"), a CommandLine Interface with command: bet /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_mid_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/enhance_and_skullstrip_bold_wf/n4_correct/template_corrected.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_mid_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_pass/template_corrected_brain.nii.gz -f 0.20 -m 190731-15:22:31,780 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.combine_masks". 190731-15:22:31,976 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_mid_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_matching_wf.enhance_and_skullstrip_bold_wf.norm". 190731-15:22:33,714 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.apply_mask" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/apply_mask". 190731-15:22:33,717 nipype.workflow INFO: [Node] Running "apply_mask" ("nipype.interfaces.fsl.maths.ApplyMask"), a CommandLine Interface with command: fslmaths /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/fixhdr_unifize/uni_xform.nii.gz -mas /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/combine_masks/ref_bold_corrected_brain_mask_maths.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/apply_mask/uni_xform_masked.nii.gz 190731-15:22:33,719 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_mid_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_matching_wf.enhance_and_skullstrip_bold_wf.map_brainmask" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_mid_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/enhance_and_skullstrip_bold_wf/map_brainmask". 190731-15:22:33,722 nipype.workflow INFO: [Node] Running "map_brainmask" ("niworkflows.interfaces.fixes.FixHeaderApplyTransforms"), a CommandLine Interface with command: antsApplyTransforms --default-value 0 --float 1 --input /home/sahad3/.cache/templateflow/tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_res-02_desc-brain_mask.nii.gz --interpolation MultiLabel --output tpl-MNI152NLin2009cAsym_res-02_desc-brain_mask_trans.nii.gz --reference-image /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_mid_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/merge/template.nii.gz --transform [ /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_mid_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/enhance_and_skullstrip_bold_wf/norm/transform0GenericAffine.mat, 1 ] 190731-15:22:33,747 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_mid_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_opposite_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_pass". 190731-15:22:33,775 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_mid_wf.bold_hmc_wf.fsl2itk" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_mid_wf/bold_hmc_wf/fsl2itk". 190731-15:22:33,798 nipype.workflow INFO: [Node] Running "fsl2itk" ("niworkflows.interfaces.itk.MCFLIRT2ITK") 190731-15:22:33,860 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.apply_mask". 190731-15:22:35,644 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_mid_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_opposite_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_dilate" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_mid_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_dilate". 190731-15:22:35,648 nipype.workflow INFO: [Node] Running "skullstrip_first_dilate" ("nipype.interfaces.fsl.maths.DilateImage"), a CommandLine Interface with command: fslmaths -dt char /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_mid_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_pass/template_corrected_brain_mask.nii.gz -kernel sphere 6.0000 -dilF /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_mid_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_dilate/template_corrected_brain_mask_dil.nii.gz 190731-15:22:36,262 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_mid_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_opposite_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_dilate". 190731-15:22:36,331 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_mid_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_matching_wf.enhance_and_skullstrip_bold_wf.map_brainmask". 190731-15:22:37,629 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_mid_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_opposite_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_mask" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_mid_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_mask". 190731-15:22:37,631 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_mid_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_matching_wf.enhance_and_skullstrip_bold_wf.pre_mask_dilate" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_mid_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/enhance_and_skullstrip_bold_wf/pre_mask_dilate". 190731-15:22:37,632 nipype.workflow INFO: [Node] Running "skullstrip_first_mask" ("nipype.interfaces.fsl.maths.ApplyMask"), a CommandLine Interface with command: fslmaths /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_mid_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_pass/template_corrected_brain.nii.gz -mas /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_mid_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_dilate/template_corrected_brain_mask_dil.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_mid_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_mask/template_corrected_brain_masked.nii.gz 190731-15:22:37,635 nipype.workflow INFO: [Node] Running "pre_mask_dilate" ("nipype.interfaces.fsl.maths.DilateImage"), a CommandLine Interface with command: fslmaths -dt char /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_mid_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/enhance_and_skullstrip_bold_wf/map_brainmask/tpl-MNI152NLin2009cAsym_res-02_desc-brain_mask_trans.nii.gz -kernel sphere 3.0000 -dilF /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_mid_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/enhance_and_skullstrip_bold_wf/pre_mask_dilate/tpl-MNI152NLin2009cAsym_res-02_desc-brain_mask_trans_dil.nii.gz 190731-15:22:37,789 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_mid_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_opposite_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_mask". 190731-15:22:37,967 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_mid_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_matching_wf.enhance_and_skullstrip_bold_wf.pre_mask_dilate". 190731-15:22:39,664 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_mid_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_opposite_wf.enhance_and_skullstrip_bold_wf.unifize" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_mid_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/enhance_and_skullstrip_bold_wf/unifize". 190731-15:22:39,668 nipype.workflow INFO: [Node] Running "unifize" ("nipype.interfaces.afni.utils.Unifize"), a CommandLine Interface with command: 3dUnifize -clfrac 0.2 -rbt 18.3 65.0 90.0 -prefix uni.nii.gz -T2 -input /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_mid_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/enhance_and_skullstrip_bold_wf/unifize/template_corrected_brain_masked.nii.gz 190731-15:22:41,70 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_mid_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_opposite_wf.enhance_and_skullstrip_bold_wf.unifize". 190731-15:22:41,682 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_mid_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_opposite_wf.enhance_and_skullstrip_bold_wf.fixhdr_unifize" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_mid_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/enhance_and_skullstrip_bold_wf/fixhdr_unifize". 190731-15:22:41,684 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_mid_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_matching_wf.enhance_and_skullstrip_bold_wf.n4_correct" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_mid_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/enhance_and_skullstrip_bold_wf/n4_correct". 190731-15:22:41,684 nipype.workflow INFO: [Node] Running "fixhdr_unifize" ("niworkflows.interfaces.utils.CopyXForm") 190731-15:22:41,687 nipype.workflow INFO: [Node] Running "n4_correct" ("nipype.interfaces.ants.segmentation.N4BiasFieldCorrection"), a CommandLine Interface with command: N4BiasFieldCorrection --bspline-fitting [ 200 ] -d 3 --input-image /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_mid_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/merge/template.nii.gz --mask-image /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_mid_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/enhance_and_skullstrip_bold_wf/check_hdr/tpl-MNI152NLin2009cAsym_res-02_desc-brain_mask_trans_dil_hdr.nii.gz --output template_corrected.nii.gz 190731-15:22:41,741 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_mid_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_opposite_wf.enhance_and_skullstrip_bold_wf.fixhdr_unifize". 190731-15:22:43,675 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_mid_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_opposite_wf.enhance_and_skullstrip_bold_wf.skullstrip_second_pass" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_mid_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/enhance_and_skullstrip_bold_wf/skullstrip_second_pass". 190731-15:22:43,679 nipype.workflow INFO: [Node] Running "skullstrip_second_pass" ("nipype.interfaces.afni.preprocess.Automask"), a CommandLine Interface with command: 3dAutomask -apply_prefix uni_xform_masked.nii.gz -dilate 1 -prefix uni_xform_mask.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_mid_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/enhance_and_skullstrip_bold_wf/skullstrip_second_pass/uni_xform.nii.gz 190731-15:22:43,879 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_mid_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_opposite_wf.enhance_and_skullstrip_bold_wf.skullstrip_second_pass". 190731-15:22:44,604 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_mid_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_matching_wf.enhance_and_skullstrip_bold_wf.n4_correct". 190731-15:22:45,656 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_mid_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_opposite_wf.enhance_and_skullstrip_bold_wf.fixhdr_skullstrip2" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_mid_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/enhance_and_skullstrip_bold_wf/fixhdr_skullstrip2". 190731-15:22:45,658 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_mid_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_matching_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_pass" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_mid_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_pass". 190731-15:22:45,659 nipype.workflow INFO: [Node] Running "fixhdr_skullstrip2" ("niworkflows.interfaces.utils.CopyXForm") 190731-15:22:45,661 nipype.workflow INFO: [Node] Running "skullstrip_first_pass" ("nipype.interfaces.fsl.preprocess.BET"), a CommandLine Interface with command: bet /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_mid_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/enhance_and_skullstrip_bold_wf/n4_correct/template_corrected.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_mid_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_pass/template_corrected_brain.nii.gz -f 0.20 -m 190731-15:22:45,691 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_mid_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_opposite_wf.enhance_and_skullstrip_bold_wf.fixhdr_skullstrip2". 190731-15:22:47,694 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_mid_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_opposite_wf.enhance_and_skullstrip_bold_wf.combine_masks" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_mid_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/enhance_and_skullstrip_bold_wf/combine_masks". 190731-15:22:47,698 nipype.workflow INFO: [Node] Running "combine_masks" ("nipype.interfaces.fsl.maths.BinaryMaths"), a CommandLine Interface with command: fslmaths /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_mid_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_pass/template_corrected_brain_mask.nii.gz -mul /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_mid_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/enhance_and_skullstrip_bold_wf/fixhdr_skullstrip2/uni_xform_mask_xform.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_mid_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/enhance_and_skullstrip_bold_wf/combine_masks/template_corrected_brain_mask_maths.nii.gz 190731-15:22:47,892 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_mid_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_opposite_wf.enhance_and_skullstrip_bold_wf.combine_masks". 190731-15:22:48,107 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_mid_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_matching_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_pass". 190731-15:22:49,669 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_mid_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_opposite_wf.enhance_and_skullstrip_bold_wf.apply_mask" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_mid_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/enhance_and_skullstrip_bold_wf/apply_mask". 190731-15:22:49,671 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_mid_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_matching_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_dilate" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_mid_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_dilate". 190731-15:22:49,672 nipype.workflow INFO: [Node] Running "apply_mask" ("nipype.interfaces.fsl.maths.ApplyMask"), a CommandLine Interface with command: fslmaths /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_mid_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/enhance_and_skullstrip_bold_wf/fixhdr_unifize/uni_xform.nii.gz -mas /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_mid_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/enhance_and_skullstrip_bold_wf/combine_masks/template_corrected_brain_mask_maths.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_mid_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/enhance_and_skullstrip_bold_wf/apply_mask/uni_xform_masked.nii.gz 190731-15:22:49,674 nipype.workflow INFO: [Node] Running "skullstrip_first_dilate" ("nipype.interfaces.fsl.maths.DilateImage"), a CommandLine Interface with command: fslmaths -dt char /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_mid_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_pass/template_corrected_brain_mask.nii.gz -kernel sphere 6.0000 -dilF /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_mid_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_dilate/template_corrected_brain_mask_dil.nii.gz 190731-15:22:49,828 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_mid_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_opposite_wf.enhance_and_skullstrip_bold_wf.apply_mask". 190731-15:22:50,226 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_mid_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_matching_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_dilate". 190731-15:22:51,652 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_mid_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_matching_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_mask" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_mid_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_mask". 190731-15:22:51,655 nipype.workflow INFO: [Node] Running "skullstrip_first_mask" ("nipype.interfaces.fsl.maths.ApplyMask"), a CommandLine Interface with command: fslmaths /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_mid_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_pass/template_corrected_brain.nii.gz -mas /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_mid_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_dilate/template_corrected_brain_mask_dil.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_mid_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_mask/template_corrected_brain_masked.nii.gz 190731-15:22:51,891 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_mid_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_matching_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_mask". 190731-15:22:53,623 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_mid_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_matching_wf.enhance_and_skullstrip_bold_wf.unifize" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_mid_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/enhance_and_skullstrip_bold_wf/unifize". 190731-15:22:53,626 nipype.workflow INFO: [Node] Running "unifize" ("nipype.interfaces.afni.utils.Unifize"), a CommandLine Interface with command: 3dUnifize -clfrac 0.2 -rbt 18.3 65.0 90.0 -prefix uni.nii.gz -T2 -input /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_mid_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/enhance_and_skullstrip_bold_wf/unifize/template_corrected_brain_masked.nii.gz 190731-15:22:55,45 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_mid_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_matching_wf.enhance_and_skullstrip_bold_wf.unifize". 190731-15:22:55,699 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_mid_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_matching_wf.enhance_and_skullstrip_bold_wf.fixhdr_unifize" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_mid_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/enhance_and_skullstrip_bold_wf/fixhdr_unifize". 190731-15:22:55,701 nipype.workflow INFO: [Node] Running "fixhdr_unifize" ("niworkflows.interfaces.utils.CopyXForm") 190731-15:22:55,753 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_mid_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_matching_wf.enhance_and_skullstrip_bold_wf.fixhdr_unifize". 190731-15:22:56,159 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_mid_wf.sdc_wf.pepolar_unwarp_wf.qwarp". 190731-15:22:57,699 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_mid_wf.sdc_wf.pepolar_unwarp_wf.cphdr_warp" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_mid_wf/sdc_wf/pepolar_unwarp_wf/cphdr_warp". 190731-15:22:57,701 nipype.workflow INFO: [Node] Running "cphdr_warp" ("niworkflows.interfaces.utils.CopyHeader") 190731-15:22:57,704 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_matching_wf.fmap2ref_reg" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/fmap2ref_reg". 190731-15:22:57,705 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_mid_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_matching_wf.enhance_and_skullstrip_bold_wf.skullstrip_second_pass" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_mid_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/enhance_and_skullstrip_bold_wf/skullstrip_second_pass". 190731-15:22:57,708 nipype.workflow INFO: [Node] Running "fmap2ref_reg" ("nipype.interfaces.ants.registration.Registration"), a CommandLine Interface with command: antsRegistration --collapse-output-transforms 1 --dimensionality 3 --float 1 --initialize-transforms-per-stage 0 --interpolation LanczosWindowedSinc --output [ transform, transform_Warped.nii.gz ] --transform Translation[ 0.05 ] --metric Mattes[ /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/apply_mask/uni_xform_masked.nii.gz, /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/enhance_and_skullstrip_bold_wf/apply_mask/uni_xform_masked.nii.gz, 1, 64, Random, 0.5 ] --convergence [ 500, 1e-07, 200 ] --smoothing-sigmas 8.0mm --shrink-factors 2 --use-estimate-learning-rate-once 1 --use-histogram-matching 1 --transform Rigid[ 0.01 ] --metric Mattes[ /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/apply_mask/uni_xform_masked.nii.gz, /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/enhance_and_skullstrip_bold_wf/apply_mask/uni_xform_masked.nii.gz, 1, 64, Random, 0.5 ] --convergence [ 200, 1e-08, 100 ] --smoothing-sigmas 2.0mm --shrink-factors 1 --use-estimate-learning-rate-once 1 --use-histogram-matching 1 --winsorize-image-intensities [ 0.005, 0.998 ] --write-composite-transform 1 190731-15:22:57,709 nipype.workflow INFO: [Node] Running "skullstrip_second_pass" ("nipype.interfaces.afni.preprocess.Automask"), a CommandLine Interface with command: 3dAutomask -apply_prefix uni_xform_masked.nii.gz -dilate 1 -prefix uni_xform_mask.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_mid_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/enhance_and_skullstrip_bold_wf/skullstrip_second_pass/uni_xform.nii.gz 190731-15:22:57,795 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_mid_wf.sdc_wf.pepolar_unwarp_wf.cphdr_warp". 190731-15:22:57,893 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_mid_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_matching_wf.enhance_and_skullstrip_bold_wf.skullstrip_second_pass". 190731-15:22:59,697 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_mid_wf.sdc_wf.pepolar_unwarp_wf.to_ants" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_mid_wf/sdc_wf/pepolar_unwarp_wf/to_ants". 190731-15:22:59,698 nipype.workflow INFO: [Node] Running "to_ants" ("nipype.interfaces.utility.wrappers.Function") 190731-15:22:59,699 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_mid_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_matching_wf.enhance_and_skullstrip_bold_wf.fixhdr_skullstrip2" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_mid_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/enhance_and_skullstrip_bold_wf/fixhdr_skullstrip2". 190731-15:22:59,701 nipype.workflow INFO: [Node] Running "fixhdr_skullstrip2" ("niworkflows.interfaces.utils.CopyXForm") 190731-15:22:59,746 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_mid_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_matching_wf.enhance_and_skullstrip_bold_wf.fixhdr_skullstrip2". 190731-15:22:59,772 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_mid_wf.sdc_wf.pepolar_unwarp_wf.to_ants". 190731-15:23:02,221 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_mid_wf.sdc_wf.pepolar_unwarp_wf.unwarp_reference" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_mid_wf/sdc_wf/pepolar_unwarp_wf/unwarp_reference". 190731-15:23:02,223 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_mid_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_matching_wf.enhance_and_skullstrip_bold_wf.combine_masks" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_mid_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/enhance_and_skullstrip_bold_wf/combine_masks". 190731-15:23:02,224 nipype.workflow INFO: [Node] Running "unwarp_reference" ("niworkflows.interfaces.registration.ANTSApplyTransformsRPT"), a CommandLine Interface with command: antsApplyTransforms --default-value 0 --dimensionality 3 --float 1 --input /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_mid_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/n4_correct/ref_bold_corrected.nii.gz --interpolation LanczosWindowedSinc --output ref_bold_corrected_trans.nii.gz --reference-image /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_mid_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/n4_correct/ref_bold_corrected.nii.gz --transform /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_mid_wf/sdc_wf/pepolar_unwarp_wf/cphdr_warp/_warpfieldQwarp_PLUS_WARP_fixhdr.nii.gz 190731-15:23:02,226 nipype.workflow INFO: [Node] Running "combine_masks" ("nipype.interfaces.fsl.maths.BinaryMaths"), a CommandLine Interface with command: fslmaths /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_mid_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_pass/template_corrected_brain_mask.nii.gz -mul /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_mid_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/enhance_and_skullstrip_bold_wf/fixhdr_skullstrip2/uni_xform_mask_xform.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_mid_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/enhance_and_skullstrip_bold_wf/combine_masks/template_corrected_brain_mask_maths.nii.gz 190731-15:23:02,352 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_mid_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_matching_wf.enhance_and_skullstrip_bold_wf.combine_masks". 190731-15:23:03,677 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_mid_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_matching_wf.enhance_and_skullstrip_bold_wf.apply_mask" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_mid_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/enhance_and_skullstrip_bold_wf/apply_mask". 190731-15:23:03,679 nipype.workflow INFO: [Node] Running "apply_mask" ("nipype.interfaces.fsl.maths.ApplyMask"), a CommandLine Interface with command: fslmaths /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_mid_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/enhance_and_skullstrip_bold_wf/fixhdr_unifize/uni_xform.nii.gz -mas /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_mid_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/enhance_and_skullstrip_bold_wf/combine_masks/template_corrected_brain_mask_maths.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_mid_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/enhance_and_skullstrip_bold_wf/apply_mask/uni_xform_masked.nii.gz 190731-15:23:03,811 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_mid_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_matching_wf.enhance_and_skullstrip_bold_wf.apply_mask". 190731-15:23:04,100 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_mid_wf.sdc_wf.pepolar_unwarp_wf.unwarp_reference". 190731-15:23:10,165 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_mid_wf.bold_hmc_wf.fsl2itk". 190731-15:23:10,228 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_matching_wf.fmap2ref_reg". 190731-15:23:11,605 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_mid_wf.sdc_wf.pepolar_unwarp_wf.enhance_and_skullstrip_bold_wf.init_aff" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_mid_wf/sdc_wf/pepolar_unwarp_wf/enhance_and_skullstrip_bold_wf/init_aff". 190731-15:23:11,607 nipype.workflow INFO: [Node] Running "init_aff" ("niworkflows.interfaces.ants.AI"), a CommandLine Interface with command: antsAI -c [10,0.000001,10] -d 3 -x /home/sahad3/.cache/templateflow/tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_res-02_desc-brain_mask.nii.gz -m Mattes[/home/sahad3/.cache/templateflow/tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_res-02_desc-fMRIPrep_boldref.nii.gz,/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_mid_wf/sdc_wf/pepolar_unwarp_wf/unwarp_reference/ref_bold_corrected_trans.nii.gz,32,Regular,0.200000] -o initialization.mat -p 0 -s [20.000000,0.120000] -t Affine[0.100000] -v 1 190731-15:23:11,638 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_mid_wf.bold_bold_trans_wf.bold_transform" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_mid_wf/bold_bold_trans_wf/bold_transform". 190731-15:23:11,662 nipype.workflow INFO: [Node] Running "bold_transform" ("niworkflows.interfaces.itk.MultiApplyTransforms") 190731-15:23:17,843 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_mid_wf.sdc_wf.pepolar_unwarp_wf.enhance_and_skullstrip_bold_wf.init_aff". 190731-15:23:19,712 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_mid_wf.sdc_wf.pepolar_unwarp_wf.enhance_and_skullstrip_bold_wf.norm" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_mid_wf/sdc_wf/pepolar_unwarp_wf/enhance_and_skullstrip_bold_wf/norm". 190731-15:23:19,719 nipype.workflow INFO: [Node] Running "norm" ("niworkflows.interfaces.fixes.FixHeaderRegistration"), a CommandLine Interface with command: antsRegistration --collapse-output-transforms 1 --dimensionality 3 --float 1 --initial-moving-transform [ /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_mid_wf/sdc_wf/pepolar_unwarp_wf/enhance_and_skullstrip_bold_wf/init_aff/initialization.mat, 0 ] --initialize-transforms-per-stage 0 --interpolation Linear --output transform --transform Affine[ 0.1 ] --metric Mattes[ /home/sahad3/.cache/templateflow/tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_res-02_desc-fMRIPrep_boldref.nii.gz, /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_mid_wf/sdc_wf/pepolar_unwarp_wf/unwarp_reference/ref_bold_corrected_trans.nii.gz, 1, 64, Random, 0.2 ] --convergence [ 200, 1e-09, 10 ] --smoothing-sigmas 2.0mm --shrink-factors 2 --use-estimate-learning-rate-once 1 --use-histogram-matching 1 --winsorize-image-intensities [ 0.05, 0.98 ] --write-composite-transform 0 190731-15:23:21,255 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_mid_wf.sdc_wf.pepolar_unwarp_wf.enhance_and_skullstrip_bold_wf.norm". 190731-15:23:23,620 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_mid_wf.sdc_wf.pepolar_unwarp_wf.enhance_and_skullstrip_bold_wf.map_brainmask" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_mid_wf/sdc_wf/pepolar_unwarp_wf/enhance_and_skullstrip_bold_wf/map_brainmask". 190731-15:23:23,624 nipype.workflow INFO: [Node] Running "map_brainmask" ("niworkflows.interfaces.fixes.FixHeaderApplyTransforms"), a CommandLine Interface with command: antsApplyTransforms --default-value 0 --float 1 --input /home/sahad3/.cache/templateflow/tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_res-02_desc-brain_mask.nii.gz --interpolation MultiLabel --output tpl-MNI152NLin2009cAsym_res-02_desc-brain_mask_trans.nii.gz --reference-image /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_mid_wf/sdc_wf/pepolar_unwarp_wf/unwarp_reference/ref_bold_corrected_trans.nii.gz --transform [ /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_mid_wf/sdc_wf/pepolar_unwarp_wf/enhance_and_skullstrip_bold_wf/norm/transform0GenericAffine.mat, 1 ] 190731-15:23:23,624 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_opposite_wf.fmap2ref_reg" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/fmap2ref_reg". 190731-15:23:23,628 nipype.workflow INFO: [Node] Running "fmap2ref_reg" ("nipype.interfaces.ants.registration.Registration"), a CommandLine Interface with command: antsRegistration --collapse-output-transforms 1 --dimensionality 3 --float 1 --initialize-transforms-per-stage 0 --interpolation LanczosWindowedSinc --output [ transform, transform_Warped.nii.gz ] --transform Translation[ 0.05 ] --metric Mattes[ /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/apply_mask/uni_xform_masked.nii.gz, /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/enhance_and_skullstrip_bold_wf/apply_mask/uni_xform_masked.nii.gz, 1, 64, Random, 0.5 ] --convergence [ 500, 1e-07, 200 ] --smoothing-sigmas 8.0mm --shrink-factors 2 --use-estimate-learning-rate-once 1 --use-histogram-matching 1 --transform Rigid[ 0.01 ] --metric Mattes[ /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/apply_mask/uni_xform_masked.nii.gz, /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/enhance_and_skullstrip_bold_wf/apply_mask/uni_xform_masked.nii.gz, 1, 64, Random, 0.5 ] --convergence [ 200, 1e-08, 100 ] --smoothing-sigmas 2.0mm --shrink-factors 1 --use-estimate-learning-rate-once 1 --use-histogram-matching 1 --winsorize-image-intensities [ 0.005, 0.998 ] --write-composite-transform 1 190731-15:23:26,159 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_mid_wf.sdc_wf.pepolar_unwarp_wf.enhance_and_skullstrip_bold_wf.map_brainmask". 190731-15:23:27,738 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_mid_wf.sdc_wf.pepolar_unwarp_wf.enhance_and_skullstrip_bold_wf.pre_mask_dilate" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_mid_wf/sdc_wf/pepolar_unwarp_wf/enhance_and_skullstrip_bold_wf/pre_mask_dilate". 190731-15:23:27,742 nipype.workflow INFO: [Node] Running "pre_mask_dilate" ("nipype.interfaces.fsl.maths.DilateImage"), a CommandLine Interface with command: fslmaths -dt char /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_mid_wf/sdc_wf/pepolar_unwarp_wf/enhance_and_skullstrip_bold_wf/map_brainmask/tpl-MNI152NLin2009cAsym_res-02_desc-brain_mask_trans.nii.gz -kernel sphere 3.0000 -dilF /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_mid_wf/sdc_wf/pepolar_unwarp_wf/enhance_and_skullstrip_bold_wf/pre_mask_dilate/tpl-MNI152NLin2009cAsym_res-02_desc-brain_mask_trans_dil.nii.gz 190731-15:23:28,29 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_mid_wf.sdc_wf.pepolar_unwarp_wf.enhance_and_skullstrip_bold_wf.pre_mask_dilate". 190731-15:23:31,673 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_mid_wf.sdc_wf.pepolar_unwarp_wf.enhance_and_skullstrip_bold_wf.n4_correct" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_mid_wf/sdc_wf/pepolar_unwarp_wf/enhance_and_skullstrip_bold_wf/n4_correct". 190731-15:23:31,677 nipype.workflow INFO: [Node] Running "n4_correct" ("nipype.interfaces.ants.segmentation.N4BiasFieldCorrection"), a CommandLine Interface with command: N4BiasFieldCorrection --bspline-fitting [ 200 ] -d 3 --input-image /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_mid_wf/sdc_wf/pepolar_unwarp_wf/unwarp_reference/ref_bold_corrected_trans.nii.gz --mask-image /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_mid_wf/sdc_wf/pepolar_unwarp_wf/enhance_and_skullstrip_bold_wf/check_hdr/tpl-MNI152NLin2009cAsym_res-02_desc-brain_mask_trans_dil_hdr.nii.gz --output ref_bold_corrected_trans_corrected.nii.gz 190731-15:23:34,764 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_mid_wf.sdc_wf.pepolar_unwarp_wf.enhance_and_skullstrip_bold_wf.n4_correct". 190731-15:23:35,686 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_mid_wf.sdc_wf.pepolar_unwarp_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_pass" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_mid_wf/sdc_wf/pepolar_unwarp_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_pass". 190731-15:23:35,689 nipype.workflow INFO: [Node] Running "skullstrip_first_pass" ("nipype.interfaces.fsl.preprocess.BET"), a CommandLine Interface with command: bet /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_mid_wf/sdc_wf/pepolar_unwarp_wf/enhance_and_skullstrip_bold_wf/n4_correct/ref_bold_corrected_trans_corrected.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_mid_wf/sdc_wf/pepolar_unwarp_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_pass/ref_bold_corrected_trans_corrected_brain.nii.gz -f 0.20 -m 190731-15:23:37,818 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_mid_wf.sdc_wf.pepolar_unwarp_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_pass". 190731-15:23:39,722 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_mid_wf.sdc_wf.pepolar_unwarp_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_dilate" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_mid_wf/sdc_wf/pepolar_unwarp_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_dilate". 190731-15:23:39,726 nipype.workflow INFO: [Node] Running "skullstrip_first_dilate" ("nipype.interfaces.fsl.maths.DilateImage"), a CommandLine Interface with command: fslmaths -dt char /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_mid_wf/sdc_wf/pepolar_unwarp_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_pass/ref_bold_corrected_trans_corrected_brain_mask.nii.gz -kernel sphere 6.0000 -dilF /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_mid_wf/sdc_wf/pepolar_unwarp_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_dilate/ref_bold_corrected_trans_corrected_brain_mask_dil.nii.gz 190731-15:23:40,427 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_mid_wf.sdc_wf.pepolar_unwarp_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_dilate". 190731-15:23:41,635 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_mid_wf.sdc_wf.pepolar_unwarp_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_mask" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_mid_wf/sdc_wf/pepolar_unwarp_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_mask". 190731-15:23:41,638 nipype.workflow INFO: [Node] Running "skullstrip_first_mask" ("nipype.interfaces.fsl.maths.ApplyMask"), a CommandLine Interface with command: fslmaths /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_mid_wf/sdc_wf/pepolar_unwarp_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_pass/ref_bold_corrected_trans_corrected_brain.nii.gz -mas /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_mid_wf/sdc_wf/pepolar_unwarp_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_dilate/ref_bold_corrected_trans_corrected_brain_mask_dil.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_mid_wf/sdc_wf/pepolar_unwarp_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_mask/ref_bold_corrected_trans_corrected_brain_masked.nii.gz 190731-15:23:41,802 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_mid_wf.sdc_wf.pepolar_unwarp_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_mask". 190731-15:23:43,663 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_mid_wf.sdc_wf.pepolar_unwarp_wf.enhance_and_skullstrip_bold_wf.unifize" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_mid_wf/sdc_wf/pepolar_unwarp_wf/enhance_and_skullstrip_bold_wf/unifize". 190731-15:23:43,667 nipype.workflow INFO: [Node] Running "unifize" ("nipype.interfaces.afni.utils.Unifize"), a CommandLine Interface with command: 3dUnifize -clfrac 0.2 -rbt 18.3 65.0 90.0 -prefix uni.nii.gz -T2 -input /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_mid_wf/sdc_wf/pepolar_unwarp_wf/enhance_and_skullstrip_bold_wf/unifize/ref_bold_corrected_trans_corrected_brain_masked.nii.gz 190731-15:23:45,298 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_mid_wf.sdc_wf.pepolar_unwarp_wf.enhance_and_skullstrip_bold_wf.unifize". 190731-15:23:47,730 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_mid_wf.sdc_wf.pepolar_unwarp_wf.enhance_and_skullstrip_bold_wf.fixhdr_unifize" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_mid_wf/sdc_wf/pepolar_unwarp_wf/enhance_and_skullstrip_bold_wf/fixhdr_unifize". 190731-15:23:47,733 nipype.workflow INFO: [Node] Running "fixhdr_unifize" ("niworkflows.interfaces.utils.CopyXForm") 190731-15:23:47,788 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_mid_wf.sdc_wf.pepolar_unwarp_wf.enhance_and_skullstrip_bold_wf.fixhdr_unifize". 190731-15:23:49,661 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_mid_wf.sdc_wf.pepolar_unwarp_wf.enhance_and_skullstrip_bold_wf.skullstrip_second_pass" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_mid_wf/sdc_wf/pepolar_unwarp_wf/enhance_and_skullstrip_bold_wf/skullstrip_second_pass". 190731-15:23:49,665 nipype.workflow INFO: [Node] Running "skullstrip_second_pass" ("nipype.interfaces.afni.preprocess.Automask"), a CommandLine Interface with command: 3dAutomask -apply_prefix uni_xform_masked.nii.gz -dilate 1 -prefix uni_xform_mask.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_mid_wf/sdc_wf/pepolar_unwarp_wf/enhance_and_skullstrip_bold_wf/skullstrip_second_pass/uni_xform.nii.gz 190731-15:23:49,792 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_opposite_wf.fmap2ref_reg". 190731-15:23:49,903 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_mid_wf.sdc_wf.pepolar_unwarp_wf.enhance_and_skullstrip_bold_wf.skullstrip_second_pass". 190731-15:23:51,741 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_mid_wf.sdc_wf.pepolar_unwarp_wf.enhance_and_skullstrip_bold_wf.fixhdr_skullstrip2" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_mid_wf/sdc_wf/pepolar_unwarp_wf/enhance_and_skullstrip_bold_wf/fixhdr_skullstrip2". 190731-15:23:51,743 nipype.workflow INFO: [Node] Running "fixhdr_skullstrip2" ("niworkflows.interfaces.utils.CopyXForm") 190731-15:23:51,745 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.sdc_wf.pepolar_unwarp_wf.qwarp" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/qwarp". 190731-15:23:51,752 nipype.workflow INFO: [Node] Running "qwarp" ("nipype.interfaces.afni.preprocess.QwarpPlusMinus"), a CommandLine Interface with command: 3dQwarp -prefix Qwarp.nii.gz -plusminus -noXdis -noZdis -base /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/qwarp/transform_Warped.nii.gz -blur -1.0 -1.0 -source /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/qwarp/transform_Warped_c0000.nii.gz -minpatch 9 -nopadWARP -noweight -pblur 0.05 0.05 190731-15:23:51,776 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_mid_wf.sdc_wf.pepolar_unwarp_wf.enhance_and_skullstrip_bold_wf.fixhdr_skullstrip2". 190731-15:23:53,735 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_mid_wf.sdc_wf.pepolar_unwarp_wf.enhance_and_skullstrip_bold_wf.combine_masks" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_mid_wf/sdc_wf/pepolar_unwarp_wf/enhance_and_skullstrip_bold_wf/combine_masks". 190731-15:23:53,739 nipype.workflow INFO: [Node] Running "combine_masks" ("nipype.interfaces.fsl.maths.BinaryMaths"), a CommandLine Interface with command: fslmaths /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_mid_wf/sdc_wf/pepolar_unwarp_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_pass/ref_bold_corrected_trans_corrected_brain_mask.nii.gz -mul /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_mid_wf/sdc_wf/pepolar_unwarp_wf/enhance_and_skullstrip_bold_wf/fixhdr_skullstrip2/uni_xform_mask_xform.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_mid_wf/sdc_wf/pepolar_unwarp_wf/enhance_and_skullstrip_bold_wf/combine_masks/ref_bold_corrected_trans_corrected_brain_mask_maths.nii.gz 190731-15:23:53,915 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_mid_wf.sdc_wf.pepolar_unwarp_wf.enhance_and_skullstrip_bold_wf.combine_masks". 190731-15:23:55,729 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_mid_wf.sdc_wf.pepolar_unwarp_wf.enhance_and_skullstrip_bold_wf.apply_mask" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_mid_wf/sdc_wf/pepolar_unwarp_wf/enhance_and_skullstrip_bold_wf/apply_mask". 190731-15:23:55,732 nipype.workflow INFO: [Node] Running "apply_mask" ("nipype.interfaces.fsl.maths.ApplyMask"), a CommandLine Interface with command: fslmaths /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_mid_wf/sdc_wf/pepolar_unwarp_wf/enhance_and_skullstrip_bold_wf/fixhdr_unifize/uni_xform.nii.gz -mas /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_mid_wf/sdc_wf/pepolar_unwarp_wf/enhance_and_skullstrip_bold_wf/combine_masks/ref_bold_corrected_trans_corrected_brain_mask_maths.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_mid_wf/sdc_wf/pepolar_unwarp_wf/enhance_and_skullstrip_bold_wf/apply_mask/uni_xform_masked.nii.gz 190731-15:23:55,873 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_mid_wf.sdc_wf.pepolar_unwarp_wf.enhance_and_skullstrip_bold_wf.apply_mask". 190731-15:24:59,501 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.sdc_wf.pepolar_unwarp_wf.qwarp". 190731-15:25:01,767 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.sdc_wf.pepolar_unwarp_wf.cphdr_warp" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/cphdr_warp". 190731-15:25:01,769 nipype.workflow INFO: [Node] Running "cphdr_warp" ("niworkflows.interfaces.utils.CopyHeader") 190731-15:25:01,771 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_mid_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.init_aff" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_mid_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/init_aff". 190731-15:25:01,773 nipype.workflow INFO: [Node] Running "init_aff" ("niworkflows.interfaces.ants.AI"), a CommandLine Interface with command: antsAI -c [10,0.000001,10] -d 3 -x /home/sahad3/.cache/templateflow/tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_res-02_desc-brain_mask.nii.gz -m Mattes[/home/sahad3/.cache/templateflow/tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_res-02_desc-fMRIPrep_boldref.nii.gz,/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_mid_wf/bold_reference_wf/gen_ref/ref_bold.nii.gz,32,Regular,0.200000] -o initialization.mat -p 0 -s [20.000000,0.120000] -t Affine[0.100000] -v 1 190731-15:25:01,873 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.sdc_wf.pepolar_unwarp_wf.cphdr_warp". 190731-15:25:03,690 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.sdc_wf.pepolar_unwarp_wf.to_ants" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/to_ants". 190731-15:25:03,692 nipype.workflow INFO: [Node] Running "to_ants" ("nipype.interfaces.utility.wrappers.Function") 190731-15:25:03,779 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.sdc_wf.pepolar_unwarp_wf.to_ants". 190731-15:25:06,213 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.sdc_wf.pepolar_unwarp_wf.unwarp_reference" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/unwarp_reference". 190731-15:25:06,217 nipype.workflow INFO: [Node] Running "unwarp_reference" ("niworkflows.interfaces.registration.ANTSApplyTransformsRPT"), a CommandLine Interface with command: antsApplyTransforms --default-value 0 --dimensionality 3 --float 1 --input /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/n4_correct/ref_bold_corrected.nii.gz --interpolation LanczosWindowedSinc --output ref_bold_corrected_trans.nii.gz --reference-image /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/n4_correct/ref_bold_corrected.nii.gz --transform /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/cphdr_warp/_warpfieldQwarp_PLUS_WARP_fixhdr.nii.gz 190731-15:25:07,985 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_mid_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.init_aff". 190731-15:25:08,59 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.sdc_wf.pepolar_unwarp_wf.unwarp_reference". 190731-15:25:08,527 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_mid_wf.bold_bold_trans_wf.bold_transform". 190731-15:25:09,692 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.sdc_wf.pepolar_unwarp_wf.enhance_and_skullstrip_bold_wf.init_aff" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/enhance_and_skullstrip_bold_wf/init_aff". 190731-15:25:09,695 nipype.workflow INFO: [Node] Running "init_aff" ("niworkflows.interfaces.ants.AI"), a CommandLine Interface with command: antsAI -c [10,0.000001,10] -d 3 -x /home/sahad3/.cache/templateflow/tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_res-02_desc-brain_mask.nii.gz -m Mattes[/home/sahad3/.cache/templateflow/tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_res-02_desc-fMRIPrep_boldref.nii.gz,/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/unwarp_reference/ref_bold_corrected_trans.nii.gz,32,Regular,0.200000] -o initialization.mat -p 0 -s [20.000000,0.120000] -t Affine[0.100000] -v 1 190731-15:25:09,717 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.bold_bold_trans_wf.bold_transform" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/bold_bold_trans_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-01..func..sub-23649_ses-01_task-rest_echo-4_bold.nii.gz/bold_transform". 190731-15:25:09,727 nipype.workflow INFO: [Node] Running "bold_transform" ("niworkflows.interfaces.itk.MultiApplyTransforms") 190731-15:25:10,31 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_mid_wf.bold_bold_trans_wf.merge" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_mid_wf/bold_bold_trans_wf/merge". 190731-15:25:10,46 nipype.workflow INFO: [Node] Running "merge" ("fmriprep.interfaces.nilearn.Merge") 190731-15:25:17,166 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.sdc_wf.pepolar_unwarp_wf.enhance_and_skullstrip_bold_wf.init_aff". 190731-15:25:17,712 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.sdc_wf.pepolar_unwarp_wf.enhance_and_skullstrip_bold_wf.norm" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/enhance_and_skullstrip_bold_wf/norm". 190731-15:25:17,717 nipype.workflow INFO: [Node] Running "norm" ("niworkflows.interfaces.fixes.FixHeaderRegistration"), a CommandLine Interface with command: antsRegistration --collapse-output-transforms 1 --dimensionality 3 --float 1 --initial-moving-transform [ /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/enhance_and_skullstrip_bold_wf/init_aff/initialization.mat, 0 ] --initialize-transforms-per-stage 0 --interpolation Linear --output transform --transform Affine[ 0.1 ] --metric Mattes[ /home/sahad3/.cache/templateflow/tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_res-02_desc-fMRIPrep_boldref.nii.gz, /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/unwarp_reference/ref_bold_corrected_trans.nii.gz, 1, 64, Random, 0.2 ] --convergence [ 200, 1e-09, 10 ] --smoothing-sigmas 2.0mm --shrink-factors 2 --use-estimate-learning-rate-once 1 --use-histogram-matching 1 --winsorize-image-intensities [ 0.05, 0.98 ] --write-composite-transform 0 190731-15:25:19,218 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.sdc_wf.pepolar_unwarp_wf.enhance_and_skullstrip_bold_wf.norm". 190731-15:25:21,714 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.sdc_wf.pepolar_unwarp_wf.enhance_and_skullstrip_bold_wf.map_brainmask" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/enhance_and_skullstrip_bold_wf/map_brainmask". 190731-15:25:21,718 nipype.workflow INFO: [Node] Running "map_brainmask" ("niworkflows.interfaces.fixes.FixHeaderApplyTransforms"), a CommandLine Interface with command: antsApplyTransforms --default-value 0 --float 1 --input /home/sahad3/.cache/templateflow/tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_res-02_desc-brain_mask.nii.gz --interpolation MultiLabel --output tpl-MNI152NLin2009cAsym_res-02_desc-brain_mask_trans.nii.gz --reference-image /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/unwarp_reference/ref_bold_corrected_trans.nii.gz --transform [ /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/enhance_and_skullstrip_bold_wf/norm/transform0GenericAffine.mat, 1 ] 190731-15:25:21,739 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.bold_bold_trans_wf.bold_transform" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/bold_bold_trans_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-01..func..sub-23649_ses-01_task-rest_echo-3_bold.nii.gz/bold_transform". 190731-15:25:21,748 nipype.workflow INFO: [Node] Running "bold_transform" ("niworkflows.interfaces.itk.MultiApplyTransforms") 190731-15:25:23,953 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.sdc_wf.pepolar_unwarp_wf.enhance_and_skullstrip_bold_wf.map_brainmask". 190731-15:25:25,732 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.sdc_wf.pepolar_unwarp_wf.enhance_and_skullstrip_bold_wf.pre_mask_dilate" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/enhance_and_skullstrip_bold_wf/pre_mask_dilate". 190731-15:25:25,735 nipype.workflow INFO: [Node] Running "pre_mask_dilate" ("nipype.interfaces.fsl.maths.DilateImage"), a CommandLine Interface with command: fslmaths -dt char /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/enhance_and_skullstrip_bold_wf/map_brainmask/tpl-MNI152NLin2009cAsym_res-02_desc-brain_mask_trans.nii.gz -kernel sphere 3.0000 -dilF /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/enhance_and_skullstrip_bold_wf/pre_mask_dilate/tpl-MNI152NLin2009cAsym_res-02_desc-brain_mask_trans_dil.nii.gz 190731-15:25:25,996 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.sdc_wf.pepolar_unwarp_wf.enhance_and_skullstrip_bold_wf.pre_mask_dilate". 190731-15:25:27,821 nipype.interface WARNING: q-forms of reference and mask are substantially different 190731-15:25:29,769 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.sdc_wf.pepolar_unwarp_wf.enhance_and_skullstrip_bold_wf.n4_correct" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/enhance_and_skullstrip_bold_wf/n4_correct". 190731-15:25:29,773 nipype.workflow INFO: [Node] Running "n4_correct" ("nipype.interfaces.ants.segmentation.N4BiasFieldCorrection"), a CommandLine Interface with command: N4BiasFieldCorrection --bspline-fitting [ 200 ] -d 3 --input-image /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/unwarp_reference/ref_bold_corrected_trans.nii.gz --mask-image /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/enhance_and_skullstrip_bold_wf/check_hdr/tpl-MNI152NLin2009cAsym_res-02_desc-brain_mask_trans_dil_hdr.nii.gz --output ref_bold_corrected_trans_corrected.nii.gz 190731-15:25:32,510 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.sdc_wf.pepolar_unwarp_wf.enhance_and_skullstrip_bold_wf.n4_correct". 190731-15:25:33,770 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.sdc_wf.pepolar_unwarp_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_pass" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_pass". 190731-15:25:33,774 nipype.workflow INFO: [Node] Running "skullstrip_first_pass" ("nipype.interfaces.fsl.preprocess.BET"), a CommandLine Interface with command: bet /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/enhance_and_skullstrip_bold_wf/n4_correct/ref_bold_corrected_trans_corrected.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_pass/ref_bold_corrected_trans_corrected_brain.nii.gz -f 0.20 -m 190731-15:25:38,33 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.sdc_wf.pepolar_unwarp_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_pass". 190731-15:25:38,192 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_mid_wf.bold_bold_trans_wf.merge". 190731-15:26:05,958 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.bold_bold_trans_wf.bold_transform". 190731-15:26:07,584 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.sdc_wf.pepolar_unwarp_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_dilate" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_dilate". 190731-15:26:07,587 nipype.workflow INFO: [Node] Running "skullstrip_first_dilate" ("nipype.interfaces.fsl.maths.DilateImage"), a CommandLine Interface with command: fslmaths -dt char /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_pass/ref_bold_corrected_trans_corrected_brain_mask.nii.gz -kernel sphere 6.0000 -dilF /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_dilate/ref_bold_corrected_trans_corrected_brain_mask_dil.nii.gz 190731-15:26:07,596 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_mid_wf.bold_bold_trans_wf.bold_reference_wf.validate" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_mid_wf/bold_bold_trans_wf/bold_reference_wf/validate". 190731-15:26:07,598 nipype.workflow INFO: [Node] Running "validate" ("niworkflows.interfaces.images.ValidateImage") 190731-15:26:07,631 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_mid_wf.bold_bold_trans_wf.bold_reference_wf.validate". 190731-15:26:08,140 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.sdc_wf.pepolar_unwarp_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_dilate". 190731-15:26:08,251 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.bold_bold_trans_wf.bold_transform" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/bold_bold_trans_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-01..func..sub-23649_ses-01_task-rest_echo-2_bold.nii.gz/bold_transform". 190731-15:26:08,261 nipype.workflow INFO: [Node] Running "bold_transform" ("niworkflows.interfaces.itk.MultiApplyTransforms") 190731-15:26:08,295 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.bold_bold_trans_wf.merge" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/bold_bold_trans_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-01..func..sub-23649_ses-01_task-rest_echo-4_bold.nii.gz/merge". 190731-15:26:08,312 nipype.workflow INFO: [Node] Running "merge" ("fmriprep.interfaces.nilearn.Merge") 190731-15:26:08,814 nipype.workflow INFO: [Node] Finished "_n4_correct0". 190731-15:26:10,193 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_mid_wf.bold_bold_trans_wf.bold_reference_wf.gen_ref" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_mid_wf/bold_bold_trans_wf/bold_reference_wf/gen_ref". 190731-15:26:10,195 nipype.workflow INFO: [Node] Running "gen_ref" ("niworkflows.interfaces.registration.EstimateReferenceImage") 190731-15:26:10,196 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.sdc_wf.pepolar_unwarp_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_mask" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_mask". 190731-15:26:10,201 nipype.workflow INFO: [Node] Running "skullstrip_first_mask" ("nipype.interfaces.fsl.maths.ApplyMask"), a CommandLine Interface with command: fslmaths /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_pass/ref_bold_corrected_trans_corrected_brain.nii.gz -mas /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_dilate/ref_bold_corrected_trans_corrected_brain_mask_dil.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_mask/ref_bold_corrected_trans_corrected_brain_masked.nii.gz 190731-15:26:10,387 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.sdc_wf.pepolar_unwarp_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_mask". 190731-15:26:10,703 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_mid_wf.bold_bold_trans_wf.bold_reference_wf.gen_ref". 190731-15:26:12,758 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.sdc_wf.pepolar_unwarp_wf.enhance_and_skullstrip_bold_wf.unifize" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/enhance_and_skullstrip_bold_wf/unifize". 190731-15:26:12,760 nipype.workflow INFO: [Node] Running "unifize" ("nipype.interfaces.afni.utils.Unifize"), a CommandLine Interface with command: 3dUnifize -clfrac 0.2 -rbt 18.3 65.0 90.0 -prefix uni.nii.gz -T2 -input /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/enhance_and_skullstrip_bold_wf/unifize/ref_bold_corrected_trans_corrected_brain_masked.nii.gz 190731-15:26:13,574 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.bold_bold_trans_wf.bold_transform". 190731-15:26:13,912 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.sdc_wf.pepolar_unwarp_wf.enhance_and_skullstrip_bold_wf.unifize". 190731-15:26:14,98 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_mid_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.init_aff" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_mid_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/init_aff". 190731-15:26:14,102 nipype.workflow INFO: [Node] Running "init_aff" ("niworkflows.interfaces.ants.AI"), a CommandLine Interface with command: antsAI -c [10,0.000001,10] -d 3 -x /home/sahad3/.cache/templateflow/tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_res-02_desc-brain_mask.nii.gz -m Mattes[/home/sahad3/.cache/templateflow/tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_res-02_desc-fMRIPrep_boldref.nii.gz,/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_mid_wf/bold_bold_trans_wf/bold_reference_wf/gen_ref/ref_bold.nii.gz,32,Regular,0.200000] -o initialization.mat -p 0 -s [20.000000,0.120000] -t Affine[0.100000] -v 1 190731-15:26:14,155 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.bold_bold_trans_wf.merge" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/bold_bold_trans_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-01..func..sub-23649_ses-01_task-rest_echo-3_bold.nii.gz/merge". 190731-15:26:14,165 nipype.workflow INFO: [Node] Running "merge" ("fmriprep.interfaces.nilearn.Merge") 190731-15:26:16,208 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.sdc_wf.pepolar_unwarp_wf.enhance_and_skullstrip_bold_wf.fixhdr_unifize" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/enhance_and_skullstrip_bold_wf/fixhdr_unifize". 190731-15:26:16,210 nipype.workflow INFO: [Node] Running "fixhdr_unifize" ("niworkflows.interfaces.utils.CopyXForm") 190731-15:26:16,249 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.sdc_wf.pepolar_unwarp_wf.enhance_and_skullstrip_bold_wf.fixhdr_unifize". 190731-15:26:18,152 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.sdc_wf.pepolar_unwarp_wf.enhance_and_skullstrip_bold_wf.skullstrip_second_pass" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/enhance_and_skullstrip_bold_wf/skullstrip_second_pass". 190731-15:26:18,157 nipype.workflow INFO: [Node] Running "skullstrip_second_pass" ("nipype.interfaces.afni.preprocess.Automask"), a CommandLine Interface with command: 3dAutomask -apply_prefix uni_xform_masked.nii.gz -dilate 1 -prefix uni_xform_mask.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/enhance_and_skullstrip_bold_wf/skullstrip_second_pass/uni_xform.nii.gz 190731-15:26:18,375 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.sdc_wf.pepolar_unwarp_wf.enhance_and_skullstrip_bold_wf.skullstrip_second_pass". 190731-15:26:19,490 nipype.workflow INFO: [Node] Finished "_n4_correct1". 190731-15:26:20,138 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.sdc_wf.pepolar_unwarp_wf.enhance_and_skullstrip_bold_wf.fixhdr_skullstrip2" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/enhance_and_skullstrip_bold_wf/fixhdr_skullstrip2". 190731-15:26:20,140 nipype.workflow INFO: [Node] Running "fixhdr_skullstrip2" ("niworkflows.interfaces.utils.CopyXForm") 190731-15:26:20,163 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.sdc_wf.pepolar_unwarp_wf.enhance_and_skullstrip_bold_wf.fixhdr_skullstrip2". 190731-15:26:20,471 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.bold_bold_trans_wf.merge". 190731-15:26:20,488 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_mid_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.init_aff". 190731-15:26:22,110 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_mid_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.norm" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_mid_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/norm". 190731-15:26:22,111 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.sdc_wf.pepolar_unwarp_wf.enhance_and_skullstrip_bold_wf.combine_masks" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/enhance_and_skullstrip_bold_wf/combine_masks". 190731-15:26:22,114 nipype.workflow INFO: [Node] Running "norm" ("niworkflows.interfaces.fixes.FixHeaderRegistration"), a CommandLine Interface with command: antsRegistration --collapse-output-transforms 1 --dimensionality 3 --float 1 --initial-moving-transform [ /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_mid_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/init_aff/initialization.mat, 0 ] --initialize-transforms-per-stage 0 --interpolation Linear --output transform --transform Affine[ 0.1 ] --metric Mattes[ /home/sahad3/.cache/templateflow/tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_res-02_desc-fMRIPrep_boldref.nii.gz, /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_mid_wf/bold_bold_trans_wf/bold_reference_wf/gen_ref/ref_bold.nii.gz, 1, 64, Random, 0.2 ] --convergence [ 200, 1e-09, 10 ] --smoothing-sigmas 2.0mm --shrink-factors 2 --use-estimate-learning-rate-once 1 --use-histogram-matching 1 --winsorize-image-intensities [ 0.05, 0.98 ] --write-composite-transform 0 190731-15:26:22,114 nipype.workflow INFO: [Node] Running "combine_masks" ("nipype.interfaces.fsl.maths.BinaryMaths"), a CommandLine Interface with command: fslmaths /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_pass/ref_bold_corrected_trans_corrected_brain_mask.nii.gz -mul /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/enhance_and_skullstrip_bold_wf/fixhdr_skullstrip2/uni_xform_mask_xform.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/enhance_and_skullstrip_bold_wf/combine_masks/ref_bold_corrected_trans_corrected_brain_mask_maths.nii.gz 190731-15:26:22,253 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.sdc_wf.pepolar_unwarp_wf.enhance_and_skullstrip_bold_wf.combine_masks". 190731-15:26:24,403 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_mid_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.norm". 190731-15:26:25,754 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.bold_bold_trans_wf.merge". 190731-15:26:29,932 nipype.workflow INFO: [Node] Finished "_n4_correct3". 190731-15:26:30,537 nipype.workflow INFO: [Node] Finished "_n4_correct2". 190731-15:26:32,935 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.skullstrip_bold_wf.skullstrip_first_pass" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-01..func..sub-23649_ses-01_task-rest_echo-4_bold.nii.gz/skullstrip_first_pass". 190731-15:26:32,942 nipype.workflow INFO: [Node] Running "skullstrip_first_pass" ("nipype.interfaces.fsl.preprocess.BET"), a CommandLine Interface with command: bet /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/bold_bold_trans_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-01..func..sub-23649_ses-01_task-rest_echo-4_bold.nii.gz/merge/vol0000_xform-00000_merged.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-01..func..sub-23649_ses-01_task-rest_echo-4_bold.nii.gz/skullstrip_first_pass/vol0000_xform-00000_merged_brain.nii.gz -f 0.20 -m 190731-15:26:32,947 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.bold_bold_trans_wf.bold_reference_wf.validate" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/bold_bold_trans_wf/bold_reference_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-01..func..sub-23649_ses-01_task-rest_echo-4_bold.nii.gz/validate". 190731-15:26:32,949 nipype.workflow INFO: [Node] Running "validate" ("niworkflows.interfaces.images.ValidateImage") 190731-15:26:33,437 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_mid_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.map_brainmask" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_mid_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/map_brainmask". 190731-15:26:33,441 nipype.workflow INFO: [Node] Running "map_brainmask" ("niworkflows.interfaces.fixes.FixHeaderApplyTransforms"), a CommandLine Interface with command: antsApplyTransforms --default-value 0 --float 1 --input /home/sahad3/.cache/templateflow/tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_res-02_desc-brain_mask.nii.gz --interpolation MultiLabel --output tpl-MNI152NLin2009cAsym_res-02_desc-brain_mask_trans.nii.gz --reference-image /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_mid_wf/bold_bold_trans_wf/bold_reference_wf/gen_ref/ref_bold.nii.gz --transform [ /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_mid_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/norm/transform0GenericAffine.mat, 1 ] 190731-15:26:33,444 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.sdc_wf.pepolar_unwarp_wf.enhance_and_skullstrip_bold_wf.apply_mask" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/enhance_and_skullstrip_bold_wf/apply_mask". 190731-15:26:33,448 nipype.workflow INFO: [Node] Running "apply_mask" ("nipype.interfaces.fsl.maths.ApplyMask"), a CommandLine Interface with command: fslmaths /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/enhance_and_skullstrip_bold_wf/fixhdr_unifize/uni_xform.nii.gz -mas /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/enhance_and_skullstrip_bold_wf/combine_masks/ref_bold_corrected_trans_corrected_brain_mask_maths.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/enhance_and_skullstrip_bold_wf/apply_mask/uni_xform_masked.nii.gz 190731-15:26:33,645 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.sdc_wf.pepolar_unwarp_wf.enhance_and_skullstrip_bold_wf.apply_mask". 190731-15:26:34,922 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.skullstrip_bold_wf.skullstrip_first_pass". 190731-15:26:35,648 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_mid_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.map_brainmask". 190731-15:26:35,923 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.bold_bold_trans_wf.bold_reference_wf.validate". 190731-15:26:43,957 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.skullstrip_bold_wf.skullstrip_first_pass" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-01..func..sub-23649_ses-01_task-rest_echo-3_bold.nii.gz/skullstrip_first_pass". 190731-15:26:43,958 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.bold_bold_trans_wf.bold_reference_wf.validate" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/bold_bold_trans_wf/bold_reference_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-01..func..sub-23649_ses-01_task-rest_echo-3_bold.nii.gz/validate". 190731-15:26:43,960 nipype.workflow INFO: [Node] Running "validate" ("niworkflows.interfaces.images.ValidateImage") 190731-15:26:43,961 nipype.workflow INFO: [Node] Running "skullstrip_first_pass" ("nipype.interfaces.fsl.preprocess.BET"), a CommandLine Interface with command: bet /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/bold_bold_trans_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-01..func..sub-23649_ses-01_task-rest_echo-3_bold.nii.gz/merge/vol0000_xform-00000_merged.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-01..func..sub-23649_ses-01_task-rest_echo-3_bold.nii.gz/skullstrip_first_pass/vol0000_xform-00000_merged_brain.nii.gz -f 0.20 -m 190731-15:26:43,982 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.anat_preproc_wf.anat_template_wf.n4_correct" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/anat_preproc_wf/anat_template_wf/n4_correct". 190731-15:26:43,988 nipype.workflow INFO: [Node] Setting-up "_n4_correct0" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/anat_preproc_wf/anat_template_wf/n4_correct/mapflow/_n4_correct0". 190731-15:26:43,989 nipype.workflow INFO: [Node] Cached "_n4_correct0" - collecting precomputed outputs 190731-15:26:43,989 nipype.workflow INFO: [Node] "_n4_correct0" found cached. 190731-15:26:43,991 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.bold_bold_trans_wf.bold_transform" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/bold_bold_trans_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-01..func..sub-23649_ses-01_task-rest_echo-1_bold.nii.gz/bold_transform". 190731-15:26:43,991 nipype.workflow INFO: [Node] Setting-up "_n4_correct1" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/anat_preproc_wf/anat_template_wf/n4_correct/mapflow/_n4_correct1". 190731-15:26:43,992 nipype.workflow INFO: [Node] Cached "_n4_correct1" - collecting precomputed outputs 190731-15:26:43,993 nipype.workflow INFO: [Node] "_n4_correct1" found cached. 190731-15:26:43,994 nipype.workflow INFO: [Node] Setting-up "_n4_correct2" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/anat_preproc_wf/anat_template_wf/n4_correct/mapflow/_n4_correct2". 190731-15:26:43,996 nipype.workflow INFO: [Node] Cached "_n4_correct2" - collecting precomputed outputs 190731-15:26:43,996 nipype.workflow INFO: [Node] "_n4_correct2" found cached. 190731-15:26:43,997 nipype.workflow INFO: [Node] Setting-up "_n4_correct3" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/anat_preproc_wf/anat_template_wf/n4_correct/mapflow/_n4_correct3". 190731-15:26:43,999 nipype.workflow INFO: [Node] Cached "_n4_correct3" - collecting precomputed outputs 190731-15:26:43,999 nipype.workflow INFO: [Node] "_n4_correct3" found cached. 190731-15:26:44,2 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.anat_preproc_wf.anat_template_wf.n4_correct". 190731-15:26:44,7 nipype.workflow INFO: [Node] Running "bold_transform" ("niworkflows.interfaces.itk.MultiApplyTransforms") 190731-15:26:44,527 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_mid_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.pre_mask_dilate" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_mid_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/pre_mask_dilate". 190731-15:26:44,528 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.skullstrip_bold_wf.skullstrip_second_pass" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-01..func..sub-23649_ses-01_task-rest_echo-4_bold.nii.gz/skullstrip_second_pass". 190731-15:26:44,530 nipype.workflow INFO: [Node] Running "pre_mask_dilate" ("nipype.interfaces.fsl.maths.DilateImage"), a CommandLine Interface with command: fslmaths -dt char /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_mid_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/map_brainmask/tpl-MNI152NLin2009cAsym_res-02_desc-brain_mask_trans.nii.gz -kernel sphere 3.0000 -dilF /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_mid_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/pre_mask_dilate/tpl-MNI152NLin2009cAsym_res-02_desc-brain_mask_trans_dil.nii.gz 190731-15:26:44,531 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.bold_bold_trans_wf.bold_reference_wf.gen_ref" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/bold_bold_trans_wf/bold_reference_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-01..func..sub-23649_ses-01_task-rest_echo-4_bold.nii.gz/gen_ref". 190731-15:26:44,531 nipype.workflow INFO: [Node] Running "skullstrip_second_pass" ("nipype.interfaces.afni.preprocess.Automask"), a CommandLine Interface with command: 3dAutomask -apply_prefix vol0000_xform-00000_merged_brain_masked.nii.gz -dilate 1 -prefix vol0000_xform-00000_merged_brain_mask.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-01..func..sub-23649_ses-01_task-rest_echo-4_bold.nii.gz/skullstrip_second_pass/vol0000_xform-00000_merged_brain.nii.gz 190731-15:26:44,533 nipype.workflow INFO: [Node] Running "gen_ref" ("niworkflows.interfaces.registration.EstimateReferenceImage") 190731-15:26:44,902 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.skullstrip_bold_wf.skullstrip_second_pass". 190731-15:26:44,947 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.bold_bold_trans_wf.bold_reference_wf.gen_ref". 190731-15:26:45,40 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_mid_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.pre_mask_dilate". 190731-15:26:46,651 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.skullstrip_bold_wf.skullstrip_first_pass". 190731-15:26:47,96 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.skullstrip_bold_wf.combine_masks" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-01..func..sub-23649_ses-01_task-rest_echo-4_bold.nii.gz/combine_masks". 190731-15:26:47,99 nipype.workflow INFO: [Node] Running "combine_masks" ("nipype.interfaces.fsl.maths.BinaryMaths"), a CommandLine Interface with command: fslmaths /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-01..func..sub-23649_ses-01_task-rest_echo-4_bold.nii.gz/skullstrip_first_pass/vol0000_xform-00000_merged_brain_mask.nii.gz -mul /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-01..func..sub-23649_ses-01_task-rest_echo-4_bold.nii.gz/skullstrip_second_pass/vol0000_xform-00000_merged_brain_mask.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-01..func..sub-23649_ses-01_task-rest_echo-4_bold.nii.gz/combine_masks/vol0000_xform-00000_merged_brain_mask_maths.nii.gz 190731-15:26:47,261 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.skullstrip_bold_wf.combine_masks". 190731-15:26:47,303 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.bold_bold_trans_wf.bold_reference_wf.validate". 190731-15:26:47,631 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.anat_preproc_wf.anat_template_wf.t1_merge" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/anat_preproc_wf/anat_template_wf/t1_merge". 190731-15:26:47,634 nipype.workflow INFO: [Node] Running "t1_merge" ("niworkflows.interfaces.freesurfer.StructuralReference"), a CommandLine Interface with command: mri_robust_template --satit --mov /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/anat_preproc_wf/anat_template_wf/n4_correct/mapflow/_n4_correct0/sub-23649_ses-01_acq-mprage_rec-ORIG_T1w_corrected.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/anat_preproc_wf/anat_template_wf/n4_correct/mapflow/_n4_correct1/sub-23649_ses-02_acq-mprage_rec-ORIG_T1w_corrected.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/anat_preproc_wf/anat_template_wf/n4_correct/mapflow/_n4_correct2/sub-23649_ses-03_acq-mprage_rec-ORIG_T1w_ras_corrected.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/anat_preproc_wf/anat_template_wf/n4_correct/mapflow/_n4_correct3/sub-23649_ses-04_acq-mprage_rec-ORIG_T1w_corrected.nii.gz --inittp 1 --iscale --template sub-23649_ses-01_acq-mprage_rec-ORIG_T1w_template.nii.gz --subsample 200 --lta /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/anat_preproc_wf/anat_template_wf/t1_merge/tp1.lta /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/anat_preproc_wf/anat_template_wf/t1_merge/tp2.lta /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/anat_preproc_wf/anat_template_wf/t1_merge/tp3.lta /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/anat_preproc_wf/anat_template_wf/t1_merge/tp4.lta 190731-15:26:48,569 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_mid_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.n4_correct" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_mid_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/n4_correct". 190731-15:26:48,572 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.skullstrip_bold_wf.mask_reportlet" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-01..func..sub-23649_ses-01_task-rest_echo-4_bold.nii.gz/mask_reportlet". 190731-15:26:48,572 nipype.workflow INFO: [Node] Running "n4_correct" ("nipype.interfaces.ants.segmentation.N4BiasFieldCorrection"), a CommandLine Interface with command: N4BiasFieldCorrection --bspline-fitting [ 200 ] -d 3 --input-image /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_mid_wf/bold_bold_trans_wf/bold_reference_wf/gen_ref/ref_bold.nii.gz --mask-image /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_mid_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/check_hdr/tpl-MNI152NLin2009cAsym_res-02_desc-brain_mask_trans_dil_hdr.nii.gz --output ref_bold_corrected.nii.gz 190731-15:26:48,575 nipype.workflow INFO: [Node] Running "mask_reportlet" ("niworkflows.interfaces.masks.SimpleShowMaskRPT") 190731-15:26:48,575 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.skullstrip_bold_wf.apply_mask" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-01..func..sub-23649_ses-01_task-rest_echo-4_bold.nii.gz/apply_mask". 190731-15:26:48,578 nipype.workflow INFO: [Node] Running "apply_mask" ("nipype.interfaces.fsl.maths.ApplyMask"), a CommandLine Interface with command: fslmaths /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/bold_bold_trans_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-01..func..sub-23649_ses-01_task-rest_echo-4_bold.nii.gz/merge/vol0000_xform-00000_merged.nii.gz -mas /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-01..func..sub-23649_ses-01_task-rest_echo-4_bold.nii.gz/combine_masks/vol0000_xform-00000_merged_brain_mask_maths.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-01..func..sub-23649_ses-01_task-rest_echo-4_bold.nii.gz/apply_mask/vol0000_xform-00000_merged_masked.nii.gz 190731-15:26:48,584 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.skullstrip_bold_wf.skullstrip_second_pass" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-01..func..sub-23649_ses-01_task-rest_echo-3_bold.nii.gz/skullstrip_second_pass". 190731-15:26:48,588 nipype.workflow INFO: [Node] Running "skullstrip_second_pass" ("nipype.interfaces.afni.preprocess.Automask"), a CommandLine Interface with command: 3dAutomask -apply_prefix vol0000_xform-00000_merged_brain_masked.nii.gz -dilate 1 -prefix vol0000_xform-00000_merged_brain_mask.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-01..func..sub-23649_ses-01_task-rest_echo-3_bold.nii.gz/skullstrip_second_pass/vol0000_xform-00000_merged_brain.nii.gz 190731-15:26:48,999 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.skullstrip_bold_wf.skullstrip_second_pass". 190731-15:26:50,582 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.skullstrip_bold_wf.combine_masks" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-01..func..sub-23649_ses-01_task-rest_echo-3_bold.nii.gz/combine_masks". 190731-15:26:50,586 nipype.workflow INFO: [Node] Running "combine_masks" ("nipype.interfaces.fsl.maths.BinaryMaths"), a CommandLine Interface with command: fslmaths /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-01..func..sub-23649_ses-01_task-rest_echo-3_bold.nii.gz/skullstrip_first_pass/vol0000_xform-00000_merged_brain_mask.nii.gz -mul /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-01..func..sub-23649_ses-01_task-rest_echo-3_bold.nii.gz/skullstrip_second_pass/vol0000_xform-00000_merged_brain_mask.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-01..func..sub-23649_ses-01_task-rest_echo-3_bold.nii.gz/combine_masks/vol0000_xform-00000_merged_brain_mask_maths.nii.gz 190731-15:26:50,715 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.skullstrip_bold_wf.combine_masks". 190731-15:26:51,955 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_mid_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.n4_correct". 190731-15:26:52,784 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.skullstrip_bold_wf.apply_mask". 190731-15:26:53,326 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_mid_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_pass" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_mid_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_pass". 190731-15:26:53,328 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.skullstrip_bold_wf.mask_reportlet" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-01..func..sub-23649_ses-01_task-rest_echo-3_bold.nii.gz/mask_reportlet". 190731-15:26:53,329 nipype.workflow INFO: [Node] Running "skullstrip_first_pass" ("nipype.interfaces.fsl.preprocess.BET"), a CommandLine Interface with command: bet /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_mid_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/n4_correct/ref_bold_corrected.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_mid_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_pass/ref_bold_corrected_brain.nii.gz -f 0.20 -m 190731-15:26:53,331 nipype.workflow INFO: [Node] Running "mask_reportlet" ("niworkflows.interfaces.masks.SimpleShowMaskRPT") 190731-15:26:54,595 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.skullstrip_bold_wf.apply_mask" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-01..func..sub-23649_ses-01_task-rest_echo-3_bold.nii.gz/apply_mask". 190731-15:26:54,597 nipype.workflow INFO: [Node] Running "apply_mask" ("nipype.interfaces.fsl.maths.ApplyMask"), a CommandLine Interface with command: fslmaths /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/bold_bold_trans_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-01..func..sub-23649_ses-01_task-rest_echo-3_bold.nii.gz/merge/vol0000_xform-00000_merged.nii.gz -mas /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-01..func..sub-23649_ses-01_task-rest_echo-3_bold.nii.gz/combine_masks/vol0000_xform-00000_merged_brain_mask_maths.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-01..func..sub-23649_ses-01_task-rest_echo-3_bold.nii.gz/apply_mask/vol0000_xform-00000_merged_masked.nii.gz 190731-15:26:54,955 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.skullstrip_bold_wf.mask_reportlet". 190731-15:26:55,838 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_mid_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_pass". 190731-15:26:56,586 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_mid_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_dilate" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_mid_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_dilate". 190731-15:26:56,588 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.bold_bold_trans_wf.bold_reference_wf.gen_ref" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/bold_bold_trans_wf/bold_reference_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-01..func..sub-23649_ses-01_task-rest_echo-3_bold.nii.gz/gen_ref". 190731-15:26:56,590 nipype.workflow INFO: [Node] Running "gen_ref" ("niworkflows.interfaces.registration.EstimateReferenceImage") 190731-15:26:56,590 nipype.workflow INFO: [Node] Running "skullstrip_first_dilate" ("nipype.interfaces.fsl.maths.DilateImage"), a CommandLine Interface with command: fslmaths -dt char /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_mid_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_pass/ref_bold_corrected_brain_mask.nii.gz -kernel sphere 6.0000 -dilF /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_mid_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_dilate/ref_bold_corrected_brain_mask_dil.nii.gz 190731-15:26:57,52 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.bold_bold_trans_wf.bold_reference_wf.gen_ref". 190731-15:26:57,291 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_mid_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_dilate". 190731-15:26:58,577 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_mid_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_mask" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_mid_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_mask". 190731-15:26:58,580 nipype.workflow INFO: [Node] Running "skullstrip_first_mask" ("nipype.interfaces.fsl.maths.ApplyMask"), a CommandLine Interface with command: fslmaths /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_mid_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_pass/ref_bold_corrected_brain.nii.gz -mas /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_mid_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_dilate/ref_bold_corrected_brain_mask_dil.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_mid_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_mask/ref_bold_corrected_brain_masked.nii.gz 190731-15:26:58,767 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_mid_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_mask". 190731-15:26:59,132 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.skullstrip_bold_wf.apply_mask". 190731-15:26:59,428 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.skullstrip_bold_wf.mask_reportlet". 190731-15:26:59,500 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.bold_bold_trans_wf.bold_transform". 190731-15:27:00,629 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_mid_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.unifize" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_mid_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/unifize". 190731-15:27:00,632 nipype.workflow INFO: [Node] Running "unifize" ("nipype.interfaces.afni.utils.Unifize"), a CommandLine Interface with command: 3dUnifize -clfrac 0.2 -rbt 18.3 65.0 90.0 -prefix uni.nii.gz -T2 -input /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_mid_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/unifize/ref_bold_corrected_brain_masked.nii.gz 190731-15:27:00,640 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.init_aff" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-01..func..sub-23649_ses-01_task-rest_echo-4_bold.nii.gz/init_aff". 190731-15:27:00,643 nipype.workflow INFO: [Node] Running "init_aff" ("niworkflows.interfaces.ants.AI"), a CommandLine Interface with command: antsAI -c [10,0.000001,10] -d 3 -x /home/sahad3/.cache/templateflow/tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_res-02_desc-brain_mask.nii.gz -m Mattes[/home/sahad3/.cache/templateflow/tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_res-02_desc-fMRIPrep_boldref.nii.gz,/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/bold_bold_trans_wf/bold_reference_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-01..func..sub-23649_ses-01_task-rest_echo-4_bold.nii.gz/gen_ref/ref_bold.nii.gz,32,Regular,0.200000] -o initialization.mat -p 0 -s [20.000000,0.120000] -t Affine[0.100000] -v 1 190731-15:27:00,703 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.bold_bold_trans_wf.merge" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/bold_bold_trans_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-01..func..sub-23649_ses-01_task-rest_echo-2_bold.nii.gz/merge". 190731-15:27:00,713 nipype.workflow INFO: [Node] Running "merge" ("fmriprep.interfaces.nilearn.Merge") 190731-15:27:02,146 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_mid_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.unifize". 190731-15:27:04,502 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_mid_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.fixhdr_unifize" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_mid_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/fixhdr_unifize". 190731-15:27:04,504 nipype.workflow INFO: [Node] Running "fixhdr_unifize" ("niworkflows.interfaces.utils.CopyXForm") 190731-15:27:04,541 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_mid_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.fixhdr_unifize". 190731-15:27:06,569 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_mid_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.skullstrip_second_pass" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_mid_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_second_pass". 190731-15:27:06,573 nipype.workflow INFO: [Node] Running "skullstrip_second_pass" ("nipype.interfaces.afni.preprocess.Automask"), a CommandLine Interface with command: 3dAutomask -apply_prefix uni_xform_masked.nii.gz -dilate 1 -prefix uni_xform_mask.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_mid_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_second_pass/uni_xform.nii.gz 190731-15:27:06,792 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_mid_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.skullstrip_second_pass". 190731-15:27:07,189 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.init_aff". 190731-15:27:08,684 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_mid_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.fixhdr_skullstrip2" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_mid_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/fixhdr_skullstrip2". 190731-15:27:08,686 nipype.workflow INFO: [Node] Running "fixhdr_skullstrip2" ("niworkflows.interfaces.utils.CopyXForm") 190731-15:27:08,693 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.norm" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-01..func..sub-23649_ses-01_task-rest_echo-4_bold.nii.gz/norm". 190731-15:27:08,700 nipype.workflow INFO: [Node] Running "norm" ("niworkflows.interfaces.fixes.FixHeaderRegistration"), a CommandLine Interface with command: antsRegistration --collapse-output-transforms 1 --dimensionality 3 --float 1 --initial-moving-transform [ /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-01..func..sub-23649_ses-01_task-rest_echo-4_bold.nii.gz/init_aff/initialization.mat, 0 ] --initialize-transforms-per-stage 0 --interpolation Linear --output transform --transform Affine[ 0.1 ] --metric Mattes[ /home/sahad3/.cache/templateflow/tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_res-02_desc-fMRIPrep_boldref.nii.gz, /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/bold_bold_trans_wf/bold_reference_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-01..func..sub-23649_ses-01_task-rest_echo-4_bold.nii.gz/gen_ref/ref_bold.nii.gz, 1, 64, Random, 0.2 ] --convergence [ 200, 1e-09, 10 ] --smoothing-sigmas 2.0mm --shrink-factors 2 --use-estimate-learning-rate-once 1 --use-histogram-matching 1 --winsorize-image-intensities [ 0.05, 0.98 ] --write-composite-transform 0 190731-15:27:08,713 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_mid_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.fixhdr_skullstrip2". 190731-15:27:09,903 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.norm". 190731-15:27:10,666 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_mid_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.combine_masks" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_mid_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/combine_masks". 190731-15:27:10,669 nipype.workflow INFO: [Node] Running "combine_masks" ("nipype.interfaces.fsl.maths.BinaryMaths"), a CommandLine Interface with command: fslmaths /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_mid_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_pass/ref_bold_corrected_brain_mask.nii.gz -mul /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_mid_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/fixhdr_skullstrip2/uni_xform_mask_xform.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_mid_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/combine_masks/ref_bold_corrected_brain_mask_maths.nii.gz 190731-15:27:10,670 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.map_brainmask" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-01..func..sub-23649_ses-01_task-rest_echo-4_bold.nii.gz/map_brainmask". 190731-15:27:10,675 nipype.workflow INFO: [Node] Running "map_brainmask" ("niworkflows.interfaces.fixes.FixHeaderApplyTransforms"), a CommandLine Interface with command: antsApplyTransforms --default-value 0 --float 1 --input /home/sahad3/.cache/templateflow/tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_res-02_desc-brain_mask.nii.gz --interpolation MultiLabel --output tpl-MNI152NLin2009cAsym_res-02_desc-brain_mask_trans.nii.gz --reference-image /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/bold_bold_trans_wf/bold_reference_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-01..func..sub-23649_ses-01_task-rest_echo-4_bold.nii.gz/gen_ref/ref_bold.nii.gz --transform [ /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-01..func..sub-23649_ses-01_task-rest_echo-4_bold.nii.gz/norm/transform0GenericAffine.mat, 1 ] 190731-15:27:10,697 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.init_aff" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-01..func..sub-23649_ses-01_task-rest_echo-3_bold.nii.gz/init_aff". 190731-15:27:10,702 nipype.workflow INFO: [Node] Running "init_aff" ("niworkflows.interfaces.ants.AI"), a CommandLine Interface with command: antsAI -c [10,0.000001,10] -d 3 -x /home/sahad3/.cache/templateflow/tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_res-02_desc-brain_mask.nii.gz -m Mattes[/home/sahad3/.cache/templateflow/tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_res-02_desc-fMRIPrep_boldref.nii.gz,/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/bold_bold_trans_wf/bold_reference_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-01..func..sub-23649_ses-01_task-rest_echo-3_bold.nii.gz/gen_ref/ref_bold.nii.gz,32,Regular,0.200000] -o initialization.mat -p 0 -s [20.000000,0.120000] -t Affine[0.100000] -v 1 190731-15:27:10,793 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_mid_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.combine_masks". 190731-15:27:12,417 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.map_brainmask". 190731-15:27:12,930 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.bold_bold_trans_wf.merge". 190731-15:27:13,170 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_mid_wf.bold_confounds_wf.dvars" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_mid_wf/bold_confounds_wf/dvars". 190731-15:27:13,172 nipype.workflow INFO: [Node] Running "dvars" ("nipype.algorithms.confounds.ComputeDVARS") 190731-15:27:13,173 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_mid_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.apply_mask" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_mid_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/apply_mask". 190731-15:27:13,176 nipype.workflow INFO: [Node] Running "apply_mask" ("nipype.interfaces.fsl.maths.ApplyMask"), a CommandLine Interface with command: fslmaths /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_mid_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/fixhdr_unifize/uni_xform.nii.gz -mas /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_mid_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/combine_masks/ref_bold_corrected_brain_mask_maths.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_mid_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/apply_mask/uni_xform_masked.nii.gz 190731-15:27:13,325 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_mid_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.apply_mask". 190731-15:27:14,592 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.pre_mask_dilate" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-01..func..sub-23649_ses-01_task-rest_echo-4_bold.nii.gz/pre_mask_dilate". 190731-15:27:14,596 nipype.workflow INFO: [Node] Running "pre_mask_dilate" ("nipype.interfaces.fsl.maths.DilateImage"), a CommandLine Interface with command: fslmaths -dt char /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-01..func..sub-23649_ses-01_task-rest_echo-4_bold.nii.gz/map_brainmask/tpl-MNI152NLin2009cAsym_res-02_desc-brain_mask_trans.nii.gz -kernel sphere 3.0000 -dilF /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-01..func..sub-23649_ses-01_task-rest_echo-4_bold.nii.gz/pre_mask_dilate/tpl-MNI152NLin2009cAsym_res-02_desc-brain_mask_trans_dil.nii.gz 190731-15:27:14,863 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.pre_mask_dilate". 190731-15:27:18,18 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.init_aff". 190731-15:27:25,188 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.skullstrip_bold_wf.skullstrip_first_pass" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-01..func..sub-23649_ses-01_task-rest_echo-2_bold.nii.gz/skullstrip_first_pass". 190731-15:27:25,190 nipype.workflow INFO: [Node] Running "skullstrip_first_pass" ("nipype.interfaces.fsl.preprocess.BET"), a CommandLine Interface with command: bet /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/bold_bold_trans_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-01..func..sub-23649_ses-01_task-rest_echo-2_bold.nii.gz/merge/vol0000_xform-00000_merged.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-01..func..sub-23649_ses-01_task-rest_echo-2_bold.nii.gz/skullstrip_first_pass/vol0000_xform-00000_merged_brain.nii.gz -f 0.20 -m 190731-15:27:25,192 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.bold_bold_trans_wf.bold_reference_wf.validate" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/bold_bold_trans_wf/bold_reference_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-01..func..sub-23649_ses-01_task-rest_echo-2_bold.nii.gz/validate". 190731-15:27:25,194 nipype.workflow INFO: [Node] Running "validate" ("niworkflows.interfaces.images.ValidateImage") 190731-15:27:25,747 nipype.interface WARNING: q-forms of reference and mask are substantially different 190731-15:27:26,295 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.norm" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-01..func..sub-23649_ses-01_task-rest_echo-3_bold.nii.gz/norm". 190731-15:27:26,299 nipype.workflow INFO: [Node] Running "norm" ("niworkflows.interfaces.fixes.FixHeaderRegistration"), a CommandLine Interface with command: antsRegistration --collapse-output-transforms 1 --dimensionality 3 --float 1 --initial-moving-transform [ /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-01..func..sub-23649_ses-01_task-rest_echo-3_bold.nii.gz/init_aff/initialization.mat, 0 ] --initialize-transforms-per-stage 0 --interpolation Linear --output transform --transform Affine[ 0.1 ] --metric Mattes[ /home/sahad3/.cache/templateflow/tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_res-02_desc-fMRIPrep_boldref.nii.gz, /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/bold_bold_trans_wf/bold_reference_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-01..func..sub-23649_ses-01_task-rest_echo-3_bold.nii.gz/gen_ref/ref_bold.nii.gz, 1, 64, Random, 0.2 ] --convergence [ 200, 1e-09, 10 ] --smoothing-sigmas 2.0mm --shrink-factors 2 --use-estimate-learning-rate-once 1 --use-histogram-matching 1 --winsorize-image-intensities [ 0.05, 0.98 ] --write-composite-transform 0 190731-15:27:26,593 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_mid_wf.bold_confounds_wf.dvars". 190731-15:27:27,396 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.skullstrip_bold_wf.skullstrip_first_pass". 190731-15:27:27,938 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.norm". 190731-15:27:28,636 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.bold_bold_trans_wf.bold_reference_wf.validate". 190731-15:27:28,852 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.n4_correct" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-01..func..sub-23649_ses-01_task-rest_echo-4_bold.nii.gz/n4_correct". 190731-15:27:28,855 nipype.workflow INFO: [Node] Running "n4_correct" ("nipype.interfaces.ants.segmentation.N4BiasFieldCorrection"), a CommandLine Interface with command: N4BiasFieldCorrection --bspline-fitting [ 200 ] -d 3 --input-image /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/bold_bold_trans_wf/bold_reference_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-01..func..sub-23649_ses-01_task-rest_echo-4_bold.nii.gz/gen_ref/ref_bold.nii.gz --mask-image /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-01..func..sub-23649_ses-01_task-rest_echo-4_bold.nii.gz/check_hdr/tpl-MNI152NLin2009cAsym_res-02_desc-brain_mask_trans_dil_hdr.nii.gz --output ref_bold_corrected.nii.gz 190731-15:27:29,869 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.map_brainmask" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-01..func..sub-23649_ses-01_task-rest_echo-3_bold.nii.gz/map_brainmask". 190731-15:27:29,871 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.skullstrip_bold_wf.skullstrip_second_pass" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-01..func..sub-23649_ses-01_task-rest_echo-2_bold.nii.gz/skullstrip_second_pass". 190731-15:27:29,873 nipype.workflow INFO: [Node] Running "map_brainmask" ("niworkflows.interfaces.fixes.FixHeaderApplyTransforms"), a CommandLine Interface with command: antsApplyTransforms --default-value 0 --float 1 --input /home/sahad3/.cache/templateflow/tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_res-02_desc-brain_mask.nii.gz --interpolation MultiLabel --output tpl-MNI152NLin2009cAsym_res-02_desc-brain_mask_trans.nii.gz --reference-image /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/bold_bold_trans_wf/bold_reference_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-01..func..sub-23649_ses-01_task-rest_echo-3_bold.nii.gz/gen_ref/ref_bold.nii.gz --transform [ /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-01..func..sub-23649_ses-01_task-rest_echo-3_bold.nii.gz/norm/transform0GenericAffine.mat, 1 ] 190731-15:27:29,875 nipype.workflow INFO: [Node] Running "skullstrip_second_pass" ("nipype.interfaces.afni.preprocess.Automask"), a CommandLine Interface with command: 3dAutomask -apply_prefix vol0000_xform-00000_merged_brain_masked.nii.gz -dilate 1 -prefix vol0000_xform-00000_merged_brain_mask.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-01..func..sub-23649_ses-01_task-rest_echo-2_bold.nii.gz/skullstrip_second_pass/vol0000_xform-00000_merged_brain.nii.gz 190731-15:27:29,879 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.bold_bold_trans_wf.bold_reference_wf.gen_ref" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/bold_bold_trans_wf/bold_reference_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-01..func..sub-23649_ses-01_task-rest_echo-2_bold.nii.gz/gen_ref". 190731-15:27:29,881 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_mid_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.norm" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_mid_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/norm". 190731-15:27:29,881 nipype.workflow INFO: [Node] Running "gen_ref" ("niworkflows.interfaces.registration.EstimateReferenceImage") 190731-15:27:29,888 nipype.workflow INFO: [Node] Running "norm" ("niworkflows.interfaces.fixes.FixHeaderRegistration"), a CommandLine Interface with command: antsRegistration --collapse-output-transforms 1 --dimensionality 3 --float 1 --initial-moving-transform [ /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_mid_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/init_aff/initialization.mat, 0 ] --initialize-transforms-per-stage 0 --interpolation Linear --output transform --transform Affine[ 0.1 ] --metric Mattes[ /home/sahad3/.cache/templateflow/tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_res-02_desc-fMRIPrep_boldref.nii.gz, /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_mid_wf/bold_reference_wf/gen_ref/ref_bold.nii.gz, 1, 64, Random, 0.2 ] --convergence [ 200, 1e-09, 10 ] --smoothing-sigmas 2.0mm --shrink-factors 2 --use-estimate-learning-rate-once 1 --use-histogram-matching 1 --winsorize-image-intensities [ 0.05, 0.98 ] --write-composite-transform 0 190731-15:27:30,79 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.skullstrip_bold_wf.skullstrip_second_pass". 190731-15:27:30,272 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.bold_bold_trans_wf.bold_reference_wf.gen_ref". 190731-15:27:31,537 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.n4_correct". 190731-15:27:31,661 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_mid_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.norm". 190731-15:27:31,780 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.skullstrip_bold_wf.combine_masks" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-01..func..sub-23649_ses-01_task-rest_echo-2_bold.nii.gz/combine_masks". 190731-15:27:31,783 nipype.workflow INFO: [Node] Running "combine_masks" ("nipype.interfaces.fsl.maths.BinaryMaths"), a CommandLine Interface with command: fslmaths /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-01..func..sub-23649_ses-01_task-rest_echo-2_bold.nii.gz/skullstrip_first_pass/vol0000_xform-00000_merged_brain_mask.nii.gz -mul /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-01..func..sub-23649_ses-01_task-rest_echo-2_bold.nii.gz/skullstrip_second_pass/vol0000_xform-00000_merged_brain_mask.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-01..func..sub-23649_ses-01_task-rest_echo-2_bold.nii.gz/combine_masks/vol0000_xform-00000_merged_brain_mask_maths.nii.gz 190731-15:27:31,934 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.skullstrip_bold_wf.combine_masks". 190731-15:27:32,35 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.map_brainmask". 190731-15:27:34,391 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_pass" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-01..func..sub-23649_ses-01_task-rest_echo-4_bold.nii.gz/skullstrip_first_pass". 190731-15:27:34,393 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.pre_mask_dilate" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-01..func..sub-23649_ses-01_task-rest_echo-3_bold.nii.gz/pre_mask_dilate". 190731-15:27:34,394 nipype.workflow INFO: [Node] Running "skullstrip_first_pass" ("nipype.interfaces.fsl.preprocess.BET"), a CommandLine Interface with command: bet /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-01..func..sub-23649_ses-01_task-rest_echo-4_bold.nii.gz/n4_correct/ref_bold_corrected.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-01..func..sub-23649_ses-01_task-rest_echo-4_bold.nii.gz/skullstrip_first_pass/ref_bold_corrected_brain.nii.gz -f 0.20 -m 190731-15:27:34,394 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.skullstrip_bold_wf.mask_reportlet" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-01..func..sub-23649_ses-01_task-rest_echo-2_bold.nii.gz/mask_reportlet". 190731-15:27:34,395 nipype.workflow INFO: [Node] Running "pre_mask_dilate" ("nipype.interfaces.fsl.maths.DilateImage"), a CommandLine Interface with command: fslmaths -dt char /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-01..func..sub-23649_ses-01_task-rest_echo-3_bold.nii.gz/map_brainmask/tpl-MNI152NLin2009cAsym_res-02_desc-brain_mask_trans.nii.gz -kernel sphere 3.0000 -dilF /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-01..func..sub-23649_ses-01_task-rest_echo-3_bold.nii.gz/pre_mask_dilate/tpl-MNI152NLin2009cAsym_res-02_desc-brain_mask_trans_dil.nii.gz 190731-15:27:34,396 nipype.workflow INFO: [Node] Running "mask_reportlet" ("niworkflows.interfaces.masks.SimpleShowMaskRPT") 190731-15:27:34,397 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.skullstrip_bold_wf.apply_mask" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-01..func..sub-23649_ses-01_task-rest_echo-2_bold.nii.gz/apply_mask". 190731-15:27:34,399 nipype.workflow INFO: [Node] Running "apply_mask" ("nipype.interfaces.fsl.maths.ApplyMask"), a CommandLine Interface with command: fslmaths /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/bold_bold_trans_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-01..func..sub-23649_ses-01_task-rest_echo-2_bold.nii.gz/merge/vol0000_xform-00000_merged.nii.gz -mas /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-01..func..sub-23649_ses-01_task-rest_echo-2_bold.nii.gz/combine_masks/vol0000_xform-00000_merged_brain_mask_maths.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-01..func..sub-23649_ses-01_task-rest_echo-2_bold.nii.gz/apply_mask/vol0000_xform-00000_merged_masked.nii.gz 190731-15:27:34,400 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.init_aff" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-01..func..sub-23649_ses-01_task-rest_echo-2_bold.nii.gz/init_aff". 190731-15:27:34,404 nipype.workflow INFO: [Node] Running "init_aff" ("niworkflows.interfaces.ants.AI"), a CommandLine Interface with command: antsAI -c [10,0.000001,10] -d 3 -x /home/sahad3/.cache/templateflow/tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_res-02_desc-brain_mask.nii.gz -m Mattes[/home/sahad3/.cache/templateflow/tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_res-02_desc-fMRIPrep_boldref.nii.gz,/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/bold_bold_trans_wf/bold_reference_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-01..func..sub-23649_ses-01_task-rest_echo-2_bold.nii.gz/gen_ref/ref_bold.nii.gz,32,Regular,0.200000] -o initialization.mat -p 0 -s [20.000000,0.120000] -t Affine[0.100000] -v 1 190731-15:27:34,575 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.pre_mask_dilate". 190731-15:27:35,782 nipype.interface WARNING: q-forms of reference and mask are substantially different 190731-15:27:36,329 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_mid_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.map_brainmask" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_mid_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/map_brainmask". 190731-15:27:36,332 nipype.workflow INFO: [Node] Running "map_brainmask" ("niworkflows.interfaces.fixes.FixHeaderApplyTransforms"), a CommandLine Interface with command: antsApplyTransforms --default-value 0 --float 1 --input /home/sahad3/.cache/templateflow/tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_res-02_desc-brain_mask.nii.gz --interpolation MultiLabel --output tpl-MNI152NLin2009cAsym_res-02_desc-brain_mask_trans.nii.gz --reference-image /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_mid_wf/bold_reference_wf/gen_ref/ref_bold.nii.gz --transform [ /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_mid_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/norm/transform0GenericAffine.mat, 1 ] 190731-15:27:36,483 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_pass". 190731-15:27:36,795 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.bold_bold_trans_wf.bold_transform". 190731-15:27:37,745 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_dilate" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-01..func..sub-23649_ses-01_task-rest_echo-4_bold.nii.gz/skullstrip_first_dilate". 190731-15:27:37,748 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.n4_correct" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-01..func..sub-23649_ses-01_task-rest_echo-3_bold.nii.gz/n4_correct". 190731-15:27:37,749 nipype.workflow INFO: [Node] Running "skullstrip_first_dilate" ("nipype.interfaces.fsl.maths.DilateImage"), a CommandLine Interface with command: fslmaths -dt char /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-01..func..sub-23649_ses-01_task-rest_echo-4_bold.nii.gz/skullstrip_first_pass/ref_bold_corrected_brain_mask.nii.gz -kernel sphere 6.0000 -dilF /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-01..func..sub-23649_ses-01_task-rest_echo-4_bold.nii.gz/skullstrip_first_dilate/ref_bold_corrected_brain_mask_dil.nii.gz 190731-15:27:37,751 nipype.workflow INFO: [Node] Running "n4_correct" ("nipype.interfaces.ants.segmentation.N4BiasFieldCorrection"), a CommandLine Interface with command: N4BiasFieldCorrection --bspline-fitting [ 200 ] -d 3 --input-image /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/bold_bold_trans_wf/bold_reference_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-01..func..sub-23649_ses-01_task-rest_echo-3_bold.nii.gz/gen_ref/ref_bold.nii.gz --mask-image /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-01..func..sub-23649_ses-01_task-rest_echo-3_bold.nii.gz/check_hdr/tpl-MNI152NLin2009cAsym_res-02_desc-brain_mask_trans_dil_hdr.nii.gz --output ref_bold_corrected.nii.gz 190731-15:27:37,765 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.bold_bold_trans_wf.merge" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/bold_bold_trans_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-01..func..sub-23649_ses-01_task-rest_echo-1_bold.nii.gz/merge". 190731-15:27:37,781 nipype.workflow INFO: [Node] Running "merge" ("fmriprep.interfaces.nilearn.Merge") 190731-15:27:37,890 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.skullstrip_bold_wf.apply_mask". 190731-15:27:38,114 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_dilate". 190731-15:27:38,501 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_mid_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.map_brainmask". 190731-15:27:39,516 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.init_aff". 190731-15:27:39,754 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_mask" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-01..func..sub-23649_ses-01_task-rest_echo-4_bold.nii.gz/skullstrip_first_mask". 190731-15:27:39,756 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_mid_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.pre_mask_dilate" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_mid_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/pre_mask_dilate". 190731-15:27:39,756 nipype.workflow INFO: [Node] Running "skullstrip_first_mask" ("nipype.interfaces.fsl.maths.ApplyMask"), a CommandLine Interface with command: fslmaths /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-01..func..sub-23649_ses-01_task-rest_echo-4_bold.nii.gz/skullstrip_first_pass/ref_bold_corrected_brain.nii.gz -mas /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-01..func..sub-23649_ses-01_task-rest_echo-4_bold.nii.gz/skullstrip_first_dilate/ref_bold_corrected_brain_mask_dil.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-01..func..sub-23649_ses-01_task-rest_echo-4_bold.nii.gz/skullstrip_first_mask/ref_bold_corrected_brain_masked.nii.gz 190731-15:27:39,758 nipype.workflow INFO: [Node] Running "pre_mask_dilate" ("nipype.interfaces.fsl.maths.DilateImage"), a CommandLine Interface with command: fslmaths -dt char /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_mid_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/map_brainmask/tpl-MNI152NLin2009cAsym_res-02_desc-brain_mask_trans.nii.gz -kernel sphere 3.0000 -dilF /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_mid_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/pre_mask_dilate/tpl-MNI152NLin2009cAsym_res-02_desc-brain_mask_trans_dil.nii.gz 190731-15:27:39,879 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_mask". 190731-15:27:39,906 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.skullstrip_bold_wf.mask_reportlet". 190731-15:27:39,971 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_mid_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.pre_mask_dilate". 190731-15:27:39,990 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.n4_correct". 190731-15:27:41,772 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.unifize" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-01..func..sub-23649_ses-01_task-rest_echo-4_bold.nii.gz/unifize". 190731-15:27:41,775 nipype.workflow INFO: [Node] Running "unifize" ("nipype.interfaces.afni.utils.Unifize"), a CommandLine Interface with command: 3dUnifize -clfrac 0.2 -rbt 18.3 65.0 90.0 -prefix uni.nii.gz -T2 -input /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-01..func..sub-23649_ses-01_task-rest_echo-4_bold.nii.gz/unifize/ref_bold_corrected_brain_masked.nii.gz 190731-15:27:42,396 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_pass" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-01..func..sub-23649_ses-01_task-rest_echo-3_bold.nii.gz/skullstrip_first_pass". 190731-15:27:42,399 nipype.workflow INFO: [Node] Running "skullstrip_first_pass" ("nipype.interfaces.fsl.preprocess.BET"), a CommandLine Interface with command: bet /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-01..func..sub-23649_ses-01_task-rest_echo-3_bold.nii.gz/n4_correct/ref_bold_corrected.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-01..func..sub-23649_ses-01_task-rest_echo-3_bold.nii.gz/skullstrip_first_pass/ref_bold_corrected_brain.nii.gz -f 0.20 -m 190731-15:27:42,401 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.norm" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-01..func..sub-23649_ses-01_task-rest_echo-2_bold.nii.gz/norm". 190731-15:27:42,408 nipype.workflow INFO: [Node] Running "norm" ("niworkflows.interfaces.fixes.FixHeaderRegistration"), a CommandLine Interface with command: antsRegistration --collapse-output-transforms 1 --dimensionality 3 --float 1 --initial-moving-transform [ /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-01..func..sub-23649_ses-01_task-rest_echo-2_bold.nii.gz/init_aff/initialization.mat, 0 ] --initialize-transforms-per-stage 0 --interpolation Linear --output transform --transform Affine[ 0.1 ] --metric Mattes[ /home/sahad3/.cache/templateflow/tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_res-02_desc-fMRIPrep_boldref.nii.gz, /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/bold_bold_trans_wf/bold_reference_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-01..func..sub-23649_ses-01_task-rest_echo-2_bold.nii.gz/gen_ref/ref_bold.nii.gz, 1, 64, Random, 0.2 ] --convergence [ 200, 1e-09, 10 ] --smoothing-sigmas 2.0mm --shrink-factors 2 --use-estimate-learning-rate-once 1 --use-histogram-matching 1 --winsorize-image-intensities [ 0.05, 0.98 ] --write-composite-transform 0 190731-15:27:42,415 nipype.interface WARNING: q-forms of reference and mask are substantially different 190731-15:27:42,831 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.unifize". 190731-15:27:42,981 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_opposite_wf.enhance_and_skullstrip_bold_wf.init_aff" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/enhance_and_skullstrip_bold_wf/init_aff". 190731-15:27:42,984 nipype.workflow INFO: [Node] Running "init_aff" ("niworkflows.interfaces.ants.AI"), a CommandLine Interface with command: antsAI -c [10,0.000001,10] -d 3 -x /home/sahad3/.cache/templateflow/tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_res-02_desc-brain_mask.nii.gz -m Mattes[/home/sahad3/.cache/templateflow/tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_res-02_desc-fMRIPrep_boldref.nii.gz,/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/merge/template.nii.gz,32,Regular,0.200000] -o initialization.mat -p 0 -s [20.000000,0.120000] -t Affine[0.100000] -v 1 190731-15:27:43,815 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.fixhdr_unifize" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-01..func..sub-23649_ses-01_task-rest_echo-4_bold.nii.gz/fixhdr_unifize". 190731-15:27:43,818 nipype.workflow INFO: [Node] Running "fixhdr_unifize" ("niworkflows.interfaces.utils.CopyXForm") 190731-15:27:43,818 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_mid_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.n4_correct" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_mid_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/n4_correct". 190731-15:27:43,822 nipype.workflow INFO: [Node] Running "n4_correct" ("nipype.interfaces.ants.segmentation.N4BiasFieldCorrection"), a CommandLine Interface with command: N4BiasFieldCorrection --bspline-fitting [ 200 ] -d 3 --input-image /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_mid_wf/bold_reference_wf/gen_ref/ref_bold.nii.gz --mask-image /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_mid_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/check_hdr/tpl-MNI152NLin2009cAsym_res-02_desc-brain_mask_trans_dil_hdr.nii.gz --output ref_bold_corrected.nii.gz 190731-15:27:43,854 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.fixhdr_unifize". 190731-15:27:43,978 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.norm". 190731-15:27:44,471 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_pass". 190731-15:27:45,764 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.skullstrip_second_pass" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-01..func..sub-23649_ses-01_task-rest_echo-4_bold.nii.gz/skullstrip_second_pass". 190731-15:27:45,766 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_dilate" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-01..func..sub-23649_ses-01_task-rest_echo-3_bold.nii.gz/skullstrip_first_dilate". 190731-15:27:45,767 nipype.workflow INFO: [Node] Running "skullstrip_second_pass" ("nipype.interfaces.afni.preprocess.Automask"), a CommandLine Interface with command: 3dAutomask -apply_prefix uni_xform_masked.nii.gz -dilate 1 -prefix uni_xform_mask.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-01..func..sub-23649_ses-01_task-rest_echo-4_bold.nii.gz/skullstrip_second_pass/uni_xform.nii.gz 190731-15:27:45,768 nipype.workflow INFO: [Node] Running "skullstrip_first_dilate" ("nipype.interfaces.fsl.maths.DilateImage"), a CommandLine Interface with command: fslmaths -dt char /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-01..func..sub-23649_ses-01_task-rest_echo-3_bold.nii.gz/skullstrip_first_pass/ref_bold_corrected_brain_mask.nii.gz -kernel sphere 6.0000 -dilF /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-01..func..sub-23649_ses-01_task-rest_echo-3_bold.nii.gz/skullstrip_first_dilate/ref_bold_corrected_brain_mask_dil.nii.gz 190731-15:27:45,770 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.map_brainmask" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-01..func..sub-23649_ses-01_task-rest_echo-2_bold.nii.gz/map_brainmask". 190731-15:27:45,772 nipype.workflow INFO: [Node] Running "map_brainmask" ("niworkflows.interfaces.fixes.FixHeaderApplyTransforms"), a CommandLine Interface with command: antsApplyTransforms --default-value 0 --float 1 --input /home/sahad3/.cache/templateflow/tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_res-02_desc-brain_mask.nii.gz --interpolation MultiLabel --output tpl-MNI152NLin2009cAsym_res-02_desc-brain_mask_trans.nii.gz --reference-image /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/bold_bold_trans_wf/bold_reference_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-01..func..sub-23649_ses-01_task-rest_echo-2_bold.nii.gz/gen_ref/ref_bold.nii.gz --transform [ /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-01..func..sub-23649_ses-01_task-rest_echo-2_bold.nii.gz/norm/transform0GenericAffine.mat, 1 ] 190731-15:27:45,935 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.skullstrip_second_pass". 190731-15:27:46,100 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_dilate". 190731-15:27:46,451 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_mid_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.n4_correct". 190731-15:27:47,714 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.fixhdr_skullstrip2" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-01..func..sub-23649_ses-01_task-rest_echo-4_bold.nii.gz/fixhdr_skullstrip2". 190731-15:27:47,717 nipype.workflow INFO: [Node] Running "fixhdr_skullstrip2" ("niworkflows.interfaces.utils.CopyXForm") 190731-15:27:47,717 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_mask" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-01..func..sub-23649_ses-01_task-rest_echo-3_bold.nii.gz/skullstrip_first_mask". 190731-15:27:47,719 nipype.workflow INFO: [Node] Running "skullstrip_first_mask" ("nipype.interfaces.fsl.maths.ApplyMask"), a CommandLine Interface with command: fslmaths /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-01..func..sub-23649_ses-01_task-rest_echo-3_bold.nii.gz/skullstrip_first_pass/ref_bold_corrected_brain.nii.gz -mas /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-01..func..sub-23649_ses-01_task-rest_echo-3_bold.nii.gz/skullstrip_first_dilate/ref_bold_corrected_brain_mask_dil.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-01..func..sub-23649_ses-01_task-rest_echo-3_bold.nii.gz/skullstrip_first_mask/ref_bold_corrected_brain_masked.nii.gz 190731-15:27:47,719 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_mid_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_pass" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_mid_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_pass". 190731-15:27:47,721 nipype.workflow INFO: [Node] Running "skullstrip_first_pass" ("nipype.interfaces.fsl.preprocess.BET"), a CommandLine Interface with command: bet /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_mid_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/n4_correct/ref_bold_corrected.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_mid_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_pass/ref_bold_corrected_brain.nii.gz -f 0.20 -m 190731-15:27:47,740 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.fixhdr_skullstrip2". 190731-15:27:47,798 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.map_brainmask". 190731-15:27:47,846 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_mask". 190731-15:27:48,306 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_opposite_wf.enhance_and_skullstrip_bold_wf.init_aff". 190731-15:27:49,474 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.bold_bold_trans_wf.merge". 190731-15:27:49,720 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.combine_masks" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-01..func..sub-23649_ses-01_task-rest_echo-4_bold.nii.gz/combine_masks". 190731-15:27:49,722 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.unifize" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-01..func..sub-23649_ses-01_task-rest_echo-3_bold.nii.gz/unifize". 190731-15:27:49,723 nipype.workflow INFO: [Node] Running "combine_masks" ("nipype.interfaces.fsl.maths.BinaryMaths"), a CommandLine Interface with command: fslmaths /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-01..func..sub-23649_ses-01_task-rest_echo-4_bold.nii.gz/skullstrip_first_pass/ref_bold_corrected_brain_mask.nii.gz -mul /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-01..func..sub-23649_ses-01_task-rest_echo-4_bold.nii.gz/fixhdr_skullstrip2/uni_xform_mask_xform.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-01..func..sub-23649_ses-01_task-rest_echo-4_bold.nii.gz/combine_masks/ref_bold_corrected_brain_mask_maths.nii.gz 190731-15:27:49,723 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.pre_mask_dilate" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-01..func..sub-23649_ses-01_task-rest_echo-2_bold.nii.gz/pre_mask_dilate". 190731-15:27:49,724 nipype.workflow INFO: [Node] Running "unifize" ("nipype.interfaces.afni.utils.Unifize"), a CommandLine Interface with command: 3dUnifize -clfrac 0.2 -rbt 18.3 65.0 90.0 -prefix uni.nii.gz -T2 -input /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-01..func..sub-23649_ses-01_task-rest_echo-3_bold.nii.gz/unifize/ref_bold_corrected_brain_masked.nii.gz 190731-15:27:49,726 nipype.workflow INFO: [Node] Running "pre_mask_dilate" ("nipype.interfaces.fsl.maths.DilateImage"), a CommandLine Interface with command: fslmaths -dt char /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-01..func..sub-23649_ses-01_task-rest_echo-2_bold.nii.gz/map_brainmask/tpl-MNI152NLin2009cAsym_res-02_desc-brain_mask_trans.nii.gz -kernel sphere 3.0000 -dilF /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-01..func..sub-23649_ses-01_task-rest_echo-2_bold.nii.gz/pre_mask_dilate/tpl-MNI152NLin2009cAsym_res-02_desc-brain_mask_trans_dil.nii.gz 190731-15:27:49,728 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_opposite_wf.enhance_and_skullstrip_bold_wf.norm" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/enhance_and_skullstrip_bold_wf/norm". 190731-15:27:49,732 nipype.workflow INFO: [Node] Running "norm" ("niworkflows.interfaces.fixes.FixHeaderRegistration"), a CommandLine Interface with command: antsRegistration --collapse-output-transforms 1 --dimensionality 3 --float 1 --initial-moving-transform [ /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/enhance_and_skullstrip_bold_wf/init_aff/initialization.mat, 0 ] --initialize-transforms-per-stage 0 --interpolation Linear --output transform --transform Affine[ 0.1 ] --metric Mattes[ /home/sahad3/.cache/templateflow/tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_res-02_desc-fMRIPrep_boldref.nii.gz, /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/merge/template.nii.gz, 1, 64, Random, 0.2 ] --convergence [ 200, 1e-09, 10 ] --smoothing-sigmas 2.0mm --shrink-factors 2 --use-estimate-learning-rate-once 1 --use-histogram-matching 1 --winsorize-image-intensities [ 0.05, 0.98 ] --write-composite-transform 0 190731-15:27:49,752 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_mid_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_pass". 190731-15:27:49,831 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.combine_masks". 190731-15:27:49,907 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.pre_mask_dilate". 190731-15:27:50,781 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.unifize". 190731-15:27:50,879 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_opposite_wf.enhance_and_skullstrip_bold_wf.norm". 190731-15:27:52,261 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.apply_mask" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-01..func..sub-23649_ses-01_task-rest_echo-4_bold.nii.gz/apply_mask". 190731-15:27:52,263 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.fixhdr_unifize" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-01..func..sub-23649_ses-01_task-rest_echo-3_bold.nii.gz/fixhdr_unifize". 190731-15:27:52,263 nipype.workflow INFO: [Node] Running "apply_mask" ("nipype.interfaces.fsl.maths.ApplyMask"), a CommandLine Interface with command: fslmaths /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-01..func..sub-23649_ses-01_task-rest_echo-4_bold.nii.gz/fixhdr_unifize/uni_xform.nii.gz -mas /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-01..func..sub-23649_ses-01_task-rest_echo-4_bold.nii.gz/combine_masks/ref_bold_corrected_brain_mask_maths.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-01..func..sub-23649_ses-01_task-rest_echo-4_bold.nii.gz/apply_mask/uni_xform_masked.nii.gz 190731-15:27:52,264 nipype.workflow INFO: [Node] Running "fixhdr_unifize" ("niworkflows.interfaces.utils.CopyXForm") 190731-15:27:52,275 nipype.interface WARNING: q-forms of reference and mask are substantially different 190731-15:27:52,297 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.fixhdr_unifize". 190731-15:27:52,412 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.apply_mask". 190731-15:28:02,929 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.skullstrip_bold_wf.skullstrip_first_pass" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-01..func..sub-23649_ses-01_task-rest_echo-1_bold.nii.gz/skullstrip_first_pass". 190731-15:28:02,931 nipype.workflow INFO: [Node] Running "skullstrip_first_pass" ("nipype.interfaces.fsl.preprocess.BET"), a CommandLine Interface with command: bet /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/bold_bold_trans_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-01..func..sub-23649_ses-01_task-rest_echo-1_bold.nii.gz/merge/vol0000_xform-00000_merged.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-01..func..sub-23649_ses-01_task-rest_echo-1_bold.nii.gz/skullstrip_first_pass/vol0000_xform-00000_merged_brain.nii.gz -f 0.20 -m 190731-15:28:02,932 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_mid_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_dilate" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_mid_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_dilate". 190731-15:28:02,934 nipype.workflow INFO: [Node] Running "skullstrip_first_dilate" ("nipype.interfaces.fsl.maths.DilateImage"), a CommandLine Interface with command: fslmaths -dt char /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_mid_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_pass/ref_bold_corrected_brain_mask.nii.gz -kernel sphere 6.0000 -dilF /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_mid_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_dilate/ref_bold_corrected_brain_mask_dil.nii.gz 190731-15:28:02,935 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_opposite_wf.enhance_and_skullstrip_bold_wf.map_brainmask" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/enhance_and_skullstrip_bold_wf/map_brainmask". 190731-15:28:02,937 nipype.workflow INFO: [Node] Running "map_brainmask" ("niworkflows.interfaces.fixes.FixHeaderApplyTransforms"), a CommandLine Interface with command: antsApplyTransforms --default-value 0 --float 1 --input /home/sahad3/.cache/templateflow/tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_res-02_desc-brain_mask.nii.gz --interpolation MultiLabel --output tpl-MNI152NLin2009cAsym_res-02_desc-brain_mask_trans.nii.gz --reference-image /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/merge/template.nii.gz --transform [ /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/enhance_and_skullstrip_bold_wf/norm/transform0GenericAffine.mat, 1 ] 190731-15:28:02,940 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_matching_wf.enhance_and_skullstrip_bold_wf.init_aff" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/enhance_and_skullstrip_bold_wf/init_aff". 190731-15:28:02,941 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.bold_bold_trans_wf.bold_reference_wf.validate" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/bold_bold_trans_wf/bold_reference_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-01..func..sub-23649_ses-01_task-rest_echo-1_bold.nii.gz/validate". 190731-15:28:02,943 nipype.workflow INFO: [Node] Running "validate" ("niworkflows.interfaces.images.ValidateImage") 190731-15:28:02,944 nipype.workflow INFO: [Node] Running "init_aff" ("niworkflows.interfaces.ants.AI"), a CommandLine Interface with command: antsAI -c [10,0.000001,10] -d 3 -x /home/sahad3/.cache/templateflow/tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_res-02_desc-brain_mask.nii.gz -m Mattes[/home/sahad3/.cache/templateflow/tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_res-02_desc-fMRIPrep_boldref.nii.gz,/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/merge/template.nii.gz,32,Regular,0.200000] -o initialization.mat -p 0 -s [20.000000,0.120000] -t Affine[0.100000] -v 1 190731-15:28:03,396 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_mid_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_dilate". 190731-15:28:03,461 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.skullstrip_second_pass" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-01..func..sub-23649_ses-01_task-rest_echo-3_bold.nii.gz/skullstrip_second_pass". 190731-15:28:03,463 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.n4_correct" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-01..func..sub-23649_ses-01_task-rest_echo-2_bold.nii.gz/n4_correct". 190731-15:28:03,464 nipype.workflow INFO: [Node] Running "skullstrip_second_pass" ("nipype.interfaces.afni.preprocess.Automask"), a CommandLine Interface with command: 3dAutomask -apply_prefix uni_xform_masked.nii.gz -dilate 1 -prefix uni_xform_mask.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-01..func..sub-23649_ses-01_task-rest_echo-3_bold.nii.gz/skullstrip_second_pass/uni_xform.nii.gz 190731-15:28:03,467 nipype.workflow INFO: [Node] Running "n4_correct" ("nipype.interfaces.ants.segmentation.N4BiasFieldCorrection"), a CommandLine Interface with command: N4BiasFieldCorrection --bspline-fitting [ 200 ] -d 3 --input-image /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/bold_bold_trans_wf/bold_reference_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-01..func..sub-23649_ses-01_task-rest_echo-2_bold.nii.gz/gen_ref/ref_bold.nii.gz --mask-image /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-01..func..sub-23649_ses-01_task-rest_echo-2_bold.nii.gz/check_hdr/tpl-MNI152NLin2009cAsym_res-02_desc-brain_mask_trans_dil_hdr.nii.gz --output ref_bold_corrected.nii.gz 190731-15:28:03,707 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.skullstrip_second_pass". 190731-15:28:04,763 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_opposite_wf.enhance_and_skullstrip_bold_wf.map_brainmask". 190731-15:28:04,850 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.skullstrip_bold_wf.skullstrip_first_pass". 190731-15:28:05,318 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.n4_correct". 190731-15:28:05,465 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.fixhdr_skullstrip2" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-01..func..sub-23649_ses-01_task-rest_echo-3_bold.nii.gz/fixhdr_skullstrip2". 190731-15:28:05,466 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.skullstrip_bold_wf.skullstrip_second_pass" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-01..func..sub-23649_ses-01_task-rest_echo-1_bold.nii.gz/skullstrip_second_pass". 190731-15:28:05,466 nipype.workflow INFO: [Node] Running "fixhdr_skullstrip2" ("niworkflows.interfaces.utils.CopyXForm") 190731-15:28:05,468 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_mid_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_mask" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_mid_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_mask". 190731-15:28:05,468 nipype.workflow INFO: [Node] Running "skullstrip_second_pass" ("nipype.interfaces.afni.preprocess.Automask"), a CommandLine Interface with command: 3dAutomask -apply_prefix vol0000_xform-00000_merged_brain_masked.nii.gz -dilate 1 -prefix vol0000_xform-00000_merged_brain_mask.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-01..func..sub-23649_ses-01_task-rest_echo-1_bold.nii.gz/skullstrip_second_pass/vol0000_xform-00000_merged_brain.nii.gz 190731-15:28:05,470 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_opposite_wf.enhance_and_skullstrip_bold_wf.pre_mask_dilate" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/enhance_and_skullstrip_bold_wf/pre_mask_dilate". 190731-15:28:05,470 nipype.workflow INFO: [Node] Running "skullstrip_first_mask" ("nipype.interfaces.fsl.maths.ApplyMask"), a CommandLine Interface with command: fslmaths /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_mid_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_pass/ref_bold_corrected_brain.nii.gz -mas /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_mid_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_dilate/ref_bold_corrected_brain_mask_dil.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_mid_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_mask/ref_bold_corrected_brain_masked.nii.gz 190731-15:28:05,474 nipype.workflow INFO: [Node] Running "pre_mask_dilate" ("nipype.interfaces.fsl.maths.DilateImage"), a CommandLine Interface with command: fslmaths -dt char /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/enhance_and_skullstrip_bold_wf/map_brainmask/tpl-MNI152NLin2009cAsym_res-02_desc-brain_mask_trans.nii.gz -kernel sphere 3.0000 -dilF /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/enhance_and_skullstrip_bold_wf/pre_mask_dilate/tpl-MNI152NLin2009cAsym_res-02_desc-brain_mask_trans_dil.nii.gz 190731-15:28:05,489 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.fixhdr_skullstrip2". 190731-15:28:05,595 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_mid_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_mask". 190731-15:28:05,679 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.skullstrip_bold_wf.skullstrip_second_pass". 190731-15:28:05,749 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_opposite_wf.enhance_and_skullstrip_bold_wf.pre_mask_dilate". 190731-15:28:06,215 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.bold_bold_trans_wf.bold_reference_wf.validate". 190731-15:28:07,470 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.combine_masks" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-01..func..sub-23649_ses-01_task-rest_echo-3_bold.nii.gz/combine_masks". 190731-15:28:07,472 nipype.workflow INFO: [Node] Running "combine_masks" ("nipype.interfaces.fsl.maths.BinaryMaths"), a CommandLine Interface with command: fslmaths /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-01..func..sub-23649_ses-01_task-rest_echo-3_bold.nii.gz/skullstrip_first_pass/ref_bold_corrected_brain_mask.nii.gz -mul /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-01..func..sub-23649_ses-01_task-rest_echo-3_bold.nii.gz/fixhdr_skullstrip2/uni_xform_mask_xform.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-01..func..sub-23649_ses-01_task-rest_echo-3_bold.nii.gz/combine_masks/ref_bold_corrected_brain_mask_maths.nii.gz 190731-15:28:07,622 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.combine_masks". 190731-15:28:07,749 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_matching_wf.enhance_and_skullstrip_bold_wf.init_aff". 190731-15:28:08,75 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_pass" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-01..func..sub-23649_ses-01_task-rest_echo-2_bold.nii.gz/skullstrip_first_pass". 190731-15:28:08,77 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.skullstrip_bold_wf.combine_masks" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-01..func..sub-23649_ses-01_task-rest_echo-1_bold.nii.gz/combine_masks". 190731-15:28:08,78 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.bold_bold_trans_wf.bold_reference_wf.gen_ref" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/bold_bold_trans_wf/bold_reference_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-01..func..sub-23649_ses-01_task-rest_echo-1_bold.nii.gz/gen_ref". 190731-15:28:08,78 nipype.workflow INFO: [Node] Running "skullstrip_first_pass" ("nipype.interfaces.fsl.preprocess.BET"), a CommandLine Interface with command: bet /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-01..func..sub-23649_ses-01_task-rest_echo-2_bold.nii.gz/n4_correct/ref_bold_corrected.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-01..func..sub-23649_ses-01_task-rest_echo-2_bold.nii.gz/skullstrip_first_pass/ref_bold_corrected_brain.nii.gz -f 0.20 -m 190731-15:28:08,79 nipype.workflow INFO: [Node] Running "combine_masks" ("nipype.interfaces.fsl.maths.BinaryMaths"), a CommandLine Interface with command: fslmaths /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-01..func..sub-23649_ses-01_task-rest_echo-1_bold.nii.gz/skullstrip_first_pass/vol0000_xform-00000_merged_brain_mask.nii.gz -mul /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-01..func..sub-23649_ses-01_task-rest_echo-1_bold.nii.gz/skullstrip_second_pass/vol0000_xform-00000_merged_brain_mask.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-01..func..sub-23649_ses-01_task-rest_echo-1_bold.nii.gz/combine_masks/vol0000_xform-00000_merged_brain_mask_maths.nii.gz 190731-15:28:08,80 nipype.workflow INFO: [Node] Running "gen_ref" ("niworkflows.interfaces.registration.EstimateReferenceImage") 190731-15:28:08,80 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_mid_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.unifize" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_mid_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/unifize". 190731-15:28:08,84 nipype.workflow INFO: [Node] Running "unifize" ("nipype.interfaces.afni.utils.Unifize"), a CommandLine Interface with command: 3dUnifize -clfrac 0.2 -rbt 18.3 65.0 90.0 -prefix uni.nii.gz -T2 -input /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_mid_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/unifize/ref_bold_corrected_brain_masked.nii.gz 190731-15:28:08,216 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.skullstrip_bold_wf.combine_masks". 190731-15:28:08,450 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.bold_bold_trans_wf.bold_reference_wf.gen_ref". 190731-15:28:09,475 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_mid_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.unifize". 190731-15:28:09,936 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_pass". 190731-15:28:10,88 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.apply_mask" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-01..func..sub-23649_ses-01_task-rest_echo-3_bold.nii.gz/apply_mask". 190731-15:28:10,90 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.skullstrip_bold_wf.mask_reportlet" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-01..func..sub-23649_ses-01_task-rest_echo-1_bold.nii.gz/mask_reportlet". 190731-15:28:10,91 nipype.workflow INFO: [Node] Running "apply_mask" ("nipype.interfaces.fsl.maths.ApplyMask"), a CommandLine Interface with command: fslmaths /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-01..func..sub-23649_ses-01_task-rest_echo-3_bold.nii.gz/fixhdr_unifize/uni_xform.nii.gz -mas /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-01..func..sub-23649_ses-01_task-rest_echo-3_bold.nii.gz/combine_masks/ref_bold_corrected_brain_mask_maths.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-01..func..sub-23649_ses-01_task-rest_echo-3_bold.nii.gz/apply_mask/uni_xform_masked.nii.gz 190731-15:28:10,92 nipype.workflow INFO: [Node] Running "mask_reportlet" ("niworkflows.interfaces.masks.SimpleShowMaskRPT") 190731-15:28:10,93 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.skullstrip_bold_wf.apply_mask" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-01..func..sub-23649_ses-01_task-rest_echo-1_bold.nii.gz/apply_mask". 190731-15:28:10,95 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.init_aff" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-01..func..sub-23649_ses-01_task-rest_echo-1_bold.nii.gz/init_aff". 190731-15:28:10,95 nipype.workflow INFO: [Node] Running "apply_mask" ("nipype.interfaces.fsl.maths.ApplyMask"), a CommandLine Interface with command: fslmaths /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/bold_bold_trans_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-01..func..sub-23649_ses-01_task-rest_echo-1_bold.nii.gz/merge/vol0000_xform-00000_merged.nii.gz -mas /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-01..func..sub-23649_ses-01_task-rest_echo-1_bold.nii.gz/combine_masks/vol0000_xform-00000_merged_brain_mask_maths.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-01..func..sub-23649_ses-01_task-rest_echo-1_bold.nii.gz/apply_mask/vol0000_xform-00000_merged_masked.nii.gz 190731-15:28:10,97 nipype.workflow INFO: [Node] Running "init_aff" ("niworkflows.interfaces.ants.AI"), a CommandLine Interface with command: antsAI -c [10,0.000001,10] -d 3 -x /home/sahad3/.cache/templateflow/tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_res-02_desc-brain_mask.nii.gz -m Mattes[/home/sahad3/.cache/templateflow/tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_res-02_desc-fMRIPrep_boldref.nii.gz,/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/bold_bold_trans_wf/bold_reference_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-01..func..sub-23649_ses-01_task-rest_echo-1_bold.nii.gz/gen_ref/ref_bold.nii.gz,32,Regular,0.200000] -o initialization.mat -p 0 -s [20.000000,0.120000] -t Affine[0.100000] -v 1 190731-15:28:10,213 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.apply_mask". 190731-15:28:10,653 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_opposite_wf.enhance_and_skullstrip_bold_wf.n4_correct" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/enhance_and_skullstrip_bold_wf/n4_correct". 190731-15:28:10,657 nipype.workflow INFO: [Node] Running "n4_correct" ("nipype.interfaces.ants.segmentation.N4BiasFieldCorrection"), a CommandLine Interface with command: N4BiasFieldCorrection --bspline-fitting [ 200 ] -d 3 --input-image /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/merge/template.nii.gz --mask-image /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/enhance_and_skullstrip_bold_wf/check_hdr/tpl-MNI152NLin2009cAsym_res-02_desc-brain_mask_trans_dil_hdr.nii.gz --output template_corrected.nii.gz 190731-15:28:11,522 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_dilate" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-01..func..sub-23649_ses-01_task-rest_echo-2_bold.nii.gz/skullstrip_first_dilate". 190731-15:28:11,523 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_mid_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.fixhdr_unifize" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_mid_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/fixhdr_unifize". 190731-15:28:11,524 nipype.workflow INFO: [Node] Running "fixhdr_unifize" ("niworkflows.interfaces.utils.CopyXForm") 190731-15:28:11,526 nipype.workflow INFO: [Node] Running "skullstrip_first_dilate" ("nipype.interfaces.fsl.maths.DilateImage"), a CommandLine Interface with command: fslmaths -dt char /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-01..func..sub-23649_ses-01_task-rest_echo-2_bold.nii.gz/skullstrip_first_pass/ref_bold_corrected_brain_mask.nii.gz -kernel sphere 6.0000 -dilF /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-01..func..sub-23649_ses-01_task-rest_echo-2_bold.nii.gz/skullstrip_first_dilate/ref_bold_corrected_brain_mask_dil.nii.gz 190731-15:28:11,563 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_mid_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.fixhdr_unifize". 190731-15:28:12,88 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_dilate". 190731-15:28:13,140 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_opposite_wf.enhance_and_skullstrip_bold_wf.n4_correct". 190731-15:28:13,467 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_mask" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-01..func..sub-23649_ses-01_task-rest_echo-2_bold.nii.gz/skullstrip_first_mask". 190731-15:28:13,468 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_mid_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.skullstrip_second_pass" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_mid_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_second_pass". 190731-15:28:13,469 nipype.workflow INFO: [Node] Running "skullstrip_first_mask" ("nipype.interfaces.fsl.maths.ApplyMask"), a CommandLine Interface with command: fslmaths /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-01..func..sub-23649_ses-01_task-rest_echo-2_bold.nii.gz/skullstrip_first_pass/ref_bold_corrected_brain.nii.gz -mas /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-01..func..sub-23649_ses-01_task-rest_echo-2_bold.nii.gz/skullstrip_first_dilate/ref_bold_corrected_brain_mask_dil.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-01..func..sub-23649_ses-01_task-rest_echo-2_bold.nii.gz/skullstrip_first_mask/ref_bold_corrected_brain_masked.nii.gz 190731-15:28:13,471 nipype.workflow INFO: [Node] Running "skullstrip_second_pass" ("nipype.interfaces.afni.preprocess.Automask"), a CommandLine Interface with command: 3dAutomask -apply_prefix uni_xform_masked.nii.gz -dilate 1 -prefix uni_xform_mask.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_mid_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_second_pass/uni_xform.nii.gz 190731-15:28:13,623 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_mask". 190731-15:28:13,641 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_mid_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.skullstrip_second_pass". 190731-15:28:13,808 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.skullstrip_bold_wf.apply_mask". 190731-15:28:14,730 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.init_aff". 190731-15:28:15,446 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.skullstrip_bold_wf.mask_reportlet". 190731-15:28:15,486 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.unifize" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-01..func..sub-23649_ses-01_task-rest_echo-2_bold.nii.gz/unifize". 190731-15:28:15,488 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.join_echos" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/join_echos". 190731-15:28:15,488 nipype.workflow INFO: [Node] Running "unifize" ("nipype.interfaces.afni.utils.Unifize"), a CommandLine Interface with command: 3dUnifize -clfrac 0.2 -rbt 18.3 65.0 90.0 -prefix uni.nii.gz -T2 -input /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-01..func..sub-23649_ses-01_task-rest_echo-2_bold.nii.gz/unifize/ref_bold_corrected_brain_masked.nii.gz 190731-15:28:15,490 nipype.workflow INFO: [Node] Running "join_echos" ("nipype.interfaces.utility.base.IdentityInterface") 190731-15:28:15,493 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.norm" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-01..func..sub-23649_ses-01_task-rest_echo-1_bold.nii.gz/norm". 190731-15:28:15,493 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.join_echos". 190731-15:28:15,494 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_mid_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.fixhdr_skullstrip2" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_mid_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/fixhdr_skullstrip2". 190731-15:28:15,496 nipype.workflow INFO: [Node] Running "fixhdr_skullstrip2" ("niworkflows.interfaces.utils.CopyXForm") 190731-15:28:15,496 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_opposite_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_pass" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_pass". 190731-15:28:15,497 nipype.workflow INFO: [Node] Running "norm" ("niworkflows.interfaces.fixes.FixHeaderRegistration"), a CommandLine Interface with command: antsRegistration --collapse-output-transforms 1 --dimensionality 3 --float 1 --initial-moving-transform [ /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-01..func..sub-23649_ses-01_task-rest_echo-1_bold.nii.gz/init_aff/initialization.mat, 0 ] --initialize-transforms-per-stage 0 --interpolation Linear --output transform --transform Affine[ 0.1 ] --metric Mattes[ /home/sahad3/.cache/templateflow/tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_res-02_desc-fMRIPrep_boldref.nii.gz, /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/bold_bold_trans_wf/bold_reference_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-01..func..sub-23649_ses-01_task-rest_echo-1_bold.nii.gz/gen_ref/ref_bold.nii.gz, 1, 64, Random, 0.2 ] --convergence [ 200, 1e-09, 10 ] --smoothing-sigmas 2.0mm --shrink-factors 2 --use-estimate-learning-rate-once 1 --use-histogram-matching 1 --winsorize-image-intensities [ 0.05, 0.98 ] --write-composite-transform 0 190731-15:28:15,500 nipype.workflow INFO: [Node] Running "skullstrip_first_pass" ("nipype.interfaces.fsl.preprocess.BET"), a CommandLine Interface with command: bet /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/enhance_and_skullstrip_bold_wf/n4_correct/template_corrected.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_pass/template_corrected_brain.nii.gz -f 0.20 -m 190731-15:28:15,515 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_mid_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.fixhdr_skullstrip2". 190731-15:28:16,747 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.unifize". 190731-15:28:16,936 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.norm". 190731-15:28:17,486 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.fixhdr_unifize" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-01..func..sub-23649_ses-01_task-rest_echo-2_bold.nii.gz/fixhdr_unifize". 190731-15:28:17,488 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.bold_t2smap_wf.t2smap_node" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/bold_t2smap_wf/t2smap_node". 190731-15:28:17,491 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.map_brainmask" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-01..func..sub-23649_ses-01_task-rest_echo-1_bold.nii.gz/map_brainmask". 190731-15:28:17,493 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_mid_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.combine_masks" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_mid_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/combine_masks". 190731-15:28:17,497 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_matching_wf.enhance_and_skullstrip_bold_wf.norm" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/enhance_and_skullstrip_bold_wf/norm". 190731-15:28:17,511 nipype.workflow INFO: [Node] Running "combine_masks" ("nipype.interfaces.fsl.maths.BinaryMaths"), a CommandLine Interface with command: fslmaths /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_mid_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_pass/ref_bold_corrected_brain_mask.nii.gz -mul /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_mid_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/fixhdr_skullstrip2/uni_xform_mask_xform.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_mid_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/combine_masks/ref_bold_corrected_brain_mask_maths.nii.gz 190731-15:28:17,511 nipype.workflow INFO: [Node] Running "fixhdr_unifize" ("niworkflows.interfaces.utils.CopyXForm") 190731-15:28:17,511 nipype.workflow INFO: [Node] Running "t2smap_node" ("fmriprep.interfaces.multiecho.T2SMap"), a CommandLine Interface with command: t2smap -d /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-01..func..sub-23649_ses-01_task-rest_echo-1_bold.nii.gz/apply_mask/vol0000_xform-00000_merged_masked.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-01..func..sub-23649_ses-01_task-rest_echo-2_bold.nii.gz/apply_mask/vol0000_xform-00000_merged_masked.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-01..func..sub-23649_ses-01_task-rest_echo-3_bold.nii.gz/apply_mask/vol0000_xform-00000_merged_masked.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-01..func..sub-23649_ses-01_task-rest_echo-4_bold.nii.gz/apply_mask/vol0000_xform-00000_merged_masked.nii.gz -e 15.2 28.799999999999997 42.4 56.0 190731-15:28:17,512 nipype.workflow INFO: [Node] Running "map_brainmask" ("niworkflows.interfaces.fixes.FixHeaderApplyTransforms"), a CommandLine Interface with command: antsApplyTransforms --default-value 0 --float 1 --input /home/sahad3/.cache/templateflow/tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_res-02_desc-brain_mask.nii.gz --interpolation MultiLabel --output tpl-MNI152NLin2009cAsym_res-02_desc-brain_mask_trans.nii.gz --reference-image /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/bold_bold_trans_wf/bold_reference_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-01..func..sub-23649_ses-01_task-rest_echo-1_bold.nii.gz/gen_ref/ref_bold.nii.gz --transform [ /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-01..func..sub-23649_ses-01_task-rest_echo-1_bold.nii.gz/norm/transform0GenericAffine.mat, 1 ] 190731-15:28:17,513 nipype.workflow INFO: [Node] Running "norm" ("niworkflows.interfaces.fixes.FixHeaderRegistration"), a CommandLine Interface with command: antsRegistration --collapse-output-transforms 1 --dimensionality 3 --float 1 --initial-moving-transform [ /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/enhance_and_skullstrip_bold_wf/init_aff/initialization.mat, 0 ] --initialize-transforms-per-stage 0 --interpolation Linear --output transform --transform Affine[ 0.1 ] --metric Mattes[ /home/sahad3/.cache/templateflow/tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_res-02_desc-fMRIPrep_boldref.nii.gz, /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/merge/template.nii.gz, 1, 64, Random, 0.2 ] --convergence [ 200, 1e-09, 10 ] --smoothing-sigmas 2.0mm --shrink-factors 2 --use-estimate-learning-rate-once 1 --use-histogram-matching 1 --winsorize-image-intensities [ 0.05, 0.98 ] --write-composite-transform 0 190731-15:28:17,513 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_opposite_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_pass". 190731-15:28:17,548 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.fixhdr_unifize". 190731-15:28:17,627 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_mid_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.combine_masks". 190731-15:28:18,746 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_matching_wf.enhance_and_skullstrip_bold_wf.norm". 190731-15:28:19,507 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.skullstrip_second_pass" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-01..func..sub-23649_ses-01_task-rest_echo-2_bold.nii.gz/skullstrip_second_pass". 190731-15:28:19,509 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_mid_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.apply_mask" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_mid_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/apply_mask". 190731-15:28:19,510 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_opposite_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_dilate" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_dilate". 190731-15:28:19,513 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_matching_wf.enhance_and_skullstrip_bold_wf.map_brainmask" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/enhance_and_skullstrip_bold_wf/map_brainmask". 190731-15:28:19,538 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.bold_hmc_wf.fsl2itk" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/bold_hmc_wf/fsl2itk". 190731-15:28:19,639 nipype.workflow INFO: [Node] Running "apply_mask" ("nipype.interfaces.fsl.maths.ApplyMask"), a CommandLine Interface with command: fslmaths /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_mid_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/fixhdr_unifize/uni_xform.nii.gz -mas /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_mid_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/combine_masks/ref_bold_corrected_brain_mask_maths.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_mid_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/apply_mask/uni_xform_masked.nii.gz 190731-15:28:19,639 nipype.workflow INFO: [Node] Running "skullstrip_second_pass" ("nipype.interfaces.afni.preprocess.Automask"), a CommandLine Interface with command: 3dAutomask -apply_prefix uni_xform_masked.nii.gz -dilate 1 -prefix uni_xform_mask.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-01..func..sub-23649_ses-01_task-rest_echo-2_bold.nii.gz/skullstrip_second_pass/uni_xform.nii.gz 190731-15:28:19,639 nipype.workflow INFO: [Node] Running "skullstrip_first_dilate" ("nipype.interfaces.fsl.maths.DilateImage"), a CommandLine Interface with command: fslmaths -dt char /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_pass/template_corrected_brain_mask.nii.gz -kernel sphere 6.0000 -dilF /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_dilate/template_corrected_brain_mask_dil.nii.gz 190731-15:28:19,639 nipype.workflow INFO: [Node] Running "map_brainmask" ("niworkflows.interfaces.fixes.FixHeaderApplyTransforms"), a CommandLine Interface with command: antsApplyTransforms --default-value 0 --float 1 --input /home/sahad3/.cache/templateflow/tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_res-02_desc-brain_mask.nii.gz --interpolation MultiLabel --output tpl-MNI152NLin2009cAsym_res-02_desc-brain_mask_trans.nii.gz --reference-image /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/merge/template.nii.gz --transform [ /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/enhance_and_skullstrip_bold_wf/norm/transform0GenericAffine.mat, 1 ] 190731-15:28:19,643 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.map_brainmask". 190731-15:28:19,645 nipype.workflow INFO: [Node] Running "fsl2itk" ("niworkflows.interfaces.itk.MCFLIRT2ITK") 190731-15:28:19,763 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_mid_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.apply_mask". 190731-15:28:19,837 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.skullstrip_second_pass". 190731-15:28:20,56 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_opposite_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_dilate". 190731-15:28:21,367 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_matching_wf.enhance_and_skullstrip_bold_wf.map_brainmask". 190731-15:28:21,531 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.fixhdr_skullstrip2" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-01..func..sub-23649_ses-01_task-rest_echo-2_bold.nii.gz/fixhdr_skullstrip2". 190731-15:28:21,533 nipype.workflow INFO: [Node] Running "fixhdr_skullstrip2" ("niworkflows.interfaces.utils.CopyXForm") 190731-15:28:21,533 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.pre_mask_dilate" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-01..func..sub-23649_ses-01_task-rest_echo-1_bold.nii.gz/pre_mask_dilate". 190731-15:28:21,536 nipype.workflow INFO: [Node] Running "pre_mask_dilate" ("nipype.interfaces.fsl.maths.DilateImage"), a CommandLine Interface with command: fslmaths -dt char /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-01..func..sub-23649_ses-01_task-rest_echo-1_bold.nii.gz/map_brainmask/tpl-MNI152NLin2009cAsym_res-02_desc-brain_mask_trans.nii.gz -kernel sphere 3.0000 -dilF /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-01..func..sub-23649_ses-01_task-rest_echo-1_bold.nii.gz/pre_mask_dilate/tpl-MNI152NLin2009cAsym_res-02_desc-brain_mask_trans_dil.nii.gz 190731-15:28:21,539 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_mid_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_matching_wf.fmap2ref_reg" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_mid_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/fmap2ref_reg". 190731-15:28:21,546 nipype.workflow INFO: [Node] Running "fmap2ref_reg" ("nipype.interfaces.ants.registration.Registration"), a CommandLine Interface with command: antsRegistration --collapse-output-transforms 1 --dimensionality 3 --float 1 --initialize-transforms-per-stage 0 --interpolation LanczosWindowedSinc --output [ transform, transform_Warped.nii.gz ] --transform Translation[ 0.05 ] --metric Mattes[ /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_mid_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/apply_mask/uni_xform_masked.nii.gz, /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_mid_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/enhance_and_skullstrip_bold_wf/apply_mask/uni_xform_masked.nii.gz, 1, 64, Random, 0.5 ] --convergence [ 500, 1e-07, 200 ] --smoothing-sigmas 8.0mm --shrink-factors 2 --use-estimate-learning-rate-once 1 --use-histogram-matching 1 --transform Rigid[ 0.01 ] --metric Mattes[ /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_mid_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/apply_mask/uni_xform_masked.nii.gz, /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_mid_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/enhance_and_skullstrip_bold_wf/apply_mask/uni_xform_masked.nii.gz, 1, 64, Random, 0.5 ] --convergence [ 200, 1e-08, 100 ] --smoothing-sigmas 2.0mm --shrink-factors 1 --use-estimate-learning-rate-once 1 --use-histogram-matching 1 --winsorize-image-intensities [ 0.005, 0.998 ] --write-composite-transform 1 190731-15:28:21,551 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.fixhdr_skullstrip2". 190731-15:28:21,722 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.pre_mask_dilate". 190731-15:28:23,539 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.combine_masks" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-01..func..sub-23649_ses-01_task-rest_echo-2_bold.nii.gz/combine_masks". 190731-15:28:23,542 nipype.workflow INFO: [Node] Running "combine_masks" ("nipype.interfaces.fsl.maths.BinaryMaths"), a CommandLine Interface with command: fslmaths /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-01..func..sub-23649_ses-01_task-rest_echo-2_bold.nii.gz/skullstrip_first_pass/ref_bold_corrected_brain_mask.nii.gz -mul /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-01..func..sub-23649_ses-01_task-rest_echo-2_bold.nii.gz/fixhdr_skullstrip2/uni_xform_mask_xform.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-01..func..sub-23649_ses-01_task-rest_echo-2_bold.nii.gz/combine_masks/ref_bold_corrected_brain_mask_maths.nii.gz 190731-15:28:23,553 nipype.interface WARNING: q-forms of reference and mask are substantially different 190731-15:28:23,723 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.combine_masks". 190731-15:28:24,118 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_opposite_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_mask" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_mask". 190731-15:28:24,120 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_matching_wf.enhance_and_skullstrip_bold_wf.pre_mask_dilate" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/enhance_and_skullstrip_bold_wf/pre_mask_dilate". 190731-15:28:24,120 nipype.workflow INFO: [Node] Running "skullstrip_first_mask" ("nipype.interfaces.fsl.maths.ApplyMask"), a CommandLine Interface with command: fslmaths /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_pass/template_corrected_brain.nii.gz -mas /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_dilate/template_corrected_brain_mask_dil.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_mask/template_corrected_brain_masked.nii.gz 190731-15:28:24,122 nipype.workflow INFO: [Node] Running "pre_mask_dilate" ("nipype.interfaces.fsl.maths.DilateImage"), a CommandLine Interface with command: fslmaths -dt char /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/enhance_and_skullstrip_bold_wf/map_brainmask/tpl-MNI152NLin2009cAsym_res-02_desc-brain_mask_trans.nii.gz -kernel sphere 3.0000 -dilF /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/enhance_and_skullstrip_bold_wf/pre_mask_dilate/tpl-MNI152NLin2009cAsym_res-02_desc-brain_mask_trans_dil.nii.gz 190731-15:28:24,269 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_opposite_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_mask". 190731-15:28:24,304 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_matching_wf.enhance_and_skullstrip_bold_wf.pre_mask_dilate". 190731-15:28:26,61 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.apply_mask" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-01..func..sub-23649_ses-01_task-rest_echo-2_bold.nii.gz/apply_mask". 190731-15:28:26,64 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.n4_correct" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-01..func..sub-23649_ses-01_task-rest_echo-1_bold.nii.gz/n4_correct". 190731-15:28:26,65 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_opposite_wf.enhance_and_skullstrip_bold_wf.unifize" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/enhance_and_skullstrip_bold_wf/unifize". 190731-15:28:26,68 nipype.workflow INFO: [Node] Running "apply_mask" ("nipype.interfaces.fsl.maths.ApplyMask"), a CommandLine Interface with command: fslmaths /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-01..func..sub-23649_ses-01_task-rest_echo-2_bold.nii.gz/fixhdr_unifize/uni_xform.nii.gz -mas /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-01..func..sub-23649_ses-01_task-rest_echo-2_bold.nii.gz/combine_masks/ref_bold_corrected_brain_mask_maths.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-01..func..sub-23649_ses-01_task-rest_echo-2_bold.nii.gz/apply_mask/uni_xform_masked.nii.gz 190731-15:28:26,68 nipype.workflow INFO: [Node] Running "n4_correct" ("nipype.interfaces.ants.segmentation.N4BiasFieldCorrection"), a CommandLine Interface with command: N4BiasFieldCorrection --bspline-fitting [ 200 ] -d 3 --input-image /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/bold_bold_trans_wf/bold_reference_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-01..func..sub-23649_ses-01_task-rest_echo-1_bold.nii.gz/gen_ref/ref_bold.nii.gz --mask-image /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-01..func..sub-23649_ses-01_task-rest_echo-1_bold.nii.gz/check_hdr/tpl-MNI152NLin2009cAsym_res-02_desc-brain_mask_trans_dil_hdr.nii.gz --output ref_bold_corrected.nii.gz 190731-15:28:26,69 nipype.workflow INFO: [Node] Running "unifize" ("nipype.interfaces.afni.utils.Unifize"), a CommandLine Interface with command: 3dUnifize -clfrac 0.2 -rbt 18.3 65.0 90.0 -prefix uni.nii.gz -T2 -input /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/enhance_and_skullstrip_bold_wf/unifize/template_corrected_brain_masked.nii.gz 190731-15:28:26,257 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.apply_mask". 190731-15:28:27,199 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_opposite_wf.enhance_and_skullstrip_bold_wf.unifize". 190731-15:28:27,943 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.bold_t2smap_wf.t2smap_node". 190731-15:28:28,263 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.n4_correct". 190731-15:28:29,494 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.bold_t1_trans_wf.bold_split" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/bold_t1_trans_wf/bold_split". 190731-15:28:29,496 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.split_opt_comb" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/split_opt_comb". 190731-15:28:29,496 nipype.workflow INFO: [Node] Running "bold_split" ("nipype.interfaces.fsl.utils.Split"), a CommandLine Interface with command: fslsplit /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/bold_t2smap_wf/t2smap_node/TED.vol0000_xform-00000_merged_masked/ts_OC.nii -t 190731-15:28:29,498 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.bold_t2smap_wf.skullstrip_t2smap_wf.skullstrip_first_pass" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/bold_t2smap_wf/skullstrip_t2smap_wf/skullstrip_first_pass". 190731-15:28:29,499 nipype.workflow INFO: [Node] Running "split_opt_comb" ("nipype.interfaces.fsl.utils.Split"), a CommandLine Interface with command: fslsplit /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/bold_t2smap_wf/t2smap_node/TED.vol0000_xform-00000_merged_masked/ts_OC.nii -t 190731-15:28:29,502 nipype.workflow INFO: [Node] Running "skullstrip_first_pass" ("nipype.interfaces.fsl.preprocess.BET"), a CommandLine Interface with command: bet /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/bold_t2smap_wf/t2smap_node/TED.vol0000_xform-00000_merged_masked/t2sv.nii /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/bold_t2smap_wf/skullstrip_t2smap_wf/skullstrip_first_pass/t2sv_brain.nii.gz -f 0.20 -m 190731-15:28:30,117 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_pass" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-01..func..sub-23649_ses-01_task-rest_echo-1_bold.nii.gz/skullstrip_first_pass". 190731-15:28:30,120 nipype.workflow INFO: [Node] Running "skullstrip_first_pass" ("nipype.interfaces.fsl.preprocess.BET"), a CommandLine Interface with command: bet /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-01..func..sub-23649_ses-01_task-rest_echo-1_bold.nii.gz/n4_correct/ref_bold_corrected.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-01..func..sub-23649_ses-01_task-rest_echo-1_bold.nii.gz/skullstrip_first_pass/ref_bold_corrected_brain.nii.gz -f 0.20 -m 190731-15:28:31,465 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.bold_t2smap_wf.skullstrip_t2smap_wf.skullstrip_first_pass". 190731-15:28:32,131 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_pass". 190731-15:28:33,485 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.bold_t2smap_wf.skullstrip_t2smap_wf.skullstrip_second_pass" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/bold_t2smap_wf/skullstrip_t2smap_wf/skullstrip_second_pass". 190731-15:28:33,487 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_dilate" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-01..func..sub-23649_ses-01_task-rest_echo-1_bold.nii.gz/skullstrip_first_dilate". 190731-15:28:33,489 nipype.workflow INFO: [Node] Running "skullstrip_second_pass" ("nipype.interfaces.afni.preprocess.Automask"), a CommandLine Interface with command: 3dAutomask -apply_prefix t2sv_brain_masked.nii.gz -dilate 1 -prefix t2sv_brain_mask.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/bold_t2smap_wf/skullstrip_t2smap_wf/skullstrip_second_pass/t2sv_brain.nii.gz 190731-15:28:33,490 nipype.workflow INFO: [Node] Running "skullstrip_first_dilate" ("nipype.interfaces.fsl.maths.DilateImage"), a CommandLine Interface with command: fslmaths -dt char /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-01..func..sub-23649_ses-01_task-rest_echo-1_bold.nii.gz/skullstrip_first_pass/ref_bold_corrected_brain_mask.nii.gz -kernel sphere 6.0000 -dilF /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-01..func..sub-23649_ses-01_task-rest_echo-1_bold.nii.gz/skullstrip_first_dilate/ref_bold_corrected_brain_mask_dil.nii.gz 190731-15:28:33,689 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.bold_t2smap_wf.skullstrip_t2smap_wf.skullstrip_second_pass". 190731-15:28:33,793 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.split_opt_comb". 190731-15:28:33,833 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_dilate". 190731-15:28:34,218 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.bold_t1_trans_wf.bold_split". 190731-15:28:35,511 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.bold_t2smap_wf.skullstrip_t2smap_wf.combine_masks" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/bold_t2smap_wf/skullstrip_t2smap_wf/combine_masks". 190731-15:28:35,513 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_mask" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-01..func..sub-23649_ses-01_task-rest_echo-1_bold.nii.gz/skullstrip_first_mask". 190731-15:28:35,513 nipype.workflow INFO: [Node] Running "combine_masks" ("nipype.interfaces.fsl.maths.BinaryMaths"), a CommandLine Interface with command: fslmaths /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/bold_t2smap_wf/skullstrip_t2smap_wf/skullstrip_first_pass/t2sv_brain_mask.nii.gz -mul /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/bold_t2smap_wf/skullstrip_t2smap_wf/skullstrip_second_pass/t2sv_brain_mask.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/bold_t2smap_wf/skullstrip_t2smap_wf/combine_masks/t2sv_brain_mask_maths.nii.gz 190731-15:28:35,515 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_opposite_wf.enhance_and_skullstrip_bold_wf.fixhdr_unifize" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/enhance_and_skullstrip_bold_wf/fixhdr_unifize". 190731-15:28:35,517 nipype.workflow INFO: [Node] Running "skullstrip_first_mask" ("nipype.interfaces.fsl.maths.ApplyMask"), a CommandLine Interface with command: fslmaths /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-01..func..sub-23649_ses-01_task-rest_echo-1_bold.nii.gz/skullstrip_first_pass/ref_bold_corrected_brain.nii.gz -mas /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-01..func..sub-23649_ses-01_task-rest_echo-1_bold.nii.gz/skullstrip_first_dilate/ref_bold_corrected_brain_mask_dil.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-01..func..sub-23649_ses-01_task-rest_echo-1_bold.nii.gz/skullstrip_first_mask/ref_bold_corrected_brain_masked.nii.gz 190731-15:28:35,517 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_matching_wf.enhance_and_skullstrip_bold_wf.n4_correct" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/enhance_and_skullstrip_bold_wf/n4_correct". 190731-15:28:35,517 nipype.workflow INFO: [Node] Running "fixhdr_unifize" ("niworkflows.interfaces.utils.CopyXForm") 190731-15:28:35,519 nipype.workflow INFO: [Node] Running "n4_correct" ("nipype.interfaces.ants.segmentation.N4BiasFieldCorrection"), a CommandLine Interface with command: N4BiasFieldCorrection --bspline-fitting [ 200 ] -d 3 --input-image /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/merge/template.nii.gz --mask-image /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/enhance_and_skullstrip_bold_wf/check_hdr/tpl-MNI152NLin2009cAsym_res-02_desc-brain_mask_trans_dil_hdr.nii.gz --output template_corrected.nii.gz 190731-15:28:35,567 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_opposite_wf.enhance_and_skullstrip_bold_wf.fixhdr_unifize". 190731-15:28:35,654 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_mask". 190731-15:28:35,663 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.bold_t2smap_wf.skullstrip_t2smap_wf.combine_masks". 190731-15:28:37,532 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.bold_confounds_wf.dvars" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/bold_confounds_wf/dvars". 190731-15:28:37,535 nipype.workflow INFO: [Node] Running "dvars" ("nipype.algorithms.confounds.ComputeDVARS") 190731-15:28:37,535 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.bold_t2smap_wf.skullstrip_t2smap_wf.mask_reportlet" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/bold_t2smap_wf/skullstrip_t2smap_wf/mask_reportlet". 190731-15:28:37,538 nipype.workflow INFO: [Node] Running "mask_reportlet" ("niworkflows.interfaces.masks.SimpleShowMaskRPT") 190731-15:28:37,539 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.bold_t2smap_wf.skullstrip_t2smap_wf.apply_mask" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/bold_t2smap_wf/skullstrip_t2smap_wf/apply_mask". 190731-15:28:37,542 nipype.workflow INFO: [Node] Running "apply_mask" ("nipype.interfaces.fsl.maths.ApplyMask"), a CommandLine Interface with command: fslmaths /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/bold_t2smap_wf/t2smap_node/TED.vol0000_xform-00000_merged_masked/t2sv.nii -mas /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/bold_t2smap_wf/skullstrip_t2smap_wf/combine_masks/t2sv_brain_mask_maths.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/bold_t2smap_wf/skullstrip_t2smap_wf/apply_mask/t2sv_masked.nii.gz 190731-15:28:37,696 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_matching_wf.enhance_and_skullstrip_bold_wf.n4_correct". 190731-15:28:37,727 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.bold_t2smap_wf.skullstrip_t2smap_wf.apply_mask". 190731-15:28:37,995 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_mid_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_matching_wf.fmap2ref_reg". 190731-15:28:38,714 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.bold_hmc_wf.fsl2itk". 190731-15:28:39,514 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.unifize" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-01..func..sub-23649_ses-01_task-rest_echo-1_bold.nii.gz/unifize". 190731-15:28:39,516 nipype.workflow INFO: [Node] Running "unifize" ("nipype.interfaces.afni.utils.Unifize"), a CommandLine Interface with command: 3dUnifize -clfrac 0.2 -rbt 18.3 65.0 90.0 -prefix uni.nii.gz -T2 -input /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-01..func..sub-23649_ses-01_task-rest_echo-1_bold.nii.gz/unifize/ref_bold_corrected_brain_masked.nii.gz 190731-15:28:39,519 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_mid_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_opposite_wf.fmap2ref_reg" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_mid_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/fmap2ref_reg". 190731-15:28:39,520 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_opposite_wf.enhance_and_skullstrip_bold_wf.skullstrip_second_pass" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/enhance_and_skullstrip_bold_wf/skullstrip_second_pass". 190731-15:28:39,521 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_matching_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_pass" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_pass". 190731-15:28:39,522 nipype.workflow INFO: [Node] Running "skullstrip_second_pass" ("nipype.interfaces.afni.preprocess.Automask"), a CommandLine Interface with command: 3dAutomask -apply_prefix uni_xform_masked.nii.gz -dilate 1 -prefix uni_xform_mask.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/enhance_and_skullstrip_bold_wf/skullstrip_second_pass/uni_xform.nii.gz 190731-15:28:39,523 nipype.workflow INFO: [Node] Running "fmap2ref_reg" ("nipype.interfaces.ants.registration.Registration"), a CommandLine Interface with command: antsRegistration --collapse-output-transforms 1 --dimensionality 3 --float 1 --initialize-transforms-per-stage 0 --interpolation LanczosWindowedSinc --output [ transform, transform_Warped.nii.gz ] --transform Translation[ 0.05 ] --metric Mattes[ /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_mid_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/apply_mask/uni_xform_masked.nii.gz, /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_mid_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/enhance_and_skullstrip_bold_wf/apply_mask/uni_xform_masked.nii.gz, 1, 64, Random, 0.5 ] --convergence [ 500, 1e-07, 200 ] --smoothing-sigmas 8.0mm --shrink-factors 2 --use-estimate-learning-rate-once 1 --use-histogram-matching 1 --transform Rigid[ 0.01 ] --metric Mattes[ /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_mid_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/apply_mask/uni_xform_masked.nii.gz, /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_mid_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/enhance_and_skullstrip_bold_wf/apply_mask/uni_xform_masked.nii.gz, 1, 64, Random, 0.5 ] --convergence [ 200, 1e-08, 100 ] --smoothing-sigmas 2.0mm --shrink-factors 1 --use-estimate-learning-rate-once 1 --use-histogram-matching 1 --winsorize-image-intensities [ 0.005, 0.998 ] --write-composite-transform 1 190731-15:28:39,524 nipype.workflow INFO: [Node] Running "skullstrip_first_pass" ("nipype.interfaces.fsl.preprocess.BET"), a CommandLine Interface with command: bet /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/enhance_and_skullstrip_bold_wf/n4_correct/template_corrected.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_pass/template_corrected_brain.nii.gz -f 0.20 -m 190731-15:28:39,677 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_opposite_wf.enhance_and_skullstrip_bold_wf.skullstrip_second_pass". 190731-15:28:40,641 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.unifize". 190731-15:28:41,659 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.fixhdr_unifize" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-01..func..sub-23649_ses-01_task-rest_echo-1_bold.nii.gz/fixhdr_unifize". 190731-15:28:41,660 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_opposite_wf.enhance_and_skullstrip_bold_wf.fixhdr_skullstrip2" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/enhance_and_skullstrip_bold_wf/fixhdr_skullstrip2". 190731-15:28:41,661 nipype.workflow INFO: [Node] Running "fixhdr_unifize" ("niworkflows.interfaces.utils.CopyXForm") 190731-15:28:41,662 nipype.workflow INFO: [Node] Running "fixhdr_skullstrip2" ("niworkflows.interfaces.utils.CopyXForm") 190731-15:28:41,686 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_opposite_wf.enhance_and_skullstrip_bold_wf.fixhdr_skullstrip2". 190731-15:28:41,718 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.fixhdr_unifize". 190731-15:28:41,722 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_matching_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_pass". 190731-15:28:42,13 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.bold_t2smap_wf.skullstrip_t2smap_wf.mask_reportlet". 190731-15:28:43,507 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.skullstrip_second_pass" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-01..func..sub-23649_ses-01_task-rest_echo-1_bold.nii.gz/skullstrip_second_pass". 190731-15:28:43,510 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_opposite_wf.enhance_and_skullstrip_bold_wf.combine_masks" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/enhance_and_skullstrip_bold_wf/combine_masks". 190731-15:28:43,511 nipype.workflow INFO: [Node] Running "skullstrip_second_pass" ("nipype.interfaces.afni.preprocess.Automask"), a CommandLine Interface with command: 3dAutomask -apply_prefix uni_xform_masked.nii.gz -dilate 1 -prefix uni_xform_mask.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-01..func..sub-23649_ses-01_task-rest_echo-1_bold.nii.gz/skullstrip_second_pass/uni_xform.nii.gz 190731-15:28:43,512 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_matching_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_dilate" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_dilate". 190731-15:28:43,514 nipype.workflow INFO: [Node] Running "combine_masks" ("nipype.interfaces.fsl.maths.BinaryMaths"), a CommandLine Interface with command: fslmaths /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_pass/template_corrected_brain_mask.nii.gz -mul /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/enhance_and_skullstrip_bold_wf/fixhdr_skullstrip2/uni_xform_mask_xform.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/enhance_and_skullstrip_bold_wf/combine_masks/template_corrected_brain_mask_maths.nii.gz 190731-15:28:43,516 nipype.workflow INFO: [Node] Running "skullstrip_first_dilate" ("nipype.interfaces.fsl.maths.DilateImage"), a CommandLine Interface with command: fslmaths -dt char /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_pass/template_corrected_brain_mask.nii.gz -kernel sphere 6.0000 -dilF /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_dilate/template_corrected_brain_mask_dil.nii.gz 190731-15:28:43,527 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.init_aff" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/init_aff". 190731-15:28:43,530 nipype.workflow INFO: [Node] Running "init_aff" ("niworkflows.interfaces.ants.AI"), a CommandLine Interface with command: antsAI -c [10,0.000001,10] -d 3 -x /home/sahad3/.cache/templateflow/tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_res-02_desc-brain_mask.nii.gz -m Mattes[/home/sahad3/.cache/templateflow/tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_res-02_desc-fMRIPrep_boldref.nii.gz,/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/bold_reference_wf/gen_ref/ref_bold.nii.gz,32,Regular,0.200000] -o initialization.mat -p 0 -s [20.000000,0.120000] -t Affine[0.100000] -v 1 190731-15:28:43,690 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_opposite_wf.enhance_and_skullstrip_bold_wf.combine_masks". 190731-15:28:43,737 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.skullstrip_second_pass". 190731-15:28:43,874 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_matching_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_dilate". 190731-15:28:45,481 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.bold_confounds_wf.dvars". 190731-15:28:45,496 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.fixhdr_skullstrip2" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-01..func..sub-23649_ses-01_task-rest_echo-1_bold.nii.gz/fixhdr_skullstrip2". 190731-15:28:45,498 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_opposite_wf.enhance_and_skullstrip_bold_wf.apply_mask" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/enhance_and_skullstrip_bold_wf/apply_mask". 190731-15:28:45,499 nipype.workflow INFO: [Node] Running "fixhdr_skullstrip2" ("niworkflows.interfaces.utils.CopyXForm") 190731-15:28:45,500 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_matching_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_mask" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_mask". 190731-15:28:45,500 nipype.workflow INFO: [Node] Running "apply_mask" ("nipype.interfaces.fsl.maths.ApplyMask"), a CommandLine Interface with command: fslmaths /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/enhance_and_skullstrip_bold_wf/fixhdr_unifize/uni_xform.nii.gz -mas /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/enhance_and_skullstrip_bold_wf/combine_masks/template_corrected_brain_mask_maths.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/enhance_and_skullstrip_bold_wf/apply_mask/uni_xform_masked.nii.gz 190731-15:28:45,502 nipype.workflow INFO: [Node] Running "skullstrip_first_mask" ("nipype.interfaces.fsl.maths.ApplyMask"), a CommandLine Interface with command: fslmaths /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_pass/template_corrected_brain.nii.gz -mas /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_dilate/template_corrected_brain_mask_dil.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_mask/template_corrected_brain_masked.nii.gz 190731-15:28:45,527 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.fixhdr_skullstrip2". 190731-15:28:45,618 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_opposite_wf.enhance_and_skullstrip_bold_wf.apply_mask". 190731-15:28:45,622 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_matching_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_mask". 190731-15:28:48,506 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.combine_masks" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-01..func..sub-23649_ses-01_task-rest_echo-1_bold.nii.gz/combine_masks". 190731-15:28:48,507 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_matching_wf.enhance_and_skullstrip_bold_wf.unifize" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/enhance_and_skullstrip_bold_wf/unifize". 190731-15:28:48,508 nipype.workflow INFO: [Node] Running "combine_masks" ("nipype.interfaces.fsl.maths.BinaryMaths"), a CommandLine Interface with command: fslmaths /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-01..func..sub-23649_ses-01_task-rest_echo-1_bold.nii.gz/skullstrip_first_pass/ref_bold_corrected_brain_mask.nii.gz -mul /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-01..func..sub-23649_ses-01_task-rest_echo-1_bold.nii.gz/fixhdr_skullstrip2/uni_xform_mask_xform.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-01..func..sub-23649_ses-01_task-rest_echo-1_bold.nii.gz/combine_masks/ref_bold_corrected_brain_mask_maths.nii.gz 190731-15:28:48,511 nipype.workflow INFO: [Node] Running "unifize" ("nipype.interfaces.afni.utils.Unifize"), a CommandLine Interface with command: 3dUnifize -clfrac 0.2 -rbt 18.3 65.0 90.0 -prefix uni.nii.gz -T2 -input /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/enhance_and_skullstrip_bold_wf/unifize/template_corrected_brain_masked.nii.gz 190731-15:28:48,687 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.combine_masks". 190731-15:28:49,836 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_matching_wf.enhance_and_skullstrip_bold_wf.unifize". 190731-15:28:50,289 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.apply_mask" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-01..func..sub-23649_ses-01_task-rest_echo-1_bold.nii.gz/apply_mask". 190731-15:28:50,292 nipype.workflow INFO: [Node] Running "apply_mask" ("nipype.interfaces.fsl.maths.ApplyMask"), a CommandLine Interface with command: fslmaths /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-01..func..sub-23649_ses-01_task-rest_echo-1_bold.nii.gz/fixhdr_unifize/uni_xform.nii.gz -mas /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-01..func..sub-23649_ses-01_task-rest_echo-1_bold.nii.gz/combine_masks/ref_bold_corrected_brain_mask_maths.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_01_task_rest_echo_1_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-01..func..sub-23649_ses-01_task-rest_echo-1_bold.nii.gz/apply_mask/uni_xform_masked.nii.gz 190731-15:28:50,408 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_01_task_rest_echo_1_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.apply_mask". 190731-15:28:50,781 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.init_aff". 190731-15:28:51,480 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_matching_wf.enhance_and_skullstrip_bold_wf.fixhdr_unifize" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/enhance_and_skullstrip_bold_wf/fixhdr_unifize". 190731-15:28:51,481 nipype.workflow INFO: [Node] Running "fixhdr_unifize" ("niworkflows.interfaces.utils.CopyXForm") 190731-15:28:51,484 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.norm" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/norm". 190731-15:28:51,489 nipype.workflow INFO: [Node] Running "norm" ("niworkflows.interfaces.fixes.FixHeaderRegistration"), a CommandLine Interface with command: antsRegistration --collapse-output-transforms 1 --dimensionality 3 --float 1 --initial-moving-transform [ /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/init_aff/initialization.mat, 0 ] --initialize-transforms-per-stage 0 --interpolation Linear --output transform --transform Affine[ 0.1 ] --metric Mattes[ /home/sahad3/.cache/templateflow/tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_res-02_desc-fMRIPrep_boldref.nii.gz, /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/bold_reference_wf/gen_ref/ref_bold.nii.gz, 1, 64, Random, 0.2 ] --convergence [ 200, 1e-09, 10 ] --smoothing-sigmas 2.0mm --shrink-factors 2 --use-estimate-learning-rate-once 1 --use-histogram-matching 1 --winsorize-image-intensities [ 0.05, 0.98 ] --write-composite-transform 0 190731-15:28:51,521 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_matching_wf.enhance_and_skullstrip_bold_wf.fixhdr_unifize". 190731-15:28:52,876 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.norm". 190731-15:28:53,488 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_matching_wf.enhance_and_skullstrip_bold_wf.skullstrip_second_pass" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/enhance_and_skullstrip_bold_wf/skullstrip_second_pass". 190731-15:28:53,490 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.map_brainmask" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/map_brainmask". 190731-15:28:53,492 nipype.workflow INFO: [Node] Running "skullstrip_second_pass" ("nipype.interfaces.afni.preprocess.Automask"), a CommandLine Interface with command: 3dAutomask -apply_prefix uni_xform_masked.nii.gz -dilate 1 -prefix uni_xform_mask.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/enhance_and_skullstrip_bold_wf/skullstrip_second_pass/uni_xform.nii.gz 190731-15:28:53,493 nipype.workflow INFO: [Node] Running "map_brainmask" ("niworkflows.interfaces.fixes.FixHeaderApplyTransforms"), a CommandLine Interface with command: antsApplyTransforms --default-value 0 --float 1 --input /home/sahad3/.cache/templateflow/tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_res-02_desc-brain_mask.nii.gz --interpolation MultiLabel --output tpl-MNI152NLin2009cAsym_res-02_desc-brain_mask_trans.nii.gz --reference-image /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/bold_reference_wf/gen_ref/ref_bold.nii.gz --transform [ /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/norm/transform0GenericAffine.mat, 1 ] 190731-15:28:53,493 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_mid_run_1_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_opposite_wf.enhance_and_skullstrip_bold_wf.init_aff" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/enhance_and_skullstrip_bold_wf/init_aff". 190731-15:28:53,496 nipype.workflow INFO: [Node] Running "init_aff" ("niworkflows.interfaces.ants.AI"), a CommandLine Interface with command: antsAI -c [10,0.000001,10] -d 3 -x /home/sahad3/.cache/templateflow/tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_res-02_desc-brain_mask.nii.gz -m Mattes[/home/sahad3/.cache/templateflow/tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_res-02_desc-fMRIPrep_boldref.nii.gz,/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/merge/template.nii.gz,32,Regular,0.200000] -o initialization.mat -p 0 -s [20.000000,0.120000] -t Affine[0.100000] -v 1 190731-15:28:53,661 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_matching_wf.enhance_and_skullstrip_bold_wf.skullstrip_second_pass". 190731-15:28:55,291 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.map_brainmask". 190731-15:28:55,492 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_matching_wf.enhance_and_skullstrip_bold_wf.fixhdr_skullstrip2" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/enhance_and_skullstrip_bold_wf/fixhdr_skullstrip2". 190731-15:28:55,494 nipype.workflow INFO: [Node] Running "fixhdr_skullstrip2" ("niworkflows.interfaces.utils.CopyXForm") 190731-15:28:55,517 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_matching_wf.enhance_and_skullstrip_bold_wf.fixhdr_skullstrip2". 190731-15:28:56,431 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_mid_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_opposite_wf.fmap2ref_reg". 190731-15:28:57,511 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_mid_wf.sdc_wf.pepolar_unwarp_wf.qwarp" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_mid_wf/sdc_wf/pepolar_unwarp_wf/qwarp". 190731-15:28:57,513 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_matching_wf.enhance_and_skullstrip_bold_wf.combine_masks" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/enhance_and_skullstrip_bold_wf/combine_masks". 190731-15:28:57,515 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.pre_mask_dilate" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/pre_mask_dilate". 190731-15:28:57,515 nipype.workflow INFO: [Node] Running "combine_masks" ("nipype.interfaces.fsl.maths.BinaryMaths"), a CommandLine Interface with command: fslmaths /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_pass/template_corrected_brain_mask.nii.gz -mul /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/enhance_and_skullstrip_bold_wf/fixhdr_skullstrip2/uni_xform_mask_xform.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/enhance_and_skullstrip_bold_wf/combine_masks/template_corrected_brain_mask_maths.nii.gz 190731-15:28:57,516 nipype.workflow INFO: [Node] Running "qwarp" ("nipype.interfaces.afni.preprocess.QwarpPlusMinus"), a CommandLine Interface with command: 3dQwarp -prefix Qwarp.nii.gz -plusminus -noXdis -noZdis -base /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_mid_wf/sdc_wf/pepolar_unwarp_wf/qwarp/transform_Warped.nii.gz -blur -1.0 -1.0 -source /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_mid_wf/sdc_wf/pepolar_unwarp_wf/qwarp/transform_Warped_c0000.nii.gz -minpatch 9 -nopadWARP -noweight -pblur 0.05 0.05 190731-15:28:57,517 nipype.workflow INFO: [Node] Running "pre_mask_dilate" ("nipype.interfaces.fsl.maths.DilateImage"), a CommandLine Interface with command: fslmaths -dt char /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/map_brainmask/tpl-MNI152NLin2009cAsym_res-02_desc-brain_mask_trans.nii.gz -kernel sphere 3.0000 -dilF /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/pre_mask_dilate/tpl-MNI152NLin2009cAsym_res-02_desc-brain_mask_trans_dil.nii.gz 190731-15:28:57,642 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_matching_wf.enhance_and_skullstrip_bold_wf.combine_masks". 190731-15:28:57,699 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.pre_mask_dilate". 190731-15:28:59,287 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_mid_run_1_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_opposite_wf.enhance_and_skullstrip_bold_wf.init_aff". 190731-15:28:59,522 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_matching_wf.enhance_and_skullstrip_bold_wf.apply_mask" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/enhance_and_skullstrip_bold_wf/apply_mask". 190731-15:28:59,526 nipype.workflow INFO: [Node] Running "apply_mask" ("nipype.interfaces.fsl.maths.ApplyMask"), a CommandLine Interface with command: fslmaths /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/enhance_and_skullstrip_bold_wf/fixhdr_unifize/uni_xform.nii.gz -mas /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/enhance_and_skullstrip_bold_wf/combine_masks/template_corrected_brain_mask_maths.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/enhance_and_skullstrip_bold_wf/apply_mask/uni_xform_masked.nii.gz 190731-15:28:59,534 nipype.interface WARNING: q-forms of reference and mask are substantially different 190731-15:28:59,671 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_matching_wf.enhance_and_skullstrip_bold_wf.apply_mask". 190731-15:29:01,487 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.n4_correct" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/n4_correct". 190731-15:29:01,490 nipype.workflow INFO: [Node] Running "n4_correct" ("nipype.interfaces.ants.segmentation.N4BiasFieldCorrection"), a CommandLine Interface with command: N4BiasFieldCorrection --bspline-fitting [ 200 ] -d 3 --input-image /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/bold_reference_wf/gen_ref/ref_bold.nii.gz --mask-image /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/check_hdr/tpl-MNI152NLin2009cAsym_res-02_desc-brain_mask_trans_dil_hdr.nii.gz --output ref_bold_corrected.nii.gz 190731-15:29:01,491 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_mid_run_1_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_opposite_wf.enhance_and_skullstrip_bold_wf.norm" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/enhance_and_skullstrip_bold_wf/norm". 190731-15:29:01,495 nipype.workflow INFO: [Node] Running "norm" ("niworkflows.interfaces.fixes.FixHeaderRegistration"), a CommandLine Interface with command: antsRegistration --collapse-output-transforms 1 --dimensionality 3 --float 1 --initial-moving-transform [ /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/enhance_and_skullstrip_bold_wf/init_aff/initialization.mat, 0 ] --initialize-transforms-per-stage 0 --interpolation Linear --output transform --transform Affine[ 0.1 ] --metric Mattes[ /home/sahad3/.cache/templateflow/tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_res-02_desc-fMRIPrep_boldref.nii.gz, /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/merge/template.nii.gz, 1, 64, Random, 0.2 ] --convergence [ 200, 1e-09, 10 ] --smoothing-sigmas 2.0mm --shrink-factors 2 --use-estimate-learning-rate-once 1 --use-histogram-matching 1 --winsorize-image-intensities [ 0.05, 0.98 ] --write-composite-transform 0 190731-15:29:04,387 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.n4_correct". 190731-15:29:05,489 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_pass" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_pass". 190731-15:29:05,491 nipype.workflow INFO: [Node] Running "skullstrip_first_pass" ("nipype.interfaces.fsl.preprocess.BET"), a CommandLine Interface with command: bet /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/n4_correct/ref_bold_corrected.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_pass/ref_bold_corrected_brain.nii.gz -f 0.20 -m 190731-15:29:07,125 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_mid_run_1_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_opposite_wf.enhance_and_skullstrip_bold_wf.norm". 190731-15:29:07,670 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_pass". 190731-15:29:09,490 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_dilate" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_dilate". 190731-15:29:09,493 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_mid_run_1_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_opposite_wf.enhance_and_skullstrip_bold_wf.map_brainmask" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/enhance_and_skullstrip_bold_wf/map_brainmask". 190731-15:29:09,493 nipype.workflow INFO: [Node] Running "skullstrip_first_dilate" ("nipype.interfaces.fsl.maths.DilateImage"), a CommandLine Interface with command: fslmaths -dt char /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_pass/ref_bold_corrected_brain_mask.nii.gz -kernel sphere 6.0000 -dilF /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_dilate/ref_bold_corrected_brain_mask_dil.nii.gz 190731-15:29:09,495 nipype.workflow INFO: [Node] Running "map_brainmask" ("niworkflows.interfaces.fixes.FixHeaderApplyTransforms"), a CommandLine Interface with command: antsApplyTransforms --default-value 0 --float 1 --input /home/sahad3/.cache/templateflow/tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_res-02_desc-brain_mask.nii.gz --interpolation MultiLabel --output tpl-MNI152NLin2009cAsym_res-02_desc-brain_mask_trans.nii.gz --reference-image /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/merge/template.nii.gz --transform [ /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/enhance_and_skullstrip_bold_wf/norm/transform0GenericAffine.mat, 1 ] 190731-15:29:09,495 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_mid_run_1_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_matching_wf.enhance_and_skullstrip_bold_wf.init_aff" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/enhance_and_skullstrip_bold_wf/init_aff". 190731-15:29:09,499 nipype.workflow INFO: [Node] Running "init_aff" ("niworkflows.interfaces.ants.AI"), a CommandLine Interface with command: antsAI -c [10,0.000001,10] -d 3 -x /home/sahad3/.cache/templateflow/tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_res-02_desc-brain_mask.nii.gz -m Mattes[/home/sahad3/.cache/templateflow/tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_res-02_desc-fMRIPrep_boldref.nii.gz,/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/merge/template.nii.gz,32,Regular,0.200000] -o initialization.mat -p 0 -s [20.000000,0.120000] -t Affine[0.100000] -v 1 190731-15:29:09,813 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_dilate". 190731-15:29:11,525 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_mask" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_mask". 190731-15:29:11,527 nipype.workflow INFO: [Node] Running "skullstrip_first_mask" ("nipype.interfaces.fsl.maths.ApplyMask"), a CommandLine Interface with command: fslmaths /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_pass/ref_bold_corrected_brain.nii.gz -mas /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_dilate/ref_bold_corrected_brain_mask_dil.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_mask/ref_bold_corrected_brain_masked.nii.gz 190731-15:29:11,703 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_mask". 190731-15:29:12,38 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_mid_run_1_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_opposite_wf.enhance_and_skullstrip_bold_wf.map_brainmask". 190731-15:29:13,486 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.unifize" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/unifize". 190731-15:29:13,488 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_mid_run_1_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_opposite_wf.enhance_and_skullstrip_bold_wf.pre_mask_dilate" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/enhance_and_skullstrip_bold_wf/pre_mask_dilate". 190731-15:29:13,489 nipype.workflow INFO: [Node] Running "unifize" ("nipype.interfaces.afni.utils.Unifize"), a CommandLine Interface with command: 3dUnifize -clfrac 0.2 -rbt 18.3 65.0 90.0 -prefix uni.nii.gz -T2 -input /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/unifize/ref_bold_corrected_brain_masked.nii.gz 190731-15:29:13,491 nipype.workflow INFO: [Node] Running "pre_mask_dilate" ("nipype.interfaces.fsl.maths.DilateImage"), a CommandLine Interface with command: fslmaths -dt char /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/enhance_and_skullstrip_bold_wf/map_brainmask/tpl-MNI152NLin2009cAsym_res-02_desc-brain_mask_trans.nii.gz -kernel sphere 3.0000 -dilF /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/enhance_and_skullstrip_bold_wf/pre_mask_dilate/tpl-MNI152NLin2009cAsym_res-02_desc-brain_mask_trans_dil.nii.gz 190731-15:29:13,899 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_mid_run_1_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_opposite_wf.enhance_and_skullstrip_bold_wf.pre_mask_dilate". 190731-15:29:14,980 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.unifize". 190731-15:29:15,508 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.fixhdr_unifize" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/fixhdr_unifize". 190731-15:29:15,510 nipype.workflow INFO: [Node] Running "fixhdr_unifize" ("niworkflows.interfaces.utils.CopyXForm") 190731-15:29:15,528 nipype.interface WARNING: q-forms of reference and mask are substantially different 190731-15:29:15,552 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.fixhdr_unifize". 190731-15:29:17,894 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.skullstrip_second_pass" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_second_pass". 190731-15:29:17,896 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_mid_run_1_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_opposite_wf.enhance_and_skullstrip_bold_wf.n4_correct" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/enhance_and_skullstrip_bold_wf/n4_correct". 190731-15:29:17,897 nipype.workflow INFO: [Node] Running "skullstrip_second_pass" ("nipype.interfaces.afni.preprocess.Automask"), a CommandLine Interface with command: 3dAutomask -apply_prefix uni_xform_masked.nii.gz -dilate 1 -prefix uni_xform_mask.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_second_pass/uni_xform.nii.gz 190731-15:29:17,898 nipype.workflow INFO: [Node] Running "n4_correct" ("nipype.interfaces.ants.segmentation.N4BiasFieldCorrection"), a CommandLine Interface with command: N4BiasFieldCorrection --bspline-fitting [ 200 ] -d 3 --input-image /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/merge/template.nii.gz --mask-image /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/enhance_and_skullstrip_bold_wf/check_hdr/tpl-MNI152NLin2009cAsym_res-02_desc-brain_mask_trans_dil_hdr.nii.gz --output template_corrected.nii.gz 190731-15:29:18,166 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.skullstrip_second_pass". 190731-15:29:19,939 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.fixhdr_skullstrip2" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/fixhdr_skullstrip2". 190731-15:29:19,942 nipype.workflow INFO: [Node] Running "fixhdr_skullstrip2" ("niworkflows.interfaces.utils.CopyXForm") 190731-15:29:19,964 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.fixhdr_skullstrip2". 190731-15:29:21,349 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_mid_run_1_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_opposite_wf.enhance_and_skullstrip_bold_wf.n4_correct". 190731-15:29:21,951 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.combine_masks" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/combine_masks". 190731-15:29:21,954 nipype.workflow INFO: [Node] Running "combine_masks" ("nipype.interfaces.fsl.maths.BinaryMaths"), a CommandLine Interface with command: fslmaths /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_pass/ref_bold_corrected_brain_mask.nii.gz -mul /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/fixhdr_skullstrip2/uni_xform_mask_xform.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/combine_masks/ref_bold_corrected_brain_mask_maths.nii.gz 190731-15:29:22,97 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.combine_masks". 190731-15:29:22,619 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_mid_run_1_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_matching_wf.enhance_and_skullstrip_bold_wf.init_aff". 190731-15:29:23,569 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.apply_mask" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/apply_mask". 190731-15:29:23,571 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_mid_run_1_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_opposite_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_pass" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_pass". 190731-15:29:23,572 nipype.workflow INFO: [Node] Running "apply_mask" ("nipype.interfaces.fsl.maths.ApplyMask"), a CommandLine Interface with command: fslmaths /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/fixhdr_unifize/uni_xform.nii.gz -mas /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/combine_masks/ref_bold_corrected_brain_mask_maths.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/apply_mask/uni_xform_masked.nii.gz 190731-15:29:23,575 nipype.workflow INFO: [Node] Running "skullstrip_first_pass" ("nipype.interfaces.fsl.preprocess.BET"), a CommandLine Interface with command: bet /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/enhance_and_skullstrip_bold_wf/n4_correct/template_corrected.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_pass/template_corrected_brain.nii.gz -f 0.20 -m 190731-15:29:23,579 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_mid_run_1_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_matching_wf.enhance_and_skullstrip_bold_wf.norm" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/enhance_and_skullstrip_bold_wf/norm". 190731-15:29:23,586 nipype.workflow INFO: [Node] Running "norm" ("niworkflows.interfaces.fixes.FixHeaderRegistration"), a CommandLine Interface with command: antsRegistration --collapse-output-transforms 1 --dimensionality 3 --float 1 --initial-moving-transform [ /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/enhance_and_skullstrip_bold_wf/init_aff/initialization.mat, 0 ] --initialize-transforms-per-stage 0 --interpolation Linear --output transform --transform Affine[ 0.1 ] --metric Mattes[ /home/sahad3/.cache/templateflow/tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_res-02_desc-fMRIPrep_boldref.nii.gz, /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/merge/template.nii.gz, 1, 64, Random, 0.2 ] --convergence [ 200, 1e-09, 10 ] --smoothing-sigmas 2.0mm --shrink-factors 2 --use-estimate-learning-rate-once 1 --use-histogram-matching 1 --winsorize-image-intensities [ 0.05, 0.98 ] --write-composite-transform 0 190731-15:29:23,718 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.apply_mask". 190731-15:29:26,278 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_mid_run_1_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_opposite_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_pass". 190731-15:29:27,529 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_mid_run_1_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_opposite_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_dilate" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_dilate". 190731-15:29:27,532 nipype.workflow INFO: [Node] Running "skullstrip_first_dilate" ("nipype.interfaces.fsl.maths.DilateImage"), a CommandLine Interface with command: fslmaths -dt char /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_pass/template_corrected_brain_mask.nii.gz -kernel sphere 6.0000 -dilF /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_dilate/template_corrected_brain_mask_dil.nii.gz 190731-15:29:28,147 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_mid_run_1_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_opposite_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_dilate". 190731-15:29:29,609 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_mid_run_1_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_opposite_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_mask" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_mask". 190731-15:29:29,613 nipype.workflow INFO: [Node] Running "skullstrip_first_mask" ("nipype.interfaces.fsl.maths.ApplyMask"), a CommandLine Interface with command: fslmaths /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_pass/template_corrected_brain.nii.gz -mas /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_dilate/template_corrected_brain_mask_dil.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_mask/template_corrected_brain_masked.nii.gz 190731-15:29:29,765 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_mid_run_1_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_opposite_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_mask". 190731-15:29:30,860 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_mid_run_1_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_matching_wf.enhance_and_skullstrip_bold_wf.norm". 190731-15:29:31,652 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_matching_wf.fmap2ref_reg" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/fmap2ref_reg". 190731-15:29:31,659 nipype.workflow INFO: [Node] Running "fmap2ref_reg" ("nipype.interfaces.ants.registration.Registration"), a CommandLine Interface with command: antsRegistration --collapse-output-transforms 1 --dimensionality 3 --float 1 --initialize-transforms-per-stage 0 --interpolation LanczosWindowedSinc --output [ transform, transform_Warped.nii.gz ] --transform Translation[ 0.05 ] --metric Mattes[ /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/apply_mask/uni_xform_masked.nii.gz, /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/enhance_and_skullstrip_bold_wf/apply_mask/uni_xform_masked.nii.gz, 1, 64, Random, 0.5 ] --convergence [ 500, 1e-07, 200 ] --smoothing-sigmas 8.0mm --shrink-factors 2 --use-estimate-learning-rate-once 1 --use-histogram-matching 1 --transform Rigid[ 0.01 ] --metric Mattes[ /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/apply_mask/uni_xform_masked.nii.gz, /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/enhance_and_skullstrip_bold_wf/apply_mask/uni_xform_masked.nii.gz, 1, 64, Random, 0.5 ] --convergence [ 200, 1e-08, 100 ] --smoothing-sigmas 2.0mm --shrink-factors 1 --use-estimate-learning-rate-once 1 --use-histogram-matching 1 --winsorize-image-intensities [ 0.005, 0.998 ] --write-composite-transform 1 190731-15:29:31,664 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_mid_run_1_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_opposite_wf.enhance_and_skullstrip_bold_wf.unifize" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/enhance_and_skullstrip_bold_wf/unifize". 190731-15:29:31,668 nipype.workflow INFO: [Node] Running "unifize" ("nipype.interfaces.afni.utils.Unifize"), a CommandLine Interface with command: 3dUnifize -clfrac 0.2 -rbt 18.3 65.0 90.0 -prefix uni.nii.gz -T2 -input /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/enhance_and_skullstrip_bold_wf/unifize/template_corrected_brain_masked.nii.gz 190731-15:29:31,668 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_mid_run_1_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_matching_wf.enhance_and_skullstrip_bold_wf.map_brainmask" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/enhance_and_skullstrip_bold_wf/map_brainmask". 190731-15:29:31,672 nipype.workflow INFO: [Node] Running "map_brainmask" ("niworkflows.interfaces.fixes.FixHeaderApplyTransforms"), a CommandLine Interface with command: antsApplyTransforms --default-value 0 --float 1 --input /home/sahad3/.cache/templateflow/tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_res-02_desc-brain_mask.nii.gz --interpolation MultiLabel --output tpl-MNI152NLin2009cAsym_res-02_desc-brain_mask_trans.nii.gz --reference-image /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/merge/template.nii.gz --transform [ /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/enhance_and_skullstrip_bold_wf/norm/transform0GenericAffine.mat, 1 ] 190731-15:29:33,517 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_mid_run_1_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_opposite_wf.enhance_and_skullstrip_bold_wf.unifize". 190731-15:29:34,857 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_mid_run_1_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_matching_wf.enhance_and_skullstrip_bold_wf.map_brainmask". 190731-15:29:35,703 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_mid_run_1_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_opposite_wf.enhance_and_skullstrip_bold_wf.fixhdr_unifize" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/enhance_and_skullstrip_bold_wf/fixhdr_unifize". 190731-15:29:35,705 nipype.workflow INFO: [Node] Running "fixhdr_unifize" ("niworkflows.interfaces.utils.CopyXForm") 190731-15:29:35,705 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_mid_run_1_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_matching_wf.enhance_and_skullstrip_bold_wf.pre_mask_dilate" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/enhance_and_skullstrip_bold_wf/pre_mask_dilate". 190731-15:29:35,709 nipype.workflow INFO: [Node] Running "pre_mask_dilate" ("nipype.interfaces.fsl.maths.DilateImage"), a CommandLine Interface with command: fslmaths -dt char /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/enhance_and_skullstrip_bold_wf/map_brainmask/tpl-MNI152NLin2009cAsym_res-02_desc-brain_mask_trans.nii.gz -kernel sphere 3.0000 -dilF /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/enhance_and_skullstrip_bold_wf/pre_mask_dilate/tpl-MNI152NLin2009cAsym_res-02_desc-brain_mask_trans_dil.nii.gz 190731-15:29:35,758 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_mid_run_1_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_opposite_wf.enhance_and_skullstrip_bold_wf.fixhdr_unifize". 190731-15:29:36,17 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_mid_run_1_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_matching_wf.enhance_and_skullstrip_bold_wf.pre_mask_dilate". 190731-15:29:37,633 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_mid_run_1_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_opposite_wf.enhance_and_skullstrip_bold_wf.skullstrip_second_pass" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/enhance_and_skullstrip_bold_wf/skullstrip_second_pass". 190731-15:29:37,637 nipype.workflow INFO: [Node] Running "skullstrip_second_pass" ("nipype.interfaces.afni.preprocess.Automask"), a CommandLine Interface with command: 3dAutomask -apply_prefix uni_xform_masked.nii.gz -dilate 1 -prefix uni_xform_mask.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/enhance_and_skullstrip_bold_wf/skullstrip_second_pass/uni_xform.nii.gz 190731-15:29:37,659 nipype.interface WARNING: q-forms of reference and mask are substantially different 190731-15:29:37,911 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_mid_run_1_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_opposite_wf.enhance_and_skullstrip_bold_wf.skullstrip_second_pass". 190731-15:29:39,575 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_mid_run_1_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_opposite_wf.enhance_and_skullstrip_bold_wf.fixhdr_skullstrip2" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/enhance_and_skullstrip_bold_wf/fixhdr_skullstrip2". 190731-15:29:39,578 nipype.workflow INFO: [Node] Running "fixhdr_skullstrip2" ("niworkflows.interfaces.utils.CopyXForm") 190731-15:29:39,579 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_mid_run_1_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_matching_wf.enhance_and_skullstrip_bold_wf.n4_correct" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/enhance_and_skullstrip_bold_wf/n4_correct". 190731-15:29:39,582 nipype.workflow INFO: [Node] Running "n4_correct" ("nipype.interfaces.ants.segmentation.N4BiasFieldCorrection"), a CommandLine Interface with command: N4BiasFieldCorrection --bspline-fitting [ 200 ] -d 3 --input-image /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/merge/template.nii.gz --mask-image /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/enhance_and_skullstrip_bold_wf/check_hdr/tpl-MNI152NLin2009cAsym_res-02_desc-brain_mask_trans_dil_hdr.nii.gz --output template_corrected.nii.gz 190731-15:29:39,614 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_mid_run_1_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_opposite_wf.enhance_and_skullstrip_bold_wf.fixhdr_skullstrip2". 190731-15:29:41,540 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_mid_run_1_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_opposite_wf.enhance_and_skullstrip_bold_wf.combine_masks" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/enhance_and_skullstrip_bold_wf/combine_masks". 190731-15:29:41,544 nipype.workflow INFO: [Node] Running "combine_masks" ("nipype.interfaces.fsl.maths.BinaryMaths"), a CommandLine Interface with command: fslmaths /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_pass/template_corrected_brain_mask.nii.gz -mul /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/enhance_and_skullstrip_bold_wf/fixhdr_skullstrip2/uni_xform_mask_xform.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/enhance_and_skullstrip_bold_wf/combine_masks/template_corrected_brain_mask_maths.nii.gz 190731-15:29:41,654 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_mid_run_1_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_opposite_wf.enhance_and_skullstrip_bold_wf.combine_masks". 190731-15:29:43,459 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_mid_run_1_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_matching_wf.enhance_and_skullstrip_bold_wf.n4_correct". 190731-15:29:43,530 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_mid_run_1_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_opposite_wf.enhance_and_skullstrip_bold_wf.apply_mask" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/enhance_and_skullstrip_bold_wf/apply_mask". 190731-15:29:43,533 nipype.workflow INFO: [Node] Running "apply_mask" ("nipype.interfaces.fsl.maths.ApplyMask"), a CommandLine Interface with command: fslmaths /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/enhance_and_skullstrip_bold_wf/fixhdr_unifize/uni_xform.nii.gz -mas /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/enhance_and_skullstrip_bold_wf/combine_masks/template_corrected_brain_mask_maths.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/enhance_and_skullstrip_bold_wf/apply_mask/uni_xform_masked.nii.gz 190731-15:29:43,660 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_mid_run_1_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_opposite_wf.enhance_and_skullstrip_bold_wf.apply_mask". 190731-15:29:45,540 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_mid_run_1_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_matching_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_pass" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_pass". 190731-15:29:45,544 nipype.workflow INFO: [Node] Running "skullstrip_first_pass" ("nipype.interfaces.fsl.preprocess.BET"), a CommandLine Interface with command: bet /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/enhance_and_skullstrip_bold_wf/n4_correct/template_corrected.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_pass/template_corrected_brain.nii.gz -f 0.20 -m 190731-15:29:48,696 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_mid_run_1_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_matching_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_pass". 190731-15:29:49,576 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_mid_run_1_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_matching_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_dilate" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_dilate". 190731-15:29:49,579 nipype.workflow INFO: [Node] Running "skullstrip_first_dilate" ("nipype.interfaces.fsl.maths.DilateImage"), a CommandLine Interface with command: fslmaths -dt char /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_pass/template_corrected_brain_mask.nii.gz -kernel sphere 6.0000 -dilF /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_dilate/template_corrected_brain_mask_dil.nii.gz 190731-15:29:50,439 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_mid_run_1_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_matching_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_dilate". 190731-15:29:51,619 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_mid_run_1_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_matching_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_mask" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_mask". 190731-15:29:51,622 nipype.workflow INFO: [Node] Running "skullstrip_first_mask" ("nipype.interfaces.fsl.maths.ApplyMask"), a CommandLine Interface with command: fslmaths /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_pass/template_corrected_brain.nii.gz -mas /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_dilate/template_corrected_brain_mask_dil.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_mask/template_corrected_brain_masked.nii.gz 190731-15:29:51,792 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_mid_run_1_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_matching_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_mask". 190731-15:29:53,536 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_mid_run_1_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_matching_wf.enhance_and_skullstrip_bold_wf.unifize" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/enhance_and_skullstrip_bold_wf/unifize". 190731-15:29:53,538 nipype.workflow INFO: [Node] Running "unifize" ("nipype.interfaces.afni.utils.Unifize"), a CommandLine Interface with command: 3dUnifize -clfrac 0.2 -rbt 18.3 65.0 90.0 -prefix uni.nii.gz -T2 -input /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/enhance_and_skullstrip_bold_wf/unifize/template_corrected_brain_masked.nii.gz 190731-15:29:55,4 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_mid_run_1_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_matching_wf.enhance_and_skullstrip_bold_wf.unifize". 190731-15:29:55,522 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_mid_run_1_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_matching_wf.enhance_and_skullstrip_bold_wf.fixhdr_unifize" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/enhance_and_skullstrip_bold_wf/fixhdr_unifize". 190731-15:29:55,524 nipype.workflow INFO: [Node] Running "fixhdr_unifize" ("niworkflows.interfaces.utils.CopyXForm") 190731-15:29:55,566 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_mid_run_1_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_matching_wf.enhance_and_skullstrip_bold_wf.fixhdr_unifize". 190731-15:29:57,511 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_mid_run_1_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_matching_wf.enhance_and_skullstrip_bold_wf.skullstrip_second_pass" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/enhance_and_skullstrip_bold_wf/skullstrip_second_pass". 190731-15:29:57,515 nipype.workflow INFO: [Node] Running "skullstrip_second_pass" ("nipype.interfaces.afni.preprocess.Automask"), a CommandLine Interface with command: 3dAutomask -apply_prefix uni_xform_masked.nii.gz -dilate 1 -prefix uni_xform_mask.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/enhance_and_skullstrip_bold_wf/skullstrip_second_pass/uni_xform.nii.gz 190731-15:29:57,775 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_mid_run_1_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_matching_wf.enhance_and_skullstrip_bold_wf.skullstrip_second_pass". 190731-15:29:59,501 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_mid_run_1_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_matching_wf.enhance_and_skullstrip_bold_wf.fixhdr_skullstrip2" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/enhance_and_skullstrip_bold_wf/fixhdr_skullstrip2". 190731-15:29:59,503 nipype.workflow INFO: [Node] Running "fixhdr_skullstrip2" ("niworkflows.interfaces.utils.CopyXForm") 190731-15:29:59,530 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_mid_run_1_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_matching_wf.enhance_and_skullstrip_bold_wf.fixhdr_skullstrip2". 190731-15:30:01,518 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_mid_run_1_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_matching_wf.enhance_and_skullstrip_bold_wf.combine_masks" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/enhance_and_skullstrip_bold_wf/combine_masks". 190731-15:30:01,520 nipype.workflow INFO: [Node] Running "combine_masks" ("nipype.interfaces.fsl.maths.BinaryMaths"), a CommandLine Interface with command: fslmaths /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_pass/template_corrected_brain_mask.nii.gz -mul /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/enhance_and_skullstrip_bold_wf/fixhdr_skullstrip2/uni_xform_mask_xform.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/enhance_and_skullstrip_bold_wf/combine_masks/template_corrected_brain_mask_maths.nii.gz 190731-15:30:01,656 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_mid_run_1_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_matching_wf.enhance_and_skullstrip_bold_wf.combine_masks". 190731-15:30:03,514 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_mid_run_1_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_matching_wf.enhance_and_skullstrip_bold_wf.apply_mask" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/enhance_and_skullstrip_bold_wf/apply_mask". 190731-15:30:03,517 nipype.workflow INFO: [Node] Running "apply_mask" ("nipype.interfaces.fsl.maths.ApplyMask"), a CommandLine Interface with command: fslmaths /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/enhance_and_skullstrip_bold_wf/fixhdr_unifize/uni_xform.nii.gz -mas /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/enhance_and_skullstrip_bold_wf/combine_masks/template_corrected_brain_mask_maths.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/enhance_and_skullstrip_bold_wf/apply_mask/uni_xform_masked.nii.gz 190731-15:30:03,609 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_mid_wf.sdc_wf.pepolar_unwarp_wf.qwarp". 190731-15:30:03,639 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_mid_run_1_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_matching_wf.enhance_and_skullstrip_bold_wf.apply_mask". 190731-15:30:05,509 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_mid_wf.sdc_wf.pepolar_unwarp_wf.cphdr_warp" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_mid_wf/sdc_wf/pepolar_unwarp_wf/cphdr_warp". 190731-15:30:05,512 nipype.workflow INFO: [Node] Running "cphdr_warp" ("niworkflows.interfaces.utils.CopyHeader") 190731-15:30:05,514 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_opposite_wf.fmap2ref_reg" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/fmap2ref_reg". 190731-15:30:05,518 nipype.workflow INFO: [Node] Running "fmap2ref_reg" ("nipype.interfaces.ants.registration.Registration"), a CommandLine Interface with command: antsRegistration --collapse-output-transforms 1 --dimensionality 3 --float 1 --initialize-transforms-per-stage 0 --interpolation LanczosWindowedSinc --output [ transform, transform_Warped.nii.gz ] --transform Translation[ 0.05 ] --metric Mattes[ /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/apply_mask/uni_xform_masked.nii.gz, /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/enhance_and_skullstrip_bold_wf/apply_mask/uni_xform_masked.nii.gz, 1, 64, Random, 0.5 ] --convergence [ 500, 1e-07, 200 ] --smoothing-sigmas 8.0mm --shrink-factors 2 --use-estimate-learning-rate-once 1 --use-histogram-matching 1 --transform Rigid[ 0.01 ] --metric Mattes[ /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/apply_mask/uni_xform_masked.nii.gz, /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/enhance_and_skullstrip_bold_wf/apply_mask/uni_xform_masked.nii.gz, 1, 64, Random, 0.5 ] --convergence [ 200, 1e-08, 100 ] --smoothing-sigmas 2.0mm --shrink-factors 1 --use-estimate-learning-rate-once 1 --use-histogram-matching 1 --winsorize-image-intensities [ 0.005, 0.998 ] --write-composite-transform 1 190731-15:30:05,641 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_mid_wf.sdc_wf.pepolar_unwarp_wf.cphdr_warp". 190731-15:30:07,503 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_mid_wf.sdc_wf.pepolar_unwarp_wf.to_ants" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_mid_wf/sdc_wf/pepolar_unwarp_wf/to_ants". 190731-15:30:07,504 nipype.workflow INFO: [Node] Running "to_ants" ("nipype.interfaces.utility.wrappers.Function") 190731-15:30:07,579 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_mid_wf.sdc_wf.pepolar_unwarp_wf.to_ants". 190731-15:30:08,356 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_matching_wf.fmap2ref_reg". 190731-15:30:09,977 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_mid_wf.sdc_wf.pepolar_unwarp_wf.unwarp_reference" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_mid_wf/sdc_wf/pepolar_unwarp_wf/unwarp_reference". 190731-15:30:09,980 nipype.workflow INFO: [Node] Running "unwarp_reference" ("niworkflows.interfaces.registration.ANTSApplyTransformsRPT"), a CommandLine Interface with command: antsApplyTransforms --default-value 0 --dimensionality 3 --float 1 --input /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_mid_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/n4_correct/ref_bold_corrected.nii.gz --interpolation LanczosWindowedSinc --output ref_bold_corrected_trans.nii.gz --reference-image /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_mid_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/n4_correct/ref_bold_corrected.nii.gz --transform /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_mid_wf/sdc_wf/pepolar_unwarp_wf/cphdr_warp/_warpfieldQwarp_PLUS_WARP_fixhdr.nii.gz 190731-15:30:09,994 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_mid_run_1_wf.bold_hmc_wf.fsl2itk" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_1_wf/bold_hmc_wf/fsl2itk". 190731-15:30:10,2 nipype.workflow INFO: [Node] Running "fsl2itk" ("niworkflows.interfaces.itk.MCFLIRT2ITK") 190731-15:30:11,603 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_mid_wf.sdc_wf.pepolar_unwarp_wf.unwarp_reference". 190731-15:30:28,306 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_opposite_wf.fmap2ref_reg". 190731-15:30:28,732 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_mid_run_1_wf.bold_hmc_wf.fsl2itk". 190731-15:30:29,580 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_mid_wf.sdc_wf.pepolar_unwarp_wf.enhance_and_skullstrip_bold_wf.init_aff" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_mid_wf/sdc_wf/pepolar_unwarp_wf/enhance_and_skullstrip_bold_wf/init_aff". 190731-15:30:29,583 nipype.workflow INFO: [Node] Running "init_aff" ("niworkflows.interfaces.ants.AI"), a CommandLine Interface with command: antsAI -c [10,0.000001,10] -d 3 -x /home/sahad3/.cache/templateflow/tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_res-02_desc-brain_mask.nii.gz -m Mattes[/home/sahad3/.cache/templateflow/tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_res-02_desc-fMRIPrep_boldref.nii.gz,/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_mid_wf/sdc_wf/pepolar_unwarp_wf/unwarp_reference/ref_bold_corrected_trans.nii.gz,32,Regular,0.200000] -o initialization.mat -p 0 -s [20.000000,0.120000] -t Affine[0.100000] -v 1 190731-15:30:29,609 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_mid_wf.bold_bold_trans_wf.bold_transform" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_mid_wf/bold_bold_trans_wf/bold_transform". 190731-15:30:29,624 nipype.workflow INFO: [Node] Running "bold_transform" ("niworkflows.interfaces.itk.MultiApplyTransforms") 190731-15:30:41,915 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_mid_wf.sdc_wf.pepolar_unwarp_wf.enhance_and_skullstrip_bold_wf.init_aff". 190731-15:30:43,535 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_mid_wf.sdc_wf.pepolar_unwarp_wf.enhance_and_skullstrip_bold_wf.norm" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_mid_wf/sdc_wf/pepolar_unwarp_wf/enhance_and_skullstrip_bold_wf/norm". 190731-15:30:43,539 nipype.workflow INFO: [Node] Running "norm" ("niworkflows.interfaces.fixes.FixHeaderRegistration"), a CommandLine Interface with command: antsRegistration --collapse-output-transforms 1 --dimensionality 3 --float 1 --initial-moving-transform [ /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_mid_wf/sdc_wf/pepolar_unwarp_wf/enhance_and_skullstrip_bold_wf/init_aff/initialization.mat, 0 ] --initialize-transforms-per-stage 0 --interpolation Linear --output transform --transform Affine[ 0.1 ] --metric Mattes[ /home/sahad3/.cache/templateflow/tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_res-02_desc-fMRIPrep_boldref.nii.gz, /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_mid_wf/sdc_wf/pepolar_unwarp_wf/unwarp_reference/ref_bold_corrected_trans.nii.gz, 1, 64, Random, 0.2 ] --convergence [ 200, 1e-09, 10 ] --smoothing-sigmas 2.0mm --shrink-factors 2 --use-estimate-learning-rate-once 1 --use-histogram-matching 1 --winsorize-image-intensities [ 0.05, 0.98 ] --write-composite-transform 0 190731-15:30:46,675 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_mid_wf.sdc_wf.pepolar_unwarp_wf.enhance_and_skullstrip_bold_wf.norm". 190731-15:30:47,553 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_mid_wf.sdc_wf.pepolar_unwarp_wf.enhance_and_skullstrip_bold_wf.map_brainmask" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_mid_wf/sdc_wf/pepolar_unwarp_wf/enhance_and_skullstrip_bold_wf/map_brainmask". 190731-15:30:47,555 nipype.workflow INFO: [Node] Running "map_brainmask" ("niworkflows.interfaces.fixes.FixHeaderApplyTransforms"), a CommandLine Interface with command: antsApplyTransforms --default-value 0 --float 1 --input /home/sahad3/.cache/templateflow/tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_res-02_desc-brain_mask.nii.gz --interpolation MultiLabel --output tpl-MNI152NLin2009cAsym_res-02_desc-brain_mask_trans.nii.gz --reference-image /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_mid_wf/sdc_wf/pepolar_unwarp_wf/unwarp_reference/ref_bold_corrected_trans.nii.gz --transform [ /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_mid_wf/sdc_wf/pepolar_unwarp_wf/enhance_and_skullstrip_bold_wf/norm/transform0GenericAffine.mat, 1 ] 190731-15:30:47,555 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.sdc_wf.pepolar_unwarp_wf.qwarp" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/qwarp". 190731-15:30:47,559 nipype.workflow INFO: [Node] Running "qwarp" ("nipype.interfaces.afni.preprocess.QwarpPlusMinus"), a CommandLine Interface with command: 3dQwarp -prefix Qwarp.nii.gz -plusminus -noXdis -noZdis -base /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/qwarp/transform_Warped.nii.gz -blur -1.0 -1.0 -source /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/qwarp/transform_Warped_c0000.nii.gz -minpatch 9 -nopadWARP -noweight -pblur 0.05 0.05 190731-15:30:49,791 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_mid_wf.sdc_wf.pepolar_unwarp_wf.enhance_and_skullstrip_bold_wf.map_brainmask". 190731-15:30:51,578 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_mid_wf.sdc_wf.pepolar_unwarp_wf.enhance_and_skullstrip_bold_wf.pre_mask_dilate" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_mid_wf/sdc_wf/pepolar_unwarp_wf/enhance_and_skullstrip_bold_wf/pre_mask_dilate". 190731-15:30:51,581 nipype.workflow INFO: [Node] Running "pre_mask_dilate" ("nipype.interfaces.fsl.maths.DilateImage"), a CommandLine Interface with command: fslmaths -dt char /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_mid_wf/sdc_wf/pepolar_unwarp_wf/enhance_and_skullstrip_bold_wf/map_brainmask/tpl-MNI152NLin2009cAsym_res-02_desc-brain_mask_trans.nii.gz -kernel sphere 3.0000 -dilF /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_mid_wf/sdc_wf/pepolar_unwarp_wf/enhance_and_skullstrip_bold_wf/pre_mask_dilate/tpl-MNI152NLin2009cAsym_res-02_desc-brain_mask_trans_dil.nii.gz 190731-15:30:52,30 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_mid_wf.sdc_wf.pepolar_unwarp_wf.enhance_and_skullstrip_bold_wf.pre_mask_dilate". 190731-15:30:53,596 nipype.interface WARNING: q-forms of reference and mask are substantially different 190731-15:30:55,587 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_mid_wf.sdc_wf.pepolar_unwarp_wf.enhance_and_skullstrip_bold_wf.n4_correct" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_mid_wf/sdc_wf/pepolar_unwarp_wf/enhance_and_skullstrip_bold_wf/n4_correct". 190731-15:30:55,591 nipype.workflow INFO: [Node] Running "n4_correct" ("nipype.interfaces.ants.segmentation.N4BiasFieldCorrection"), a CommandLine Interface with command: N4BiasFieldCorrection --bspline-fitting [ 200 ] -d 3 --input-image /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_mid_wf/sdc_wf/pepolar_unwarp_wf/unwarp_reference/ref_bold_corrected_trans.nii.gz --mask-image /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_mid_wf/sdc_wf/pepolar_unwarp_wf/enhance_and_skullstrip_bold_wf/check_hdr/tpl-MNI152NLin2009cAsym_res-02_desc-brain_mask_trans_dil_hdr.nii.gz --output ref_bold_corrected_trans_corrected.nii.gz 190731-15:30:58,396 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_mid_wf.sdc_wf.pepolar_unwarp_wf.enhance_and_skullstrip_bold_wf.n4_correct". 190731-15:30:59,678 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_mid_wf.sdc_wf.pepolar_unwarp_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_pass" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_mid_wf/sdc_wf/pepolar_unwarp_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_pass". 190731-15:30:59,682 nipype.workflow INFO: [Node] Running "skullstrip_first_pass" ("nipype.interfaces.fsl.preprocess.BET"), a CommandLine Interface with command: bet /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_mid_wf/sdc_wf/pepolar_unwarp_wf/enhance_and_skullstrip_bold_wf/n4_correct/ref_bold_corrected_trans_corrected.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_mid_wf/sdc_wf/pepolar_unwarp_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_pass/ref_bold_corrected_trans_corrected_brain.nii.gz -f 0.20 -m 190731-15:31:01,892 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_mid_wf.sdc_wf.pepolar_unwarp_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_pass". 190731-15:31:03,585 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_mid_wf.sdc_wf.pepolar_unwarp_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_dilate" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_mid_wf/sdc_wf/pepolar_unwarp_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_dilate". 190731-15:31:03,588 nipype.workflow INFO: [Node] Running "skullstrip_first_dilate" ("nipype.interfaces.fsl.maths.DilateImage"), a CommandLine Interface with command: fslmaths -dt char /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_mid_wf/sdc_wf/pepolar_unwarp_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_pass/ref_bold_corrected_trans_corrected_brain_mask.nii.gz -kernel sphere 6.0000 -dilF /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_mid_wf/sdc_wf/pepolar_unwarp_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_dilate/ref_bold_corrected_trans_corrected_brain_mask_dil.nii.gz 190731-15:31:04,102 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_mid_wf.sdc_wf.pepolar_unwarp_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_dilate". 190731-15:31:05,686 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_mid_wf.sdc_wf.pepolar_unwarp_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_mask" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_mid_wf/sdc_wf/pepolar_unwarp_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_mask". 190731-15:31:05,689 nipype.workflow INFO: [Node] Running "skullstrip_first_mask" ("nipype.interfaces.fsl.maths.ApplyMask"), a CommandLine Interface with command: fslmaths /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_mid_wf/sdc_wf/pepolar_unwarp_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_pass/ref_bold_corrected_trans_corrected_brain.nii.gz -mas /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_mid_wf/sdc_wf/pepolar_unwarp_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_dilate/ref_bold_corrected_trans_corrected_brain_mask_dil.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_mid_wf/sdc_wf/pepolar_unwarp_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_mask/ref_bold_corrected_trans_corrected_brain_masked.nii.gz 190731-15:31:05,832 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_mid_wf.sdc_wf.pepolar_unwarp_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_mask". 190731-15:31:07,639 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_mid_wf.sdc_wf.pepolar_unwarp_wf.enhance_and_skullstrip_bold_wf.unifize" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_mid_wf/sdc_wf/pepolar_unwarp_wf/enhance_and_skullstrip_bold_wf/unifize". 190731-15:31:07,643 nipype.workflow INFO: [Node] Running "unifize" ("nipype.interfaces.afni.utils.Unifize"), a CommandLine Interface with command: 3dUnifize -clfrac 0.2 -rbt 18.3 65.0 90.0 -prefix uni.nii.gz -T2 -input /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_mid_wf/sdc_wf/pepolar_unwarp_wf/enhance_and_skullstrip_bold_wf/unifize/ref_bold_corrected_trans_corrected_brain_masked.nii.gz 190731-15:31:09,136 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_mid_wf.sdc_wf.pepolar_unwarp_wf.enhance_and_skullstrip_bold_wf.unifize". 190731-15:31:11,655 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_mid_wf.sdc_wf.pepolar_unwarp_wf.enhance_and_skullstrip_bold_wf.fixhdr_unifize" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_mid_wf/sdc_wf/pepolar_unwarp_wf/enhance_and_skullstrip_bold_wf/fixhdr_unifize". 190731-15:31:11,657 nipype.workflow INFO: [Node] Running "fixhdr_unifize" ("niworkflows.interfaces.utils.CopyXForm") 190731-15:31:11,704 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_mid_wf.sdc_wf.pepolar_unwarp_wf.enhance_and_skullstrip_bold_wf.fixhdr_unifize". 190731-15:31:13,683 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_mid_wf.sdc_wf.pepolar_unwarp_wf.enhance_and_skullstrip_bold_wf.skullstrip_second_pass" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_mid_wf/sdc_wf/pepolar_unwarp_wf/enhance_and_skullstrip_bold_wf/skullstrip_second_pass". 190731-15:31:13,687 nipype.workflow INFO: [Node] Running "skullstrip_second_pass" ("nipype.interfaces.afni.preprocess.Automask"), a CommandLine Interface with command: 3dAutomask -apply_prefix uni_xform_masked.nii.gz -dilate 1 -prefix uni_xform_mask.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_mid_wf/sdc_wf/pepolar_unwarp_wf/enhance_and_skullstrip_bold_wf/skullstrip_second_pass/uni_xform.nii.gz 190731-15:31:13,891 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_mid_wf.sdc_wf.pepolar_unwarp_wf.enhance_and_skullstrip_bold_wf.skullstrip_second_pass". 190731-15:31:15,638 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_mid_wf.sdc_wf.pepolar_unwarp_wf.enhance_and_skullstrip_bold_wf.fixhdr_skullstrip2" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_mid_wf/sdc_wf/pepolar_unwarp_wf/enhance_and_skullstrip_bold_wf/fixhdr_skullstrip2". 190731-15:31:15,643 nipype.workflow INFO: [Node] Running "fixhdr_skullstrip2" ("niworkflows.interfaces.utils.CopyXForm") 190731-15:31:15,675 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_mid_wf.sdc_wf.pepolar_unwarp_wf.enhance_and_skullstrip_bold_wf.fixhdr_skullstrip2". 190731-15:31:17,666 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_mid_wf.sdc_wf.pepolar_unwarp_wf.enhance_and_skullstrip_bold_wf.combine_masks" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_mid_wf/sdc_wf/pepolar_unwarp_wf/enhance_and_skullstrip_bold_wf/combine_masks". 190731-15:31:17,669 nipype.workflow INFO: [Node] Running "combine_masks" ("nipype.interfaces.fsl.maths.BinaryMaths"), a CommandLine Interface with command: fslmaths /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_mid_wf/sdc_wf/pepolar_unwarp_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_pass/ref_bold_corrected_trans_corrected_brain_mask.nii.gz -mul /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_mid_wf/sdc_wf/pepolar_unwarp_wf/enhance_and_skullstrip_bold_wf/fixhdr_skullstrip2/uni_xform_mask_xform.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_mid_wf/sdc_wf/pepolar_unwarp_wf/enhance_and_skullstrip_bold_wf/combine_masks/ref_bold_corrected_trans_corrected_brain_mask_maths.nii.gz 190731-15:31:17,842 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_mid_wf.sdc_wf.pepolar_unwarp_wf.enhance_and_skullstrip_bold_wf.combine_masks". 190731-15:31:19,709 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_mid_wf.sdc_wf.pepolar_unwarp_wf.enhance_and_skullstrip_bold_wf.apply_mask" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_mid_wf/sdc_wf/pepolar_unwarp_wf/enhance_and_skullstrip_bold_wf/apply_mask". 190731-15:31:19,713 nipype.workflow INFO: [Node] Running "apply_mask" ("nipype.interfaces.fsl.maths.ApplyMask"), a CommandLine Interface with command: fslmaths /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_mid_wf/sdc_wf/pepolar_unwarp_wf/enhance_and_skullstrip_bold_wf/fixhdr_unifize/uni_xform.nii.gz -mas /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_mid_wf/sdc_wf/pepolar_unwarp_wf/enhance_and_skullstrip_bold_wf/combine_masks/ref_bold_corrected_trans_corrected_brain_mask_maths.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_mid_wf/sdc_wf/pepolar_unwarp_wf/enhance_and_skullstrip_bold_wf/apply_mask/uni_xform_masked.nii.gz 190731-15:31:19,844 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_mid_wf.sdc_wf.pepolar_unwarp_wf.enhance_and_skullstrip_bold_wf.apply_mask". 190731-15:31:51,582 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.sdc_wf.pepolar_unwarp_wf.qwarp". 190731-15:31:53,601 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.sdc_wf.pepolar_unwarp_wf.cphdr_warp" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/cphdr_warp". 190731-15:31:53,603 nipype.workflow INFO: [Node] Running "cphdr_warp" ("niworkflows.interfaces.utils.CopyHeader") 190731-15:31:53,620 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_mid_run_1_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.init_aff" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_1_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/init_aff". 190731-15:31:53,624 nipype.workflow INFO: [Node] Running "init_aff" ("niworkflows.interfaces.ants.AI"), a CommandLine Interface with command: antsAI -c [10,0.000001,10] -d 3 -x /home/sahad3/.cache/templateflow/tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_res-02_desc-brain_mask.nii.gz -m Mattes[/home/sahad3/.cache/templateflow/tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_res-02_desc-fMRIPrep_boldref.nii.gz,/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_1_wf/bold_reference_wf/gen_ref/ref_bold.nii.gz,32,Regular,0.200000] -o initialization.mat -p 0 -s [20.000000,0.120000] -t Affine[0.100000] -v 1 190731-15:31:53,711 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.sdc_wf.pepolar_unwarp_wf.cphdr_warp". 190731-15:31:55,625 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.sdc_wf.pepolar_unwarp_wf.to_ants" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/to_ants". 190731-15:31:55,627 nipype.workflow INFO: [Node] Running "to_ants" ("nipype.interfaces.utility.wrappers.Function") 190731-15:31:55,693 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.sdc_wf.pepolar_unwarp_wf.to_ants". 190731-15:31:58,179 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.sdc_wf.pepolar_unwarp_wf.unwarp_reference" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/unwarp_reference". 190731-15:31:58,183 nipype.workflow INFO: [Node] Running "unwarp_reference" ("niworkflows.interfaces.registration.ANTSApplyTransformsRPT"), a CommandLine Interface with command: antsApplyTransforms --default-value 0 --dimensionality 3 --float 1 --input /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/n4_correct/ref_bold_corrected.nii.gz --interpolation LanczosWindowedSinc --output ref_bold_corrected_trans.nii.gz --reference-image /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/n4_correct/ref_bold_corrected.nii.gz --transform /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/cphdr_warp/_warpfieldQwarp_PLUS_WARP_fixhdr.nii.gz 190731-15:31:58,329 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_mid_run_1_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.init_aff". 190731-15:31:59,577 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.sdc_wf.pepolar_unwarp_wf.unwarp_reference". 190731-15:31:59,599 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.bold_bold_trans_wf.bold_transform" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/bold_bold_trans_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-02..func..sub-23649_ses-02_task-rest_echo-4_bold.nii.gz/bold_transform". 190731-15:31:59,609 nipype.workflow INFO: [Node] Running "bold_transform" ("niworkflows.interfaces.itk.MultiApplyTransforms") 190731-15:32:19,428 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_mid_wf.bold_bold_trans_wf.bold_transform". 190731-15:32:21,681 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.sdc_wf.pepolar_unwarp_wf.enhance_and_skullstrip_bold_wf.init_aff" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/enhance_and_skullstrip_bold_wf/init_aff". 190731-15:32:21,684 nipype.workflow INFO: [Node] Running "init_aff" ("niworkflows.interfaces.ants.AI"), a CommandLine Interface with command: antsAI -c [10,0.000001,10] -d 3 -x /home/sahad3/.cache/templateflow/tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_res-02_desc-brain_mask.nii.gz -m Mattes[/home/sahad3/.cache/templateflow/tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_res-02_desc-fMRIPrep_boldref.nii.gz,/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/unwarp_reference/ref_bold_corrected_trans.nii.gz,32,Regular,0.200000] -o initialization.mat -p 0 -s [20.000000,0.120000] -t Affine[0.100000] -v 1 190731-15:32:22,50 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_mid_wf.bold_bold_trans_wf.merge" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_mid_wf/bold_bold_trans_wf/merge". 190731-15:32:22,73 nipype.workflow INFO: [Node] Running "merge" ("fmriprep.interfaces.nilearn.Merge") 190731-15:32:26,811 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.sdc_wf.pepolar_unwarp_wf.enhance_and_skullstrip_bold_wf.init_aff". 190731-15:32:27,608 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.sdc_wf.pepolar_unwarp_wf.enhance_and_skullstrip_bold_wf.norm" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/enhance_and_skullstrip_bold_wf/norm". 190731-15:32:27,612 nipype.workflow INFO: [Node] Running "norm" ("niworkflows.interfaces.fixes.FixHeaderRegistration"), a CommandLine Interface with command: antsRegistration --collapse-output-transforms 1 --dimensionality 3 --float 1 --initial-moving-transform [ /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/enhance_and_skullstrip_bold_wf/init_aff/initialization.mat, 0 ] --initialize-transforms-per-stage 0 --interpolation Linear --output transform --transform Affine[ 0.1 ] --metric Mattes[ /home/sahad3/.cache/templateflow/tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_res-02_desc-fMRIPrep_boldref.nii.gz, /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/unwarp_reference/ref_bold_corrected_trans.nii.gz, 1, 64, Random, 0.2 ] --convergence [ 200, 1e-09, 10 ] --smoothing-sigmas 2.0mm --shrink-factors 2 --use-estimate-learning-rate-once 1 --use-histogram-matching 1 --winsorize-image-intensities [ 0.05, 0.98 ] --write-composite-transform 0 190731-15:32:29,758 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.sdc_wf.pepolar_unwarp_wf.enhance_and_skullstrip_bold_wf.norm". 190731-15:32:31,643 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.sdc_wf.pepolar_unwarp_wf.enhance_and_skullstrip_bold_wf.map_brainmask" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/enhance_and_skullstrip_bold_wf/map_brainmask". 190731-15:32:31,645 nipype.workflow INFO: [Node] Running "map_brainmask" ("niworkflows.interfaces.fixes.FixHeaderApplyTransforms"), a CommandLine Interface with command: antsApplyTransforms --default-value 0 --float 1 --input /home/sahad3/.cache/templateflow/tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_res-02_desc-brain_mask.nii.gz --interpolation MultiLabel --output tpl-MNI152NLin2009cAsym_res-02_desc-brain_mask_trans.nii.gz --reference-image /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/unwarp_reference/ref_bold_corrected_trans.nii.gz --transform [ /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/enhance_and_skullstrip_bold_wf/norm/transform0GenericAffine.mat, 1 ] 190731-15:32:31,670 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.bold_bold_trans_wf.bold_transform" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/bold_bold_trans_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-02..func..sub-23649_ses-02_task-rest_echo-3_bold.nii.gz/bold_transform". 190731-15:32:31,680 nipype.workflow INFO: [Node] Running "bold_transform" ("niworkflows.interfaces.itk.MultiApplyTransforms") 190731-15:32:33,783 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.sdc_wf.pepolar_unwarp_wf.enhance_and_skullstrip_bold_wf.map_brainmask". 190731-15:32:35,662 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.sdc_wf.pepolar_unwarp_wf.enhance_and_skullstrip_bold_wf.pre_mask_dilate" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/enhance_and_skullstrip_bold_wf/pre_mask_dilate". 190731-15:32:35,665 nipype.workflow INFO: [Node] Running "pre_mask_dilate" ("nipype.interfaces.fsl.maths.DilateImage"), a CommandLine Interface with command: fslmaths -dt char /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/enhance_and_skullstrip_bold_wf/map_brainmask/tpl-MNI152NLin2009cAsym_res-02_desc-brain_mask_trans.nii.gz -kernel sphere 3.0000 -dilF /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/enhance_and_skullstrip_bold_wf/pre_mask_dilate/tpl-MNI152NLin2009cAsym_res-02_desc-brain_mask_trans_dil.nii.gz 190731-15:32:35,868 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.sdc_wf.pepolar_unwarp_wf.enhance_and_skullstrip_bold_wf.pre_mask_dilate". 190731-15:32:37,670 nipype.interface WARNING: q-forms of reference and mask are substantially different 190731-15:32:39,662 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.sdc_wf.pepolar_unwarp_wf.enhance_and_skullstrip_bold_wf.n4_correct" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/enhance_and_skullstrip_bold_wf/n4_correct". 190731-15:32:39,665 nipype.workflow INFO: [Node] Running "n4_correct" ("nipype.interfaces.ants.segmentation.N4BiasFieldCorrection"), a CommandLine Interface with command: N4BiasFieldCorrection --bspline-fitting [ 200 ] -d 3 --input-image /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/unwarp_reference/ref_bold_corrected_trans.nii.gz --mask-image /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/enhance_and_skullstrip_bold_wf/check_hdr/tpl-MNI152NLin2009cAsym_res-02_desc-brain_mask_trans_dil_hdr.nii.gz --output ref_bold_corrected_trans_corrected.nii.gz 190731-15:32:41,875 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.sdc_wf.pepolar_unwarp_wf.enhance_and_skullstrip_bold_wf.n4_correct". 190731-15:32:43,645 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.sdc_wf.pepolar_unwarp_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_pass" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_pass". 190731-15:32:43,648 nipype.workflow INFO: [Node] Running "skullstrip_first_pass" ("nipype.interfaces.fsl.preprocess.BET"), a CommandLine Interface with command: bet /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/enhance_and_skullstrip_bold_wf/n4_correct/ref_bold_corrected_trans_corrected.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_pass/ref_bold_corrected_trans_corrected_brain.nii.gz -f 0.20 -m 190731-15:32:45,773 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.sdc_wf.pepolar_unwarp_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_pass". 190731-15:32:47,696 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.sdc_wf.pepolar_unwarp_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_dilate" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_dilate". 190731-15:32:47,698 nipype.workflow INFO: [Node] Running "skullstrip_first_dilate" ("nipype.interfaces.fsl.maths.DilateImage"), a CommandLine Interface with command: fslmaths -dt char /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_pass/ref_bold_corrected_trans_corrected_brain_mask.nii.gz -kernel sphere 6.0000 -dilF /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_dilate/ref_bold_corrected_trans_corrected_brain_mask_dil.nii.gz 190731-15:32:48,27 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.sdc_wf.pepolar_unwarp_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_dilate". 190731-15:32:49,101 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_mid_wf.bold_bold_trans_wf.merge". 190731-15:32:51,865 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.bold_bold_trans_wf.bold_transform". 190731-15:33:14,756 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_mid_wf.bold_bold_trans_wf.bold_reference_wf.validate" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_mid_wf/bold_bold_trans_wf/bold_reference_wf/validate". 190731-15:33:14,759 nipype.workflow INFO: [Node] Running "validate" ("niworkflows.interfaces.images.ValidateImage") 190731-15:33:14,770 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.sdc_wf.pepolar_unwarp_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_mask" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_mask". 190731-15:33:14,772 nipype.workflow INFO: [Node] Running "skullstrip_first_mask" ("nipype.interfaces.fsl.maths.ApplyMask"), a CommandLine Interface with command: fslmaths /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_pass/ref_bold_corrected_trans_corrected_brain.nii.gz -mas /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_dilate/ref_bold_corrected_trans_corrected_brain_mask_dil.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_mask/ref_bold_corrected_trans_corrected_brain_masked.nii.gz 190731-15:33:14,938 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.sdc_wf.pepolar_unwarp_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_mask". 190731-15:33:15,334 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.bold_bold_trans_wf.bold_transform" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/bold_bold_trans_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-02..func..sub-23649_ses-02_task-rest_echo-2_bold.nii.gz/bold_transform". 190731-15:33:15,343 nipype.workflow INFO: [Node] Running "bold_transform" ("niworkflows.interfaces.itk.MultiApplyTransforms") 190731-15:33:15,366 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.bold_bold_trans_wf.merge" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/bold_bold_trans_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-02..func..sub-23649_ses-02_task-rest_echo-4_bold.nii.gz/merge". 190731-15:33:15,376 nipype.workflow INFO: [Node] Running "merge" ("fmriprep.interfaces.nilearn.Merge") 190731-15:33:17,322 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.sdc_wf.pepolar_unwarp_wf.enhance_and_skullstrip_bold_wf.unifize" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/enhance_and_skullstrip_bold_wf/unifize". 190731-15:33:17,434 nipype.workflow INFO: [Node] Running "unifize" ("nipype.interfaces.afni.utils.Unifize"), a CommandLine Interface with command: 3dUnifize -clfrac 0.2 -rbt 18.3 65.0 90.0 -prefix uni.nii.gz -T2 -input /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/enhance_and_skullstrip_bold_wf/unifize/ref_bold_corrected_trans_corrected_brain_masked.nii.gz 190731-15:33:18,613 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.sdc_wf.pepolar_unwarp_wf.enhance_and_skullstrip_bold_wf.unifize". 190731-15:33:19,323 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.sdc_wf.pepolar_unwarp_wf.enhance_and_skullstrip_bold_wf.fixhdr_unifize" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/enhance_and_skullstrip_bold_wf/fixhdr_unifize". 190731-15:33:19,326 nipype.workflow INFO: [Node] Running "fixhdr_unifize" ("niworkflows.interfaces.utils.CopyXForm") 190731-15:33:19,391 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.sdc_wf.pepolar_unwarp_wf.enhance_and_skullstrip_bold_wf.fixhdr_unifize". 190731-15:33:21,357 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.sdc_wf.pepolar_unwarp_wf.enhance_and_skullstrip_bold_wf.skullstrip_second_pass" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/enhance_and_skullstrip_bold_wf/skullstrip_second_pass". 190731-15:33:21,359 nipype.workflow INFO: [Node] Running "skullstrip_second_pass" ("nipype.interfaces.afni.preprocess.Automask"), a CommandLine Interface with command: 3dAutomask -apply_prefix uni_xform_masked.nii.gz -dilate 1 -prefix uni_xform_mask.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/enhance_and_skullstrip_bold_wf/skullstrip_second_pass/uni_xform.nii.gz 190731-15:33:21,535 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.sdc_wf.pepolar_unwarp_wf.enhance_and_skullstrip_bold_wf.skullstrip_second_pass". 190731-15:33:22,210 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.bold_bold_trans_wf.bold_transform". 190731-15:33:22,841 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_mid_wf.bold_bold_trans_wf.bold_reference_wf.validate". 190731-15:33:23,350 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.sdc_wf.pepolar_unwarp_wf.enhance_and_skullstrip_bold_wf.fixhdr_skullstrip2" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/enhance_and_skullstrip_bold_wf/fixhdr_skullstrip2". 190731-15:33:23,352 nipype.workflow INFO: [Node] Running "fixhdr_skullstrip2" ("niworkflows.interfaces.utils.CopyXForm") 190731-15:33:23,382 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.sdc_wf.pepolar_unwarp_wf.enhance_and_skullstrip_bold_wf.fixhdr_skullstrip2". 190731-15:33:23,396 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.bold_bold_trans_wf.bold_transform" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/bold_bold_trans_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-02..func..sub-23649_ses-02_task-rest_echo-1_bold.nii.gz/bold_transform". 190731-15:33:23,413 nipype.workflow INFO: [Node] Running "bold_transform" ("niworkflows.interfaces.itk.MultiApplyTransforms") 190731-15:33:23,438 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.bold_bold_trans_wf.merge" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/bold_bold_trans_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-02..func..sub-23649_ses-02_task-rest_echo-3_bold.nii.gz/merge". 190731-15:33:23,456 nipype.workflow INFO: [Node] Running "merge" ("fmriprep.interfaces.nilearn.Merge") 190731-15:33:25,347 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_mid_wf.bold_bold_trans_wf.bold_reference_wf.gen_ref" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_mid_wf/bold_bold_trans_wf/bold_reference_wf/gen_ref". 190731-15:33:25,349 nipype.workflow INFO: [Node] Running "gen_ref" ("niworkflows.interfaces.registration.EstimateReferenceImage") 190731-15:33:25,351 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.sdc_wf.pepolar_unwarp_wf.enhance_and_skullstrip_bold_wf.combine_masks" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/enhance_and_skullstrip_bold_wf/combine_masks". 190731-15:33:25,354 nipype.workflow INFO: [Node] Running "combine_masks" ("nipype.interfaces.fsl.maths.BinaryMaths"), a CommandLine Interface with command: fslmaths /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_pass/ref_bold_corrected_trans_corrected_brain_mask.nii.gz -mul /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/enhance_and_skullstrip_bold_wf/fixhdr_skullstrip2/uni_xform_mask_xform.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/enhance_and_skullstrip_bold_wf/combine_masks/ref_bold_corrected_trans_corrected_brain_mask_maths.nii.gz 190731-15:33:25,501 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.sdc_wf.pepolar_unwarp_wf.enhance_and_skullstrip_bold_wf.combine_masks". 190731-15:33:25,890 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_mid_wf.bold_bold_trans_wf.bold_reference_wf.gen_ref". 190731-15:33:27,356 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.bold_bold_trans_wf.merge". 190731-15:33:27,908 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.sdc_wf.pepolar_unwarp_wf.enhance_and_skullstrip_bold_wf.apply_mask" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/enhance_and_skullstrip_bold_wf/apply_mask". 190731-15:33:27,911 nipype.workflow INFO: [Node] Running "apply_mask" ("nipype.interfaces.fsl.maths.ApplyMask"), a CommandLine Interface with command: fslmaths /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/enhance_and_skullstrip_bold_wf/fixhdr_unifize/uni_xform.nii.gz -mas /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/enhance_and_skullstrip_bold_wf/combine_masks/ref_bold_corrected_trans_corrected_brain_mask_maths.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/enhance_and_skullstrip_bold_wf/apply_mask/uni_xform_masked.nii.gz 190731-15:33:28,73 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.sdc_wf.pepolar_unwarp_wf.enhance_and_skullstrip_bold_wf.apply_mask". 190731-15:33:35,563 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.bold_bold_trans_wf.merge". 190731-15:33:42,198 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.skullstrip_bold_wf.skullstrip_first_pass" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-02..func..sub-23649_ses-02_task-rest_echo-4_bold.nii.gz/skullstrip_first_pass". 190731-15:33:42,202 nipype.workflow INFO: [Node] Running "skullstrip_first_pass" ("nipype.interfaces.fsl.preprocess.BET"), a CommandLine Interface with command: bet /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/bold_bold_trans_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-02..func..sub-23649_ses-02_task-rest_echo-4_bold.nii.gz/merge/vol0000_xform-00000_merged.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-02..func..sub-23649_ses-02_task-rest_echo-4_bold.nii.gz/skullstrip_first_pass/vol0000_xform-00000_merged_brain.nii.gz -f 0.20 -m 190731-15:33:42,219 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.bold_bold_trans_wf.bold_reference_wf.validate" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/bold_bold_trans_wf/bold_reference_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-02..func..sub-23649_ses-02_task-rest_echo-4_bold.nii.gz/validate". 190731-15:33:42,221 nipype.workflow INFO: [Node] Running "validate" ("niworkflows.interfaces.images.ValidateImage") 190731-15:33:44,570 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.skullstrip_bold_wf.skullstrip_first_pass". 190731-15:33:45,346 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.bold_bold_trans_wf.bold_reference_wf.validate". 190731-15:33:55,424 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.skullstrip_bold_wf.skullstrip_first_pass" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-02..func..sub-23649_ses-02_task-rest_echo-3_bold.nii.gz/skullstrip_first_pass". 190731-15:33:55,428 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.bold_bold_trans_wf.bold_reference_wf.validate" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/bold_bold_trans_wf/bold_reference_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-02..func..sub-23649_ses-02_task-rest_echo-3_bold.nii.gz/validate". 190731-15:33:55,428 nipype.workflow INFO: [Node] Running "skullstrip_first_pass" ("nipype.interfaces.fsl.preprocess.BET"), a CommandLine Interface with command: bet /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/bold_bold_trans_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-02..func..sub-23649_ses-02_task-rest_echo-3_bold.nii.gz/merge/vol0000_xform-00000_merged.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-02..func..sub-23649_ses-02_task-rest_echo-3_bold.nii.gz/skullstrip_first_pass/vol0000_xform-00000_merged_brain.nii.gz -f 0.20 -m 190731-15:33:55,430 nipype.workflow INFO: [Node] Running "validate" ("niworkflows.interfaces.images.ValidateImage") 190731-15:33:56,31 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.skullstrip_bold_wf.skullstrip_second_pass" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-02..func..sub-23649_ses-02_task-rest_echo-4_bold.nii.gz/skullstrip_second_pass". 190731-15:33:56,32 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.bold_bold_trans_wf.bold_reference_wf.gen_ref" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/bold_bold_trans_wf/bold_reference_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-02..func..sub-23649_ses-02_task-rest_echo-4_bold.nii.gz/gen_ref". 190731-15:33:56,33 nipype.workflow INFO: [Node] Running "skullstrip_second_pass" ("nipype.interfaces.afni.preprocess.Automask"), a CommandLine Interface with command: 3dAutomask -apply_prefix vol0000_xform-00000_merged_brain_masked.nii.gz -dilate 1 -prefix vol0000_xform-00000_merged_brain_mask.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-02..func..sub-23649_ses-02_task-rest_echo-4_bold.nii.gz/skullstrip_second_pass/vol0000_xform-00000_merged_brain.nii.gz 190731-15:33:56,35 nipype.workflow INFO: [Node] Running "gen_ref" ("niworkflows.interfaces.registration.EstimateReferenceImage") 190731-15:33:56,339 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.skullstrip_bold_wf.skullstrip_second_pass". 190731-15:33:56,484 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.bold_bold_trans_wf.bold_reference_wf.gen_ref". 190731-15:33:57,850 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.skullstrip_bold_wf.skullstrip_first_pass". 190731-15:33:58,7 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.skullstrip_bold_wf.combine_masks" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-02..func..sub-23649_ses-02_task-rest_echo-4_bold.nii.gz/combine_masks". 190731-15:33:58,9 nipype.workflow INFO: [Node] Running "combine_masks" ("nipype.interfaces.fsl.maths.BinaryMaths"), a CommandLine Interface with command: fslmaths /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-02..func..sub-23649_ses-02_task-rest_echo-4_bold.nii.gz/skullstrip_first_pass/vol0000_xform-00000_merged_brain_mask.nii.gz -mul /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-02..func..sub-23649_ses-02_task-rest_echo-4_bold.nii.gz/skullstrip_second_pass/vol0000_xform-00000_merged_brain_mask.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-02..func..sub-23649_ses-02_task-rest_echo-4_bold.nii.gz/combine_masks/vol0000_xform-00000_merged_brain_mask_maths.nii.gz 190731-15:33:58,183 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.skullstrip_bold_wf.combine_masks". 190731-15:33:58,715 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.bold_bold_trans_wf.bold_reference_wf.validate". 190731-15:33:59,968 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.skullstrip_bold_wf.mask_reportlet" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-02..func..sub-23649_ses-02_task-rest_echo-4_bold.nii.gz/mask_reportlet". 190731-15:33:59,971 nipype.workflow INFO: [Node] Running "mask_reportlet" ("niworkflows.interfaces.masks.SimpleShowMaskRPT") 190731-15:33:59,971 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.skullstrip_bold_wf.apply_mask" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-02..func..sub-23649_ses-02_task-rest_echo-4_bold.nii.gz/apply_mask". 190731-15:33:59,973 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.skullstrip_bold_wf.skullstrip_second_pass" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-02..func..sub-23649_ses-02_task-rest_echo-3_bold.nii.gz/skullstrip_second_pass". 190731-15:33:59,975 nipype.workflow INFO: [Node] Running "apply_mask" ("nipype.interfaces.fsl.maths.ApplyMask"), a CommandLine Interface with command: fslmaths /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/bold_bold_trans_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-02..func..sub-23649_ses-02_task-rest_echo-4_bold.nii.gz/merge/vol0000_xform-00000_merged.nii.gz -mas /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-02..func..sub-23649_ses-02_task-rest_echo-4_bold.nii.gz/combine_masks/vol0000_xform-00000_merged_brain_mask_maths.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-02..func..sub-23649_ses-02_task-rest_echo-4_bold.nii.gz/apply_mask/vol0000_xform-00000_merged_masked.nii.gz 190731-15:33:59,975 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.bold_bold_trans_wf.bold_reference_wf.gen_ref" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/bold_bold_trans_wf/bold_reference_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-02..func..sub-23649_ses-02_task-rest_echo-3_bold.nii.gz/gen_ref". 190731-15:33:59,977 nipype.workflow INFO: [Node] Running "skullstrip_second_pass" ("nipype.interfaces.afni.preprocess.Automask"), a CommandLine Interface with command: 3dAutomask -apply_prefix vol0000_xform-00000_merged_brain_masked.nii.gz -dilate 1 -prefix vol0000_xform-00000_merged_brain_mask.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-02..func..sub-23649_ses-02_task-rest_echo-3_bold.nii.gz/skullstrip_second_pass/vol0000_xform-00000_merged_brain.nii.gz 190731-15:33:59,977 nipype.workflow INFO: [Node] Running "gen_ref" ("niworkflows.interfaces.registration.EstimateReferenceImage") 190731-15:34:00,303 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.skullstrip_bold_wf.skullstrip_second_pass". 190731-15:34:00,433 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.bold_bold_trans_wf.bold_reference_wf.gen_ref". 190731-15:34:01,959 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.skullstrip_bold_wf.combine_masks" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-02..func..sub-23649_ses-02_task-rest_echo-3_bold.nii.gz/combine_masks". 190731-15:34:01,963 nipype.workflow INFO: [Node] Running "combine_masks" ("nipype.interfaces.fsl.maths.BinaryMaths"), a CommandLine Interface with command: fslmaths /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-02..func..sub-23649_ses-02_task-rest_echo-3_bold.nii.gz/skullstrip_first_pass/vol0000_xform-00000_merged_brain_mask.nii.gz -mul /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-02..func..sub-23649_ses-02_task-rest_echo-3_bold.nii.gz/skullstrip_second_pass/vol0000_xform-00000_merged_brain_mask.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-02..func..sub-23649_ses-02_task-rest_echo-3_bold.nii.gz/combine_masks/vol0000_xform-00000_merged_brain_mask_maths.nii.gz 190731-15:34:02,100 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.skullstrip_bold_wf.combine_masks". 190731-15:34:04,22 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.skullstrip_bold_wf.mask_reportlet" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-02..func..sub-23649_ses-02_task-rest_echo-3_bold.nii.gz/mask_reportlet". 190731-15:34:04,24 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.skullstrip_bold_wf.apply_mask" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-02..func..sub-23649_ses-02_task-rest_echo-3_bold.nii.gz/apply_mask". 190731-15:34:04,24 nipype.workflow INFO: [Node] Running "mask_reportlet" ("niworkflows.interfaces.masks.SimpleShowMaskRPT") 190731-15:34:04,27 nipype.workflow INFO: [Node] Running "apply_mask" ("nipype.interfaces.fsl.maths.ApplyMask"), a CommandLine Interface with command: fslmaths /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/bold_bold_trans_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-02..func..sub-23649_ses-02_task-rest_echo-3_bold.nii.gz/merge/vol0000_xform-00000_merged.nii.gz -mas /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-02..func..sub-23649_ses-02_task-rest_echo-3_bold.nii.gz/combine_masks/vol0000_xform-00000_merged_brain_mask_maths.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-02..func..sub-23649_ses-02_task-rest_echo-3_bold.nii.gz/apply_mask/vol0000_xform-00000_merged_masked.nii.gz 190731-15:34:05,344 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.skullstrip_bold_wf.apply_mask". 190731-15:34:05,625 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.skullstrip_bold_wf.mask_reportlet". 190731-15:34:08,448 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.skullstrip_bold_wf.apply_mask". 190731-15:34:09,760 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.skullstrip_bold_wf.mask_reportlet". 190731-15:34:10,604 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.bold_bold_trans_wf.bold_transform". 190731-15:34:11,982 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.bold_bold_trans_wf.merge" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/bold_bold_trans_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-02..func..sub-23649_ses-02_task-rest_echo-2_bold.nii.gz/merge". 190731-15:34:11,982 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_mid_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.init_aff" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_mid_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/init_aff". 190731-15:34:11,986 nipype.workflow INFO: [Node] Running "init_aff" ("niworkflows.interfaces.ants.AI"), a CommandLine Interface with command: antsAI -c [10,0.000001,10] -d 3 -x /home/sahad3/.cache/templateflow/tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_res-02_desc-brain_mask.nii.gz -m Mattes[/home/sahad3/.cache/templateflow/tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_res-02_desc-fMRIPrep_boldref.nii.gz,/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_mid_wf/bold_bold_trans_wf/bold_reference_wf/gen_ref/ref_bold.nii.gz,32,Regular,0.200000] -o initialization.mat -p 0 -s [20.000000,0.120000] -t Affine[0.100000] -v 1 190731-15:34:11,992 nipype.workflow INFO: [Node] Running "merge" ("fmriprep.interfaces.nilearn.Merge") 190731-15:34:13,215 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.bold_bold_trans_wf.bold_transform". 190731-15:34:14,107 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.init_aff" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-02..func..sub-23649_ses-02_task-rest_echo-4_bold.nii.gz/init_aff". 190731-15:34:14,111 nipype.workflow INFO: [Node] Running "init_aff" ("niworkflows.interfaces.ants.AI"), a CommandLine Interface with command: antsAI -c [10,0.000001,10] -d 3 -x /home/sahad3/.cache/templateflow/tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_res-02_desc-brain_mask.nii.gz -m Mattes[/home/sahad3/.cache/templateflow/tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_res-02_desc-fMRIPrep_boldref.nii.gz,/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/bold_bold_trans_wf/bold_reference_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-02..func..sub-23649_ses-02_task-rest_echo-4_bold.nii.gz/gen_ref/ref_bold.nii.gz,32,Regular,0.200000] -o initialization.mat -p 0 -s [20.000000,0.120000] -t Affine[0.100000] -v 1 190731-15:34:14,177 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.bold_bold_trans_wf.merge" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/bold_bold_trans_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-02..func..sub-23649_ses-02_task-rest_echo-1_bold.nii.gz/merge". 190731-15:34:14,187 nipype.workflow INFO: [Node] Running "merge" ("fmriprep.interfaces.nilearn.Merge") 190731-15:34:16,291 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_mid_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.init_aff". 190731-15:34:17,992 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_mid_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.norm" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_mid_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/norm". 190731-15:34:17,996 nipype.workflow INFO: [Node] Running "norm" ("niworkflows.interfaces.fixes.FixHeaderRegistration"), a CommandLine Interface with command: antsRegistration --collapse-output-transforms 1 --dimensionality 3 --float 1 --initial-moving-transform [ /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_mid_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/init_aff/initialization.mat, 0 ] --initialize-transforms-per-stage 0 --interpolation Linear --output transform --transform Affine[ 0.1 ] --metric Mattes[ /home/sahad3/.cache/templateflow/tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_res-02_desc-fMRIPrep_boldref.nii.gz, /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_mid_wf/bold_bold_trans_wf/bold_reference_wf/gen_ref/ref_bold.nii.gz, 1, 64, Random, 0.2 ] --convergence [ 200, 1e-09, 10 ] --smoothing-sigmas 2.0mm --shrink-factors 2 --use-estimate-learning-rate-once 1 --use-histogram-matching 1 --winsorize-image-intensities [ 0.05, 0.98 ] --write-composite-transform 0 190731-15:34:19,101 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.init_aff". 190731-15:34:19,269 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_mid_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.norm". 190731-15:34:19,961 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_mid_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.map_brainmask" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_mid_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/map_brainmask". 190731-15:34:19,964 nipype.workflow INFO: [Node] Running "map_brainmask" ("niworkflows.interfaces.fixes.FixHeaderApplyTransforms"), a CommandLine Interface with command: antsApplyTransforms --default-value 0 --float 1 --input /home/sahad3/.cache/templateflow/tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_res-02_desc-brain_mask.nii.gz --interpolation MultiLabel --output tpl-MNI152NLin2009cAsym_res-02_desc-brain_mask_trans.nii.gz --reference-image /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_mid_wf/bold_bold_trans_wf/bold_reference_wf/gen_ref/ref_bold.nii.gz --transform [ /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_mid_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/norm/transform0GenericAffine.mat, 1 ] 190731-15:34:19,966 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.norm" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-02..func..sub-23649_ses-02_task-rest_echo-4_bold.nii.gz/norm". 190731-15:34:19,967 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.init_aff" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-02..func..sub-23649_ses-02_task-rest_echo-3_bold.nii.gz/init_aff". 190731-15:34:19,970 nipype.workflow INFO: [Node] Running "init_aff" ("niworkflows.interfaces.ants.AI"), a CommandLine Interface with command: antsAI -c [10,0.000001,10] -d 3 -x /home/sahad3/.cache/templateflow/tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_res-02_desc-brain_mask.nii.gz -m Mattes[/home/sahad3/.cache/templateflow/tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_res-02_desc-fMRIPrep_boldref.nii.gz,/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/bold_bold_trans_wf/bold_reference_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-02..func..sub-23649_ses-02_task-rest_echo-3_bold.nii.gz/gen_ref/ref_bold.nii.gz,32,Regular,0.200000] -o initialization.mat -p 0 -s [20.000000,0.120000] -t Affine[0.100000] -v 1 190731-15:34:19,971 nipype.workflow INFO: [Node] Running "norm" ("niworkflows.interfaces.fixes.FixHeaderRegistration"), a CommandLine Interface with command: antsRegistration --collapse-output-transforms 1 --dimensionality 3 --float 1 --initial-moving-transform [ /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-02..func..sub-23649_ses-02_task-rest_echo-4_bold.nii.gz/init_aff/initialization.mat, 0 ] --initialize-transforms-per-stage 0 --interpolation Linear --output transform --transform Affine[ 0.1 ] --metric Mattes[ /home/sahad3/.cache/templateflow/tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_res-02_desc-fMRIPrep_boldref.nii.gz, /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/bold_bold_trans_wf/bold_reference_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-02..func..sub-23649_ses-02_task-rest_echo-4_bold.nii.gz/gen_ref/ref_bold.nii.gz, 1, 64, Random, 0.2 ] --convergence [ 200, 1e-09, 10 ] --smoothing-sigmas 2.0mm --shrink-factors 2 --use-estimate-learning-rate-once 1 --use-histogram-matching 1 --winsorize-image-intensities [ 0.05, 0.98 ] --write-composite-transform 0 190731-15:34:21,946 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.norm". 190731-15:34:22,142 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_mid_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.map_brainmask". 190731-15:34:23,488 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.bold_bold_trans_wf.merge". 190731-15:34:23,964 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_mid_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.pre_mask_dilate" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_mid_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/pre_mask_dilate". 190731-15:34:23,966 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.map_brainmask" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-02..func..sub-23649_ses-02_task-rest_echo-4_bold.nii.gz/map_brainmask". 190731-15:34:23,966 nipype.workflow INFO: [Node] Running "pre_mask_dilate" ("nipype.interfaces.fsl.maths.DilateImage"), a CommandLine Interface with command: fslmaths -dt char /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_mid_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/map_brainmask/tpl-MNI152NLin2009cAsym_res-02_desc-brain_mask_trans.nii.gz -kernel sphere 3.0000 -dilF /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_mid_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/pre_mask_dilate/tpl-MNI152NLin2009cAsym_res-02_desc-brain_mask_trans_dil.nii.gz 190731-15:34:23,969 nipype.workflow INFO: [Node] Running "map_brainmask" ("niworkflows.interfaces.fixes.FixHeaderApplyTransforms"), a CommandLine Interface with command: antsApplyTransforms --default-value 0 --float 1 --input /home/sahad3/.cache/templateflow/tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_res-02_desc-brain_mask.nii.gz --interpolation MultiLabel --output tpl-MNI152NLin2009cAsym_res-02_desc-brain_mask_trans.nii.gz --reference-image /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/bold_bold_trans_wf/bold_reference_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-02..func..sub-23649_ses-02_task-rest_echo-4_bold.nii.gz/gen_ref/ref_bold.nii.gz --transform [ /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-02..func..sub-23649_ses-02_task-rest_echo-4_bold.nii.gz/norm/transform0GenericAffine.mat, 1 ] 190731-15:34:23,970 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_mid_run_1_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.norm" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_1_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/norm". 190731-15:34:23,974 nipype.workflow INFO: [Node] Running "norm" ("niworkflows.interfaces.fixes.FixHeaderRegistration"), a CommandLine Interface with command: antsRegistration --collapse-output-transforms 1 --dimensionality 3 --float 1 --initial-moving-transform [ /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_1_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/init_aff/initialization.mat, 0 ] --initialize-transforms-per-stage 0 --interpolation Linear --output transform --transform Affine[ 0.1 ] --metric Mattes[ /home/sahad3/.cache/templateflow/tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_res-02_desc-fMRIPrep_boldref.nii.gz, /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_1_wf/bold_reference_wf/gen_ref/ref_bold.nii.gz, 1, 64, Random, 0.2 ] --convergence [ 200, 1e-09, 10 ] --smoothing-sigmas 2.0mm --shrink-factors 2 --use-estimate-learning-rate-once 1 --use-histogram-matching 1 --winsorize-image-intensities [ 0.05, 0.98 ] --write-composite-transform 0 190731-15:34:24,237 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_mid_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.pre_mask_dilate". 190731-15:34:24,914 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.init_aff". 190731-15:34:25,334 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_mid_run_1_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.norm". 190731-15:34:25,617 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.bold_bold_trans_wf.merge". 190731-15:34:25,863 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.map_brainmask". 190731-15:34:25,983 nipype.interface WARNING: q-forms of reference and mask are substantially different 190731-15:34:26,477 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.norm" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-02..func..sub-23649_ses-02_task-rest_echo-3_bold.nii.gz/norm". 190731-15:34:26,482 nipype.workflow INFO: [Node] Running "norm" ("niworkflows.interfaces.fixes.FixHeaderRegistration"), a CommandLine Interface with command: antsRegistration --collapse-output-transforms 1 --dimensionality 3 --float 1 --initial-moving-transform [ /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-02..func..sub-23649_ses-02_task-rest_echo-3_bold.nii.gz/init_aff/initialization.mat, 0 ] --initialize-transforms-per-stage 0 --interpolation Linear --output transform --transform Affine[ 0.1 ] --metric Mattes[ /home/sahad3/.cache/templateflow/tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_res-02_desc-fMRIPrep_boldref.nii.gz, /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/bold_bold_trans_wf/bold_reference_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-02..func..sub-23649_ses-02_task-rest_echo-3_bold.nii.gz/gen_ref/ref_bold.nii.gz, 1, 64, Random, 0.2 ] --convergence [ 200, 1e-09, 10 ] --smoothing-sigmas 2.0mm --shrink-factors 2 --use-estimate-learning-rate-once 1 --use-histogram-matching 1 --winsorize-image-intensities [ 0.05, 0.98 ] --write-composite-transform 0 190731-15:34:27,400 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.norm". 190731-15:34:37,716 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.skullstrip_bold_wf.skullstrip_first_pass" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-02..func..sub-23649_ses-02_task-rest_echo-2_bold.nii.gz/skullstrip_first_pass". 190731-15:34:37,717 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.bold_bold_trans_wf.bold_reference_wf.validate" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/bold_bold_trans_wf/bold_reference_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-02..func..sub-23649_ses-02_task-rest_echo-2_bold.nii.gz/validate". 190731-15:34:37,719 nipype.workflow INFO: [Node] Running "skullstrip_first_pass" ("nipype.interfaces.fsl.preprocess.BET"), a CommandLine Interface with command: bet /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/bold_bold_trans_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-02..func..sub-23649_ses-02_task-rest_echo-2_bold.nii.gz/merge/vol0000_xform-00000_merged.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-02..func..sub-23649_ses-02_task-rest_echo-2_bold.nii.gz/skullstrip_first_pass/vol0000_xform-00000_merged_brain.nii.gz -f 0.20 -m 190731-15:34:37,719 nipype.workflow INFO: [Node] Running "validate" ("niworkflows.interfaces.images.ValidateImage") 190731-15:34:37,729 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_mid_run_1_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.map_brainmask" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_1_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/map_brainmask". 190731-15:34:37,732 nipype.workflow INFO: [Node] Running "map_brainmask" ("niworkflows.interfaces.fixes.FixHeaderApplyTransforms"), a CommandLine Interface with command: antsApplyTransforms --default-value 0 --float 1 --input /home/sahad3/.cache/templateflow/tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_res-02_desc-brain_mask.nii.gz --interpolation MultiLabel --output tpl-MNI152NLin2009cAsym_res-02_desc-brain_mask_trans.nii.gz --reference-image /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_1_wf/bold_reference_wf/gen_ref/ref_bold.nii.gz --transform [ /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_1_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/norm/transform0GenericAffine.mat, 1 ] 190731-15:34:38,220 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_mid_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.n4_correct" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_mid_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/n4_correct". 190731-15:34:38,222 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.pre_mask_dilate" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-02..func..sub-23649_ses-02_task-rest_echo-4_bold.nii.gz/pre_mask_dilate". 190731-15:34:38,222 nipype.workflow INFO: [Node] Running "n4_correct" ("nipype.interfaces.ants.segmentation.N4BiasFieldCorrection"), a CommandLine Interface with command: N4BiasFieldCorrection --bspline-fitting [ 200 ] -d 3 --input-image /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_mid_wf/bold_bold_trans_wf/bold_reference_wf/gen_ref/ref_bold.nii.gz --mask-image /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_mid_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/check_hdr/tpl-MNI152NLin2009cAsym_res-02_desc-brain_mask_trans_dil_hdr.nii.gz --output ref_bold_corrected.nii.gz 190731-15:34:38,224 nipype.workflow INFO: [Node] Running "pre_mask_dilate" ("nipype.interfaces.fsl.maths.DilateImage"), a CommandLine Interface with command: fslmaths -dt char /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-02..func..sub-23649_ses-02_task-rest_echo-4_bold.nii.gz/map_brainmask/tpl-MNI152NLin2009cAsym_res-02_desc-brain_mask_trans.nii.gz -kernel sphere 3.0000 -dilF /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-02..func..sub-23649_ses-02_task-rest_echo-4_bold.nii.gz/pre_mask_dilate/tpl-MNI152NLin2009cAsym_res-02_desc-brain_mask_trans_dil.nii.gz 190731-15:34:38,225 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.map_brainmask" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-02..func..sub-23649_ses-02_task-rest_echo-3_bold.nii.gz/map_brainmask". 190731-15:34:38,227 nipype.workflow INFO: [Node] Running "map_brainmask" ("niworkflows.interfaces.fixes.FixHeaderApplyTransforms"), a CommandLine Interface with command: antsApplyTransforms --default-value 0 --float 1 --input /home/sahad3/.cache/templateflow/tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_res-02_desc-brain_mask.nii.gz --interpolation MultiLabel --output tpl-MNI152NLin2009cAsym_res-02_desc-brain_mask_trans.nii.gz --reference-image /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/bold_bold_trans_wf/bold_reference_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-02..func..sub-23649_ses-02_task-rest_echo-3_bold.nii.gz/gen_ref/ref_bold.nii.gz --transform [ /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-02..func..sub-23649_ses-02_task-rest_echo-3_bold.nii.gz/norm/transform0GenericAffine.mat, 1 ] 190731-15:34:38,397 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.pre_mask_dilate". 190731-15:34:39,573 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.skullstrip_bold_wf.skullstrip_first_pass". 190731-15:34:39,811 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_mid_run_1_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.map_brainmask". 190731-15:34:39,948 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.map_brainmask". 190731-15:34:40,651 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_mid_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.n4_correct". 190731-15:34:40,665 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.bold_bold_trans_wf.bold_reference_wf.validate". 190731-15:34:48,773 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.skullstrip_bold_wf.skullstrip_first_pass" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-02..func..sub-23649_ses-02_task-rest_echo-1_bold.nii.gz/skullstrip_first_pass". 190731-15:34:48,775 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.bold_bold_trans_wf.bold_reference_wf.validate" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/bold_bold_trans_wf/bold_reference_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-02..func..sub-23649_ses-02_task-rest_echo-1_bold.nii.gz/validate". 190731-15:34:48,777 nipype.workflow INFO: [Node] Running "skullstrip_first_pass" ("nipype.interfaces.fsl.preprocess.BET"), a CommandLine Interface with command: bet /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/bold_bold_trans_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-02..func..sub-23649_ses-02_task-rest_echo-1_bold.nii.gz/merge/vol0000_xform-00000_merged.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-02..func..sub-23649_ses-02_task-rest_echo-1_bold.nii.gz/skullstrip_first_pass/vol0000_xform-00000_merged_brain.nii.gz -f 0.20 -m 190731-15:34:48,777 nipype.workflow INFO: [Node] Running "validate" ("niworkflows.interfaces.images.ValidateImage") 190731-15:34:48,777 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_mid_run_2_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_opposite_wf.enhance_and_skullstrip_bold_wf.init_aff" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_2_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/enhance_and_skullstrip_bold_wf/init_aff". 190731-15:34:48,780 nipype.workflow INFO: [Node] Running "init_aff" ("niworkflows.interfaces.ants.AI"), a CommandLine Interface with command: antsAI -c [10,0.000001,10] -d 3 -x /home/sahad3/.cache/templateflow/tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_res-02_desc-brain_mask.nii.gz -m Mattes[/home/sahad3/.cache/templateflow/tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_res-02_desc-fMRIPrep_boldref.nii.gz,/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_2_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/merge/template.nii.gz,32,Regular,0.200000] -o initialization.mat -p 0 -s [20.000000,0.120000] -t Affine[0.100000] -v 1 190731-15:34:49,942 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_mid_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_pass" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_mid_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_pass". 190731-15:34:49,946 nipype.workflow INFO: [Node] Running "skullstrip_first_pass" ("nipype.interfaces.fsl.preprocess.BET"), a CommandLine Interface with command: bet /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_mid_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/n4_correct/ref_bold_corrected.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_mid_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_pass/ref_bold_corrected_brain.nii.gz -f 0.20 -m 190731-15:34:49,954 nipype.interface WARNING: q-forms of reference and mask are substantially different 190731-15:34:50,461 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.pre_mask_dilate" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-02..func..sub-23649_ses-02_task-rest_echo-3_bold.nii.gz/pre_mask_dilate". 190731-15:34:50,463 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.skullstrip_bold_wf.skullstrip_second_pass" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-02..func..sub-23649_ses-02_task-rest_echo-2_bold.nii.gz/skullstrip_second_pass". 190731-15:34:50,464 nipype.workflow INFO: [Node] Running "pre_mask_dilate" ("nipype.interfaces.fsl.maths.DilateImage"), a CommandLine Interface with command: fslmaths -dt char /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-02..func..sub-23649_ses-02_task-rest_echo-3_bold.nii.gz/map_brainmask/tpl-MNI152NLin2009cAsym_res-02_desc-brain_mask_trans.nii.gz -kernel sphere 3.0000 -dilF /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-02..func..sub-23649_ses-02_task-rest_echo-3_bold.nii.gz/pre_mask_dilate/tpl-MNI152NLin2009cAsym_res-02_desc-brain_mask_trans_dil.nii.gz 190731-15:34:50,464 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.bold_bold_trans_wf.bold_reference_wf.gen_ref" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/bold_bold_trans_wf/bold_reference_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-02..func..sub-23649_ses-02_task-rest_echo-2_bold.nii.gz/gen_ref". 190731-15:34:50,466 nipype.workflow INFO: [Node] Running "skullstrip_second_pass" ("nipype.interfaces.afni.preprocess.Automask"), a CommandLine Interface with command: 3dAutomask -apply_prefix vol0000_xform-00000_merged_brain_masked.nii.gz -dilate 1 -prefix vol0000_xform-00000_merged_brain_mask.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-02..func..sub-23649_ses-02_task-rest_echo-2_bold.nii.gz/skullstrip_second_pass/vol0000_xform-00000_merged_brain.nii.gz 190731-15:34:50,466 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_mid_run_1_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.pre_mask_dilate" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_1_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/pre_mask_dilate". 190731-15:34:50,467 nipype.workflow INFO: [Node] Running "gen_ref" ("niworkflows.interfaces.registration.EstimateReferenceImage") 190731-15:34:50,468 nipype.workflow INFO: [Node] Running "pre_mask_dilate" ("nipype.interfaces.fsl.maths.DilateImage"), a CommandLine Interface with command: fslmaths -dt char /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_1_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/map_brainmask/tpl-MNI152NLin2009cAsym_res-02_desc-brain_mask_trans.nii.gz -kernel sphere 3.0000 -dilF /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_1_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/pre_mask_dilate/tpl-MNI152NLin2009cAsym_res-02_desc-brain_mask_trans_dil.nii.gz 190731-15:34:50,629 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.skullstrip_bold_wf.skullstrip_second_pass". 190731-15:34:50,677 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.skullstrip_bold_wf.skullstrip_first_pass". 190731-15:34:50,765 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_mid_run_1_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.pre_mask_dilate". 190731-15:34:50,769 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.pre_mask_dilate". 190731-15:34:50,859 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.bold_bold_trans_wf.bold_reference_wf.gen_ref". 190731-15:34:51,301 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.n4_correct" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-02..func..sub-23649_ses-02_task-rest_echo-4_bold.nii.gz/n4_correct". 190731-15:34:51,304 nipype.workflow INFO: [Node] Running "n4_correct" ("nipype.interfaces.ants.segmentation.N4BiasFieldCorrection"), a CommandLine Interface with command: N4BiasFieldCorrection --bspline-fitting [ 200 ] -d 3 --input-image /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/bold_bold_trans_wf/bold_reference_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-02..func..sub-23649_ses-02_task-rest_echo-4_bold.nii.gz/gen_ref/ref_bold.nii.gz --mask-image /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-02..func..sub-23649_ses-02_task-rest_echo-4_bold.nii.gz/check_hdr/tpl-MNI152NLin2009cAsym_res-02_desc-brain_mask_trans_dil_hdr.nii.gz --output ref_bold_corrected.nii.gz 190731-15:34:51,313 nipype.interface WARNING: q-forms of reference and mask are substantially different 190731-15:34:51,817 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.skullstrip_bold_wf.combine_masks" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-02..func..sub-23649_ses-02_task-rest_echo-2_bold.nii.gz/combine_masks". 190731-15:34:51,819 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.skullstrip_bold_wf.skullstrip_second_pass" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-02..func..sub-23649_ses-02_task-rest_echo-1_bold.nii.gz/skullstrip_second_pass". 190731-15:34:51,820 nipype.workflow INFO: [Node] Running "combine_masks" ("nipype.interfaces.fsl.maths.BinaryMaths"), a CommandLine Interface with command: fslmaths /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-02..func..sub-23649_ses-02_task-rest_echo-2_bold.nii.gz/skullstrip_first_pass/vol0000_xform-00000_merged_brain_mask.nii.gz -mul /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-02..func..sub-23649_ses-02_task-rest_echo-2_bold.nii.gz/skullstrip_second_pass/vol0000_xform-00000_merged_brain_mask.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-02..func..sub-23649_ses-02_task-rest_echo-2_bold.nii.gz/combine_masks/vol0000_xform-00000_merged_brain_mask_maths.nii.gz 190731-15:34:51,822 nipype.workflow INFO: [Node] Running "skullstrip_second_pass" ("nipype.interfaces.afni.preprocess.Automask"), a CommandLine Interface with command: 3dAutomask -apply_prefix vol0000_xform-00000_merged_brain_masked.nii.gz -dilate 1 -prefix vol0000_xform-00000_merged_brain_mask.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-02..func..sub-23649_ses-02_task-rest_echo-1_bold.nii.gz/skullstrip_second_pass/vol0000_xform-00000_merged_brain.nii.gz 190731-15:34:51,847 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.bold_bold_trans_wf.bold_reference_wf.validate". 190731-15:34:51,934 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_mid_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_pass". 190731-15:34:51,962 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.skullstrip_bold_wf.combine_masks". 190731-15:34:51,987 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.skullstrip_bold_wf.skullstrip_second_pass". 190731-15:34:53,353 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_mid_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_dilate" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_mid_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_dilate". 190731-15:34:53,355 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.n4_correct" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-02..func..sub-23649_ses-02_task-rest_echo-3_bold.nii.gz/n4_correct". 190731-15:34:53,356 nipype.workflow INFO: [Node] Running "skullstrip_first_dilate" ("nipype.interfaces.fsl.maths.DilateImage"), a CommandLine Interface with command: fslmaths -dt char /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_mid_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_pass/ref_bold_corrected_brain_mask.nii.gz -kernel sphere 6.0000 -dilF /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_mid_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_dilate/ref_bold_corrected_brain_mask_dil.nii.gz 190731-15:34:53,357 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.skullstrip_bold_wf.mask_reportlet" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-02..func..sub-23649_ses-02_task-rest_echo-2_bold.nii.gz/mask_reportlet". 190731-15:34:53,357 nipype.workflow INFO: [Node] Running "n4_correct" ("nipype.interfaces.ants.segmentation.N4BiasFieldCorrection"), a CommandLine Interface with command: N4BiasFieldCorrection --bspline-fitting [ 200 ] -d 3 --input-image /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/bold_bold_trans_wf/bold_reference_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-02..func..sub-23649_ses-02_task-rest_echo-3_bold.nii.gz/gen_ref/ref_bold.nii.gz --mask-image /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-02..func..sub-23649_ses-02_task-rest_echo-3_bold.nii.gz/check_hdr/tpl-MNI152NLin2009cAsym_res-02_desc-brain_mask_trans_dil_hdr.nii.gz --output ref_bold_corrected.nii.gz 190731-15:34:53,358 nipype.workflow INFO: [Node] Running "mask_reportlet" ("niworkflows.interfaces.masks.SimpleShowMaskRPT") 190731-15:34:53,359 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.skullstrip_bold_wf.apply_mask" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-02..func..sub-23649_ses-02_task-rest_echo-2_bold.nii.gz/apply_mask". 190731-15:34:53,362 nipype.workflow INFO: [Node] Running "apply_mask" ("nipype.interfaces.fsl.maths.ApplyMask"), a CommandLine Interface with command: fslmaths /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/bold_bold_trans_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-02..func..sub-23649_ses-02_task-rest_echo-2_bold.nii.gz/merge/vol0000_xform-00000_merged.nii.gz -mas /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-02..func..sub-23649_ses-02_task-rest_echo-2_bold.nii.gz/combine_masks/vol0000_xform-00000_merged_brain_mask_maths.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-02..func..sub-23649_ses-02_task-rest_echo-2_bold.nii.gz/apply_mask/vol0000_xform-00000_merged_masked.nii.gz 190731-15:34:53,517 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.n4_correct". 190731-15:34:53,808 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_mid_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_dilate". 190731-15:34:53,910 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.skullstrip_bold_wf.combine_masks" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-02..func..sub-23649_ses-02_task-rest_echo-1_bold.nii.gz/combine_masks". 190731-15:34:53,911 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.bold_bold_trans_wf.bold_reference_wf.gen_ref" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/bold_bold_trans_wf/bold_reference_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-02..func..sub-23649_ses-02_task-rest_echo-1_bold.nii.gz/gen_ref". 190731-15:34:53,913 nipype.workflow INFO: [Node] Running "gen_ref" ("niworkflows.interfaces.registration.EstimateReferenceImage") 190731-15:34:53,913 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_mid_run_1_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.n4_correct" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_1_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/n4_correct". 190731-15:34:53,914 nipype.workflow INFO: [Node] Running "combine_masks" ("nipype.interfaces.fsl.maths.BinaryMaths"), a CommandLine Interface with command: fslmaths /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-02..func..sub-23649_ses-02_task-rest_echo-1_bold.nii.gz/skullstrip_first_pass/vol0000_xform-00000_merged_brain_mask.nii.gz -mul /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-02..func..sub-23649_ses-02_task-rest_echo-1_bold.nii.gz/skullstrip_second_pass/vol0000_xform-00000_merged_brain_mask.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-02..func..sub-23649_ses-02_task-rest_echo-1_bold.nii.gz/combine_masks/vol0000_xform-00000_merged_brain_mask_maths.nii.gz 190731-15:34:53,916 nipype.workflow INFO: [Node] Running "n4_correct" ("nipype.interfaces.ants.segmentation.N4BiasFieldCorrection"), a CommandLine Interface with command: N4BiasFieldCorrection --bspline-fitting [ 200 ] -d 3 --input-image /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_1_wf/bold_reference_wf/gen_ref/ref_bold.nii.gz --mask-image /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_1_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/check_hdr/tpl-MNI152NLin2009cAsym_res-02_desc-brain_mask_trans_dil_hdr.nii.gz --output ref_bold_corrected.nii.gz 190731-15:34:54,60 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_mid_run_2_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_opposite_wf.enhance_and_skullstrip_bold_wf.init_aff". 190731-15:34:54,61 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.skullstrip_bold_wf.combine_masks". 190731-15:34:54,277 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.bold_bold_trans_wf.bold_reference_wf.gen_ref". 190731-15:34:55,362 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_mid_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_mask" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_mid_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_mask". 190731-15:34:55,365 nipype.workflow INFO: [Node] Running "skullstrip_first_mask" ("nipype.interfaces.fsl.maths.ApplyMask"), a CommandLine Interface with command: fslmaths /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_mid_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_pass/ref_bold_corrected_brain.nii.gz -mas /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_mid_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_dilate/ref_bold_corrected_brain_mask_dil.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_mid_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_mask/ref_bold_corrected_brain_masked.nii.gz 190731-15:34:55,489 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.n4_correct". 190731-15:34:55,521 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_mid_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_mask". 190731-15:34:55,947 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_pass" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-02..func..sub-23649_ses-02_task-rest_echo-4_bold.nii.gz/skullstrip_first_pass". 190731-15:34:55,950 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.init_aff" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-02..func..sub-23649_ses-02_task-rest_echo-2_bold.nii.gz/init_aff". 190731-15:34:55,950 nipype.workflow INFO: [Node] Running "skullstrip_first_pass" ("nipype.interfaces.fsl.preprocess.BET"), a CommandLine Interface with command: bet /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-02..func..sub-23649_ses-02_task-rest_echo-4_bold.nii.gz/n4_correct/ref_bold_corrected.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-02..func..sub-23649_ses-02_task-rest_echo-4_bold.nii.gz/skullstrip_first_pass/ref_bold_corrected_brain.nii.gz -f 0.20 -m 190731-15:34:55,951 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.skullstrip_bold_wf.mask_reportlet" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-02..func..sub-23649_ses-02_task-rest_echo-1_bold.nii.gz/mask_reportlet". 190731-15:34:55,953 nipype.workflow INFO: [Node] Running "init_aff" ("niworkflows.interfaces.ants.AI"), a CommandLine Interface with command: antsAI -c [10,0.000001,10] -d 3 -x /home/sahad3/.cache/templateflow/tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_res-02_desc-brain_mask.nii.gz -m Mattes[/home/sahad3/.cache/templateflow/tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_res-02_desc-fMRIPrep_boldref.nii.gz,/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/bold_bold_trans_wf/bold_reference_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-02..func..sub-23649_ses-02_task-rest_echo-2_bold.nii.gz/gen_ref/ref_bold.nii.gz,32,Regular,0.200000] -o initialization.mat -p 0 -s [20.000000,0.120000] -t Affine[0.100000] -v 1 190731-15:34:55,954 nipype.workflow INFO: [Node] Running "mask_reportlet" ("niworkflows.interfaces.masks.SimpleShowMaskRPT") 190731-15:34:55,955 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.skullstrip_bold_wf.apply_mask" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-02..func..sub-23649_ses-02_task-rest_echo-1_bold.nii.gz/apply_mask". 190731-15:34:55,957 nipype.workflow INFO: [Node] Running "apply_mask" ("nipype.interfaces.fsl.maths.ApplyMask"), a CommandLine Interface with command: fslmaths /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/bold_bold_trans_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-02..func..sub-23649_ses-02_task-rest_echo-1_bold.nii.gz/merge/vol0000_xform-00000_merged.nii.gz -mas /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-02..func..sub-23649_ses-02_task-rest_echo-1_bold.nii.gz/combine_masks/vol0000_xform-00000_merged_brain_mask_maths.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-02..func..sub-23649_ses-02_task-rest_echo-1_bold.nii.gz/apply_mask/vol0000_xform-00000_merged_masked.nii.gz 190731-15:34:56,460 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_mid_run_1_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.n4_correct". 190731-15:34:57,359 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_mid_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.unifize" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_mid_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/unifize". 190731-15:34:57,363 nipype.workflow INFO: [Node] Running "unifize" ("nipype.interfaces.afni.utils.Unifize"), a CommandLine Interface with command: 3dUnifize -clfrac 0.2 -rbt 18.3 65.0 90.0 -prefix uni.nii.gz -T2 -input /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_mid_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/unifize/ref_bold_corrected_brain_masked.nii.gz 190731-15:34:57,396 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.skullstrip_bold_wf.apply_mask". 190731-15:34:57,940 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_pass" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-02..func..sub-23649_ses-02_task-rest_echo-3_bold.nii.gz/skullstrip_first_pass". 190731-15:34:57,943 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_mid_run_1_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_pass" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_1_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_pass". 190731-15:34:57,944 nipype.workflow INFO: [Node] Running "skullstrip_first_pass" ("nipype.interfaces.fsl.preprocess.BET"), a CommandLine Interface with command: bet /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-02..func..sub-23649_ses-02_task-rest_echo-3_bold.nii.gz/n4_correct/ref_bold_corrected.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-02..func..sub-23649_ses-02_task-rest_echo-3_bold.nii.gz/skullstrip_first_pass/ref_bold_corrected_brain.nii.gz -f 0.20 -m 190731-15:34:57,945 nipype.workflow INFO: [Node] Running "skullstrip_first_pass" ("nipype.interfaces.fsl.preprocess.BET"), a CommandLine Interface with command: bet /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_1_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/n4_correct/ref_bold_corrected.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_1_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_pass/ref_bold_corrected_brain.nii.gz -f 0.20 -m 190731-15:34:57,954 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_pass". 190731-15:34:58,713 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.skullstrip_bold_wf.mask_reportlet". 190731-15:34:58,904 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_mid_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.unifize". 190731-15:34:59,354 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_dilate" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-02..func..sub-23649_ses-02_task-rest_echo-4_bold.nii.gz/skullstrip_first_dilate". 190731-15:34:59,358 nipype.workflow INFO: [Node] Running "skullstrip_first_dilate" ("nipype.interfaces.fsl.maths.DilateImage"), a CommandLine Interface with command: fslmaths -dt char /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-02..func..sub-23649_ses-02_task-rest_echo-4_bold.nii.gz/skullstrip_first_pass/ref_bold_corrected_brain_mask.nii.gz -kernel sphere 6.0000 -dilF /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-02..func..sub-23649_ses-02_task-rest_echo-4_bold.nii.gz/skullstrip_first_dilate/ref_bold_corrected_brain_mask_dil.nii.gz 190731-15:34:59,765 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_dilate". 190731-15:34:59,881 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_pass". 190731-15:34:59,884 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.skullstrip_bold_wf.apply_mask". 190731-15:35:00,524 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_mid_run_1_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_pass". 190731-15:35:01,286 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.init_aff". 190731-15:35:01,308 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_mid_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.fixhdr_unifize" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_mid_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/fixhdr_unifize". 190731-15:35:01,309 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_mask" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-02..func..sub-23649_ses-02_task-rest_echo-4_bold.nii.gz/skullstrip_first_mask". 190731-15:35:01,310 nipype.workflow INFO: [Node] Running "fixhdr_unifize" ("niworkflows.interfaces.utils.CopyXForm") 190731-15:35:01,312 nipype.workflow INFO: [Node] Running "skullstrip_first_mask" ("nipype.interfaces.fsl.maths.ApplyMask"), a CommandLine Interface with command: fslmaths /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-02..func..sub-23649_ses-02_task-rest_echo-4_bold.nii.gz/skullstrip_first_pass/ref_bold_corrected_brain.nii.gz -mas /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-02..func..sub-23649_ses-02_task-rest_echo-4_bold.nii.gz/skullstrip_first_dilate/ref_bold_corrected_brain_mask_dil.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-02..func..sub-23649_ses-02_task-rest_echo-4_bold.nii.gz/skullstrip_first_mask/ref_bold_corrected_brain_masked.nii.gz 190731-15:35:01,312 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_dilate" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-02..func..sub-23649_ses-02_task-rest_echo-3_bold.nii.gz/skullstrip_first_dilate". 190731-15:35:01,314 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.join_echos" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/join_echos". 190731-15:35:01,315 nipype.workflow INFO: [Node] Running "skullstrip_first_dilate" ("nipype.interfaces.fsl.maths.DilateImage"), a CommandLine Interface with command: fslmaths -dt char /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-02..func..sub-23649_ses-02_task-rest_echo-3_bold.nii.gz/skullstrip_first_pass/ref_bold_corrected_brain_mask.nii.gz -kernel sphere 6.0000 -dilF /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-02..func..sub-23649_ses-02_task-rest_echo-3_bold.nii.gz/skullstrip_first_dilate/ref_bold_corrected_brain_mask_dil.nii.gz 190731-15:35:01,315 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_mid_run_1_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_dilate" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_1_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_dilate". 190731-15:35:01,316 nipype.workflow INFO: [Node] Running "join_echos" ("nipype.interfaces.utility.base.IdentityInterface") 190731-15:35:01,318 nipype.workflow INFO: [Node] Running "skullstrip_first_dilate" ("nipype.interfaces.fsl.maths.DilateImage"), a CommandLine Interface with command: fslmaths -dt char /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_1_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_pass/ref_bold_corrected_brain_mask.nii.gz -kernel sphere 6.0000 -dilF /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_1_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_dilate/ref_bold_corrected_brain_mask_dil.nii.gz 190731-15:35:01,319 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.join_echos". 190731-15:35:01,359 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_mid_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.fixhdr_unifize". 190731-15:35:01,456 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_mask". 190731-15:35:01,463 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.skullstrip_bold_wf.mask_reportlet". 190731-15:35:01,656 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_dilate". 190731-15:35:01,743 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_mid_run_1_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_dilate". 190731-15:35:03,297 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_mid_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.skullstrip_second_pass" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_mid_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_second_pass". 190731-15:35:03,299 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.unifize" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-02..func..sub-23649_ses-02_task-rest_echo-4_bold.nii.gz/unifize". 190731-15:35:03,300 nipype.workflow INFO: [Node] Running "skullstrip_second_pass" ("nipype.interfaces.afni.preprocess.Automask"), a CommandLine Interface with command: 3dAutomask -apply_prefix uni_xform_masked.nii.gz -dilate 1 -prefix uni_xform_mask.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_mid_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_second_pass/uni_xform.nii.gz 190731-15:35:03,302 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_mask" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-02..func..sub-23649_ses-02_task-rest_echo-3_bold.nii.gz/skullstrip_first_mask". 190731-15:35:03,302 nipype.workflow INFO: [Node] Running "unifize" ("nipype.interfaces.afni.utils.Unifize"), a CommandLine Interface with command: 3dUnifize -clfrac 0.2 -rbt 18.3 65.0 90.0 -prefix uni.nii.gz -T2 -input /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-02..func..sub-23649_ses-02_task-rest_echo-4_bold.nii.gz/unifize/ref_bold_corrected_brain_masked.nii.gz 190731-15:35:03,304 nipype.workflow INFO: [Node] Running "skullstrip_first_mask" ("nipype.interfaces.fsl.maths.ApplyMask"), a CommandLine Interface with command: fslmaths /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-02..func..sub-23649_ses-02_task-rest_echo-3_bold.nii.gz/skullstrip_first_pass/ref_bold_corrected_brain.nii.gz -mas /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-02..func..sub-23649_ses-02_task-rest_echo-3_bold.nii.gz/skullstrip_first_dilate/ref_bold_corrected_brain_mask_dil.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-02..func..sub-23649_ses-02_task-rest_echo-3_bold.nii.gz/skullstrip_first_mask/ref_bold_corrected_brain_masked.nii.gz 190731-15:35:03,309 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.norm" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-02..func..sub-23649_ses-02_task-rest_echo-2_bold.nii.gz/norm". 190731-15:35:03,310 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.bold_t2smap_wf.t2smap_node" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/bold_t2smap_wf/t2smap_node". 190731-15:35:03,312 nipype.workflow INFO: [Node] Running "t2smap_node" ("fmriprep.interfaces.multiecho.T2SMap"), a CommandLine Interface with command: t2smap -d /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-02..func..sub-23649_ses-02_task-rest_echo-1_bold.nii.gz/apply_mask/vol0000_xform-00000_merged_masked.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-02..func..sub-23649_ses-02_task-rest_echo-2_bold.nii.gz/apply_mask/vol0000_xform-00000_merged_masked.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-02..func..sub-23649_ses-02_task-rest_echo-3_bold.nii.gz/apply_mask/vol0000_xform-00000_merged_masked.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-02..func..sub-23649_ses-02_task-rest_echo-4_bold.nii.gz/apply_mask/vol0000_xform-00000_merged_masked.nii.gz -e 15.2 28.799999999999997 42.4 56.0 190731-15:35:03,313 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.init_aff" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-02..func..sub-23649_ses-02_task-rest_echo-1_bold.nii.gz/init_aff". 190731-15:35:03,315 nipype.workflow INFO: [Node] Running "init_aff" ("niworkflows.interfaces.ants.AI"), a CommandLine Interface with command: antsAI -c [10,0.000001,10] -d 3 -x /home/sahad3/.cache/templateflow/tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_res-02_desc-brain_mask.nii.gz -m Mattes[/home/sahad3/.cache/templateflow/tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_res-02_desc-fMRIPrep_boldref.nii.gz,/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/bold_bold_trans_wf/bold_reference_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-02..func..sub-23649_ses-02_task-rest_echo-1_bold.nii.gz/gen_ref/ref_bold.nii.gz,32,Regular,0.200000] -o initialization.mat -p 0 -s [20.000000,0.120000] -t Affine[0.100000] -v 1 190731-15:35:03,315 nipype.workflow INFO: [Node] Running "norm" ("niworkflows.interfaces.fixes.FixHeaderRegistration"), a CommandLine Interface with command: antsRegistration --collapse-output-transforms 1 --dimensionality 3 --float 1 --initial-moving-transform [ /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-02..func..sub-23649_ses-02_task-rest_echo-2_bold.nii.gz/init_aff/initialization.mat, 0 ] --initialize-transforms-per-stage 0 --interpolation Linear --output transform --transform Affine[ 0.1 ] --metric Mattes[ /home/sahad3/.cache/templateflow/tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_res-02_desc-fMRIPrep_boldref.nii.gz, /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/bold_bold_trans_wf/bold_reference_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-02..func..sub-23649_ses-02_task-rest_echo-2_bold.nii.gz/gen_ref/ref_bold.nii.gz, 1, 64, Random, 0.2 ] --convergence [ 200, 1e-09, 10 ] --smoothing-sigmas 2.0mm --shrink-factors 2 --use-estimate-learning-rate-once 1 --use-histogram-matching 1 --winsorize-image-intensities [ 0.05, 0.98 ] --write-composite-transform 0 190731-15:35:03,459 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_mask". 190731-15:35:03,481 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_mid_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.skullstrip_second_pass". 190731-15:35:04,508 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.unifize". 190731-15:35:05,178 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.norm". 190731-15:35:05,334 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_mid_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.fixhdr_skullstrip2" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_mid_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/fixhdr_skullstrip2". 190731-15:35:05,336 nipype.workflow INFO: [Node] Running "fixhdr_skullstrip2" ("niworkflows.interfaces.utils.CopyXForm") 190731-15:35:05,337 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.fixhdr_unifize" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-02..func..sub-23649_ses-02_task-rest_echo-4_bold.nii.gz/fixhdr_unifize". 190731-15:35:05,339 nipype.workflow INFO: [Node] Running "fixhdr_unifize" ("niworkflows.interfaces.utils.CopyXForm") 190731-15:35:05,347 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.unifize" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-02..func..sub-23649_ses-02_task-rest_echo-3_bold.nii.gz/unifize". 190731-15:35:05,349 nipype.workflow INFO: [Node] Running "unifize" ("nipype.interfaces.afni.utils.Unifize"), a CommandLine Interface with command: 3dUnifize -clfrac 0.2 -rbt 18.3 65.0 90.0 -prefix uni.nii.gz -T2 -input /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-02..func..sub-23649_ses-02_task-rest_echo-3_bold.nii.gz/unifize/ref_bold_corrected_brain_masked.nii.gz 190731-15:35:05,365 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_mid_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.fixhdr_skullstrip2". 190731-15:35:05,375 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.fixhdr_unifize". 190731-15:35:06,414 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.unifize". 190731-15:35:07,430 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_mid_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.combine_masks" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_mid_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/combine_masks". 190731-15:35:07,431 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.skullstrip_second_pass" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-02..func..sub-23649_ses-02_task-rest_echo-4_bold.nii.gz/skullstrip_second_pass". 190731-15:35:07,432 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.fixhdr_unifize" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-02..func..sub-23649_ses-02_task-rest_echo-3_bold.nii.gz/fixhdr_unifize". 190731-15:35:07,433 nipype.workflow INFO: [Node] Running "skullstrip_second_pass" ("nipype.interfaces.afni.preprocess.Automask"), a CommandLine Interface with command: 3dAutomask -apply_prefix uni_xform_masked.nii.gz -dilate 1 -prefix uni_xform_mask.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-02..func..sub-23649_ses-02_task-rest_echo-4_bold.nii.gz/skullstrip_second_pass/uni_xform.nii.gz 190731-15:35:07,434 nipype.workflow INFO: [Node] Running "fixhdr_unifize" ("niworkflows.interfaces.utils.CopyXForm") 190731-15:35:07,434 nipype.workflow INFO: [Node] Running "combine_masks" ("nipype.interfaces.fsl.maths.BinaryMaths"), a CommandLine Interface with command: fslmaths /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_mid_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_pass/ref_bold_corrected_brain_mask.nii.gz -mul /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_mid_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/fixhdr_skullstrip2/uni_xform_mask_xform.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_mid_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/combine_masks/ref_bold_corrected_brain_mask_maths.nii.gz 190731-15:35:07,435 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.map_brainmask" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-02..func..sub-23649_ses-02_task-rest_echo-2_bold.nii.gz/map_brainmask". 190731-15:35:07,438 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_mid_run_1_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_mask" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_1_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_mask". 190731-15:35:07,439 nipype.workflow INFO: [Node] Running "map_brainmask" ("niworkflows.interfaces.fixes.FixHeaderApplyTransforms"), a CommandLine Interface with command: antsApplyTransforms --default-value 0 --float 1 --input /home/sahad3/.cache/templateflow/tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_res-02_desc-brain_mask.nii.gz --interpolation MultiLabel --output tpl-MNI152NLin2009cAsym_res-02_desc-brain_mask_trans.nii.gz --reference-image /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/bold_bold_trans_wf/bold_reference_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-02..func..sub-23649_ses-02_task-rest_echo-2_bold.nii.gz/gen_ref/ref_bold.nii.gz --transform [ /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-02..func..sub-23649_ses-02_task-rest_echo-2_bold.nii.gz/norm/transform0GenericAffine.mat, 1 ] 190731-15:35:07,441 nipype.workflow INFO: [Node] Running "skullstrip_first_mask" ("nipype.interfaces.fsl.maths.ApplyMask"), a CommandLine Interface with command: fslmaths /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_1_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_pass/ref_bold_corrected_brain.nii.gz -mas /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_1_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_dilate/ref_bold_corrected_brain_mask_dil.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_1_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_mask/ref_bold_corrected_brain_masked.nii.gz 190731-15:35:07,472 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.fixhdr_unifize". 190731-15:35:07,569 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_mid_run_1_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_mask". 190731-15:35:07,626 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.skullstrip_second_pass". 190731-15:35:07,658 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_mid_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.combine_masks". 190731-15:35:08,622 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.init_aff". 190731-15:35:09,248 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.map_brainmask". 190731-15:35:09,877 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_mid_wf.bold_confounds_wf.dvars" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_mid_wf/bold_confounds_wf/dvars". 190731-15:35:09,879 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_mid_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.apply_mask" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_mid_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/apply_mask". 190731-15:35:09,879 nipype.workflow INFO: [Node] Running "dvars" ("nipype.algorithms.confounds.ComputeDVARS") 190731-15:35:09,881 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.fixhdr_skullstrip2" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-02..func..sub-23649_ses-02_task-rest_echo-4_bold.nii.gz/fixhdr_skullstrip2". 190731-15:35:09,881 nipype.workflow INFO: [Node] Running "apply_mask" ("nipype.interfaces.fsl.maths.ApplyMask"), a CommandLine Interface with command: fslmaths /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_mid_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/fixhdr_unifize/uni_xform.nii.gz -mas /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_mid_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/combine_masks/ref_bold_corrected_brain_mask_maths.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_mid_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/apply_mask/uni_xform_masked.nii.gz 190731-15:35:09,882 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.skullstrip_second_pass" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-02..func..sub-23649_ses-02_task-rest_echo-3_bold.nii.gz/skullstrip_second_pass". 190731-15:35:09,882 nipype.workflow INFO: [Node] Running "fixhdr_skullstrip2" ("niworkflows.interfaces.utils.CopyXForm") 190731-15:35:09,884 nipype.workflow INFO: [Node] Running "skullstrip_second_pass" ("nipype.interfaces.afni.preprocess.Automask"), a CommandLine Interface with command: 3dAutomask -apply_prefix uni_xform_masked.nii.gz -dilate 1 -prefix uni_xform_mask.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-02..func..sub-23649_ses-02_task-rest_echo-3_bold.nii.gz/skullstrip_second_pass/uni_xform.nii.gz 190731-15:35:09,887 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.norm" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-02..func..sub-23649_ses-02_task-rest_echo-1_bold.nii.gz/norm". 190731-15:35:09,895 nipype.workflow INFO: [Node] Running "norm" ("niworkflows.interfaces.fixes.FixHeaderRegistration"), a CommandLine Interface with command: antsRegistration --collapse-output-transforms 1 --dimensionality 3 --float 1 --initial-moving-transform [ /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-02..func..sub-23649_ses-02_task-rest_echo-1_bold.nii.gz/init_aff/initialization.mat, 0 ] --initialize-transforms-per-stage 0 --interpolation Linear --output transform --transform Affine[ 0.1 ] --metric Mattes[ /home/sahad3/.cache/templateflow/tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_res-02_desc-fMRIPrep_boldref.nii.gz, /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/bold_bold_trans_wf/bold_reference_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-02..func..sub-23649_ses-02_task-rest_echo-1_bold.nii.gz/gen_ref/ref_bold.nii.gz, 1, 64, Random, 0.2 ] --convergence [ 200, 1e-09, 10 ] --smoothing-sigmas 2.0mm --shrink-factors 2 --use-estimate-learning-rate-once 1 --use-histogram-matching 1 --winsorize-image-intensities [ 0.05, 0.98 ] --write-composite-transform 0 190731-15:35:09,894 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_mid_run_1_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.unifize" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_1_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/unifize". 190731-15:35:09,902 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.fixhdr_skullstrip2". 190731-15:35:09,903 nipype.workflow INFO: [Node] Running "unifize" ("nipype.interfaces.afni.utils.Unifize"), a CommandLine Interface with command: 3dUnifize -clfrac 0.2 -rbt 18.3 65.0 90.0 -prefix uni.nii.gz -T2 -input /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_1_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/unifize/ref_bold_corrected_brain_masked.nii.gz 190731-15:35:10,35 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_mid_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.apply_mask". 190731-15:35:10,80 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.skullstrip_second_pass". 190731-15:35:11,238 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_mid_run_1_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.unifize". 190731-15:35:11,307 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.norm". 190731-15:35:11,308 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.combine_masks" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-02..func..sub-23649_ses-02_task-rest_echo-4_bold.nii.gz/combine_masks". 190731-15:35:11,310 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.fixhdr_skullstrip2" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-02..func..sub-23649_ses-02_task-rest_echo-3_bold.nii.gz/fixhdr_skullstrip2". 190731-15:35:11,311 nipype.workflow INFO: [Node] Running "combine_masks" ("nipype.interfaces.fsl.maths.BinaryMaths"), a CommandLine Interface with command: fslmaths /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-02..func..sub-23649_ses-02_task-rest_echo-4_bold.nii.gz/skullstrip_first_pass/ref_bold_corrected_brain_mask.nii.gz -mul /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-02..func..sub-23649_ses-02_task-rest_echo-4_bold.nii.gz/fixhdr_skullstrip2/uni_xform_mask_xform.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-02..func..sub-23649_ses-02_task-rest_echo-4_bold.nii.gz/combine_masks/ref_bold_corrected_brain_mask_maths.nii.gz 190731-15:35:11,311 nipype.workflow INFO: [Node] Running "fixhdr_skullstrip2" ("niworkflows.interfaces.utils.CopyXForm") 190731-15:35:11,312 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.pre_mask_dilate" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-02..func..sub-23649_ses-02_task-rest_echo-2_bold.nii.gz/pre_mask_dilate". 190731-15:35:11,315 nipype.workflow INFO: [Node] Running "pre_mask_dilate" ("nipype.interfaces.fsl.maths.DilateImage"), a CommandLine Interface with command: fslmaths -dt char /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-02..func..sub-23649_ses-02_task-rest_echo-2_bold.nii.gz/map_brainmask/tpl-MNI152NLin2009cAsym_res-02_desc-brain_mask_trans.nii.gz -kernel sphere 3.0000 -dilF /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-02..func..sub-23649_ses-02_task-rest_echo-2_bold.nii.gz/pre_mask_dilate/tpl-MNI152NLin2009cAsym_res-02_desc-brain_mask_trans_dil.nii.gz 190731-15:35:11,339 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.fixhdr_skullstrip2". 190731-15:35:11,445 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.combine_masks". 190731-15:35:11,495 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.pre_mask_dilate". 190731-15:35:13,512 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.bold_t2smap_wf.t2smap_node". 190731-15:35:13,816 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.apply_mask" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-02..func..sub-23649_ses-02_task-rest_echo-4_bold.nii.gz/apply_mask". 190731-15:35:13,817 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.combine_masks" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-02..func..sub-23649_ses-02_task-rest_echo-3_bold.nii.gz/combine_masks". 190731-15:35:13,818 nipype.workflow INFO: [Node] Running "apply_mask" ("nipype.interfaces.fsl.maths.ApplyMask"), a CommandLine Interface with command: fslmaths /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-02..func..sub-23649_ses-02_task-rest_echo-4_bold.nii.gz/fixhdr_unifize/uni_xform.nii.gz -mas /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-02..func..sub-23649_ses-02_task-rest_echo-4_bold.nii.gz/combine_masks/ref_bold_corrected_brain_mask_maths.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-02..func..sub-23649_ses-02_task-rest_echo-4_bold.nii.gz/apply_mask/uni_xform_masked.nii.gz 190731-15:35:13,820 nipype.workflow INFO: [Node] Running "combine_masks" ("nipype.interfaces.fsl.maths.BinaryMaths"), a CommandLine Interface with command: fslmaths /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-02..func..sub-23649_ses-02_task-rest_echo-3_bold.nii.gz/skullstrip_first_pass/ref_bold_corrected_brain_mask.nii.gz -mul /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-02..func..sub-23649_ses-02_task-rest_echo-3_bold.nii.gz/fixhdr_skullstrip2/uni_xform_mask_xform.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-02..func..sub-23649_ses-02_task-rest_echo-3_bold.nii.gz/combine_masks/ref_bold_corrected_brain_mask_maths.nii.gz 190731-15:35:13,830 nipype.interface WARNING: q-forms of reference and mask are substantially different 190731-15:35:13,935 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.apply_mask". 190731-15:35:13,940 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.combine_masks". 190731-15:35:14,315 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.map_brainmask" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-02..func..sub-23649_ses-02_task-rest_echo-1_bold.nii.gz/map_brainmask". 190731-15:35:14,316 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_mid_run_1_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.fixhdr_unifize" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_1_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/fixhdr_unifize". 190731-15:35:14,317 nipype.workflow INFO: [Node] Running "map_brainmask" ("niworkflows.interfaces.fixes.FixHeaderApplyTransforms"), a CommandLine Interface with command: antsApplyTransforms --default-value 0 --float 1 --input /home/sahad3/.cache/templateflow/tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_res-02_desc-brain_mask.nii.gz --interpolation MultiLabel --output tpl-MNI152NLin2009cAsym_res-02_desc-brain_mask_trans.nii.gz --reference-image /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/bold_bold_trans_wf/bold_reference_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-02..func..sub-23649_ses-02_task-rest_echo-1_bold.nii.gz/gen_ref/ref_bold.nii.gz --transform [ /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-02..func..sub-23649_ses-02_task-rest_echo-1_bold.nii.gz/norm/transform0GenericAffine.mat, 1 ] 190731-15:35:14,318 nipype.workflow INFO: [Node] Running "fixhdr_unifize" ("niworkflows.interfaces.utils.CopyXForm") 190731-15:35:14,321 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_mid_run_2_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_opposite_wf.enhance_and_skullstrip_bold_wf.norm" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_2_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/enhance_and_skullstrip_bold_wf/norm". 190731-15:35:14,325 nipype.workflow INFO: [Node] Running "norm" ("niworkflows.interfaces.fixes.FixHeaderRegistration"), a CommandLine Interface with command: antsRegistration --collapse-output-transforms 1 --dimensionality 3 --float 1 --initial-moving-transform [ /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_2_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/enhance_and_skullstrip_bold_wf/init_aff/initialization.mat, 0 ] --initialize-transforms-per-stage 0 --interpolation Linear --output transform --transform Affine[ 0.1 ] --metric Mattes[ /home/sahad3/.cache/templateflow/tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_res-02_desc-fMRIPrep_boldref.nii.gz, /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_2_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/merge/template.nii.gz, 1, 64, Random, 0.2 ] --convergence [ 200, 1e-09, 10 ] --smoothing-sigmas 2.0mm --shrink-factors 2 --use-estimate-learning-rate-once 1 --use-histogram-matching 1 --winsorize-image-intensities [ 0.05, 0.98 ] --write-composite-transform 0 190731-15:35:14,357 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_mid_run_1_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.fixhdr_unifize". 190731-15:35:15,839 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.apply_mask" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-02..func..sub-23649_ses-02_task-rest_echo-3_bold.nii.gz/apply_mask". 190731-15:35:15,841 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.n4_correct" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-02..func..sub-23649_ses-02_task-rest_echo-2_bold.nii.gz/n4_correct". 190731-15:35:15,841 nipype.workflow INFO: [Node] Running "apply_mask" ("nipype.interfaces.fsl.maths.ApplyMask"), a CommandLine Interface with command: fslmaths /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-02..func..sub-23649_ses-02_task-rest_echo-3_bold.nii.gz/fixhdr_unifize/uni_xform.nii.gz -mas /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-02..func..sub-23649_ses-02_task-rest_echo-3_bold.nii.gz/combine_masks/ref_bold_corrected_brain_mask_maths.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-02..func..sub-23649_ses-02_task-rest_echo-3_bold.nii.gz/apply_mask/uni_xform_masked.nii.gz 190731-15:35:15,843 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.bold_t1_trans_wf.bold_split" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/bold_t1_trans_wf/bold_split". 190731-15:35:15,843 nipype.workflow INFO: [Node] Running "n4_correct" ("nipype.interfaces.ants.segmentation.N4BiasFieldCorrection"), a CommandLine Interface with command: N4BiasFieldCorrection --bspline-fitting [ 200 ] -d 3 --input-image /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/bold_bold_trans_wf/bold_reference_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-02..func..sub-23649_ses-02_task-rest_echo-2_bold.nii.gz/gen_ref/ref_bold.nii.gz --mask-image /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-02..func..sub-23649_ses-02_task-rest_echo-2_bold.nii.gz/check_hdr/tpl-MNI152NLin2009cAsym_res-02_desc-brain_mask_trans_dil_hdr.nii.gz --output ref_bold_corrected.nii.gz 190731-15:35:15,845 nipype.workflow INFO: [Node] Running "bold_split" ("nipype.interfaces.fsl.utils.Split"), a CommandLine Interface with command: fslsplit /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/bold_t2smap_wf/t2smap_node/TED.vol0000_xform-00000_merged_masked/ts_OC.nii -t 190731-15:35:15,847 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.split_opt_comb" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/split_opt_comb". 190731-15:35:15,847 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.bold_t2smap_wf.skullstrip_t2smap_wf.skullstrip_first_pass" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/bold_t2smap_wf/skullstrip_t2smap_wf/skullstrip_first_pass". 190731-15:35:15,849 nipype.workflow INFO: [Node] Running "split_opt_comb" ("nipype.interfaces.fsl.utils.Split"), a CommandLine Interface with command: fslsplit /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/bold_t2smap_wf/t2smap_node/TED.vol0000_xform-00000_merged_masked/ts_OC.nii -t 190731-15:35:15,850 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_mid_run_1_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.skullstrip_second_pass" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_1_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_second_pass". 190731-15:35:15,851 nipype.workflow INFO: [Node] Running "skullstrip_first_pass" ("nipype.interfaces.fsl.preprocess.BET"), a CommandLine Interface with command: bet /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/bold_t2smap_wf/t2smap_node/TED.vol0000_xform-00000_merged_masked/t2sv.nii /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/bold_t2smap_wf/skullstrip_t2smap_wf/skullstrip_first_pass/t2sv_brain.nii.gz -f 0.20 -m 190731-15:35:15,853 nipype.workflow INFO: [Node] Running "skullstrip_second_pass" ("nipype.interfaces.afni.preprocess.Automask"), a CommandLine Interface with command: 3dAutomask -apply_prefix uni_xform_masked.nii.gz -dilate 1 -prefix uni_xform_mask.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_1_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_second_pass/uni_xform.nii.gz 190731-15:35:16,11 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.apply_mask". 190731-15:35:16,70 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_mid_run_1_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.skullstrip_second_pass". 190731-15:35:16,147 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.map_brainmask". 190731-15:35:16,413 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_mid_run_2_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_opposite_wf.enhance_and_skullstrip_bold_wf.norm". 190731-15:35:17,327 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.pre_mask_dilate" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-02..func..sub-23649_ses-02_task-rest_echo-1_bold.nii.gz/pre_mask_dilate". 190731-15:35:17,328 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_mid_run_1_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.fixhdr_skullstrip2" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_1_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/fixhdr_skullstrip2". 190731-15:35:17,329 nipype.workflow INFO: [Node] Running "pre_mask_dilate" ("nipype.interfaces.fsl.maths.DilateImage"), a CommandLine Interface with command: fslmaths -dt char /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-02..func..sub-23649_ses-02_task-rest_echo-1_bold.nii.gz/map_brainmask/tpl-MNI152NLin2009cAsym_res-02_desc-brain_mask_trans.nii.gz -kernel sphere 3.0000 -dilF /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-02..func..sub-23649_ses-02_task-rest_echo-1_bold.nii.gz/pre_mask_dilate/tpl-MNI152NLin2009cAsym_res-02_desc-brain_mask_trans_dil.nii.gz 190731-15:35:17,331 nipype.workflow INFO: [Node] Running "fixhdr_skullstrip2" ("niworkflows.interfaces.utils.CopyXForm") 190731-15:35:17,332 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_mid_run_2_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_opposite_wf.enhance_and_skullstrip_bold_wf.map_brainmask" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_2_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/enhance_and_skullstrip_bold_wf/map_brainmask". 190731-15:35:17,333 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_mid_run_2_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_matching_wf.enhance_and_skullstrip_bold_wf.init_aff" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_2_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/enhance_and_skullstrip_bold_wf/init_aff". 190731-15:35:17,335 nipype.workflow INFO: [Node] Running "map_brainmask" ("niworkflows.interfaces.fixes.FixHeaderApplyTransforms"), a CommandLine Interface with command: antsApplyTransforms --default-value 0 --float 1 --input /home/sahad3/.cache/templateflow/tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_res-02_desc-brain_mask.nii.gz --interpolation MultiLabel --output tpl-MNI152NLin2009cAsym_res-02_desc-brain_mask_trans.nii.gz --reference-image /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_2_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/merge/template.nii.gz --transform [ /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_2_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/enhance_and_skullstrip_bold_wf/norm/transform0GenericAffine.mat, 1 ] 190731-15:35:17,336 nipype.workflow INFO: [Node] Running "init_aff" ("niworkflows.interfaces.ants.AI"), a CommandLine Interface with command: antsAI -c [10,0.000001,10] -d 3 -x /home/sahad3/.cache/templateflow/tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_res-02_desc-brain_mask.nii.gz -m Mattes[/home/sahad3/.cache/templateflow/tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_res-02_desc-fMRIPrep_boldref.nii.gz,/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_2_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/merge/template.nii.gz,32,Regular,0.200000] -o initialization.mat -p 0 -s [20.000000,0.120000] -t Affine[0.100000] -v 1 190731-15:35:17,357 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_mid_run_1_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.fixhdr_skullstrip2". 190731-15:35:17,646 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.pre_mask_dilate". 190731-15:35:18,188 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.bold_t2smap_wf.skullstrip_t2smap_wf.skullstrip_first_pass". 190731-15:35:18,307 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.n4_correct". 190731-15:35:19,943 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_mid_run_2_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_opposite_wf.enhance_and_skullstrip_bold_wf.map_brainmask". 190731-15:35:20,92 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.split_opt_comb". 190731-15:35:20,105 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_pass" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-02..func..sub-23649_ses-02_task-rest_echo-2_bold.nii.gz/skullstrip_first_pass". 190731-15:35:20,105 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.bold_t2smap_wf.skullstrip_t2smap_wf.skullstrip_second_pass" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/bold_t2smap_wf/skullstrip_t2smap_wf/skullstrip_second_pass". 190731-15:35:20,108 nipype.workflow INFO: [Node] Running "skullstrip_second_pass" ("nipype.interfaces.afni.preprocess.Automask"), a CommandLine Interface with command: 3dAutomask -apply_prefix t2sv_brain_masked.nii.gz -dilate 1 -prefix t2sv_brain_mask.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/bold_t2smap_wf/skullstrip_t2smap_wf/skullstrip_second_pass/t2sv_brain.nii.gz 190731-15:35:20,109 nipype.workflow INFO: [Node] Running "skullstrip_first_pass" ("nipype.interfaces.fsl.preprocess.BET"), a CommandLine Interface with command: bet /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-02..func..sub-23649_ses-02_task-rest_echo-2_bold.nii.gz/n4_correct/ref_bold_corrected.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-02..func..sub-23649_ses-02_task-rest_echo-2_bold.nii.gz/skullstrip_first_pass/ref_bold_corrected_brain.nii.gz -f 0.20 -m 190731-15:35:20,114 nipype.interface WARNING: q-forms of reference and mask are substantially different 190731-15:35:20,226 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.bold_t1_trans_wf.bold_split". 190731-15:35:20,285 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.bold_t2smap_wf.skullstrip_t2smap_wf.skullstrip_second_pass". 190731-15:35:20,632 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_mid_run_1_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.combine_masks" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_1_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/combine_masks". 190731-15:35:20,635 nipype.workflow INFO: [Node] Running "combine_masks" ("nipype.interfaces.fsl.maths.BinaryMaths"), a CommandLine Interface with command: fslmaths /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_1_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_pass/ref_bold_corrected_brain_mask.nii.gz -mul /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_1_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/fixhdr_skullstrip2/uni_xform_mask_xform.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_1_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/combine_masks/ref_bold_corrected_brain_mask_maths.nii.gz 190731-15:35:20,780 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_mid_run_1_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.combine_masks". 190731-15:35:21,340 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.bold_t2smap_wf.skullstrip_t2smap_wf.combine_masks" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/bold_t2smap_wf/skullstrip_t2smap_wf/combine_masks". 190731-15:35:21,342 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.n4_correct" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-02..func..sub-23649_ses-02_task-rest_echo-1_bold.nii.gz/n4_correct". 190731-15:35:21,343 nipype.workflow INFO: [Node] Running "combine_masks" ("nipype.interfaces.fsl.maths.BinaryMaths"), a CommandLine Interface with command: fslmaths /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/bold_t2smap_wf/skullstrip_t2smap_wf/skullstrip_first_pass/t2sv_brain_mask.nii.gz -mul /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/bold_t2smap_wf/skullstrip_t2smap_wf/skullstrip_second_pass/t2sv_brain_mask.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/bold_t2smap_wf/skullstrip_t2smap_wf/combine_masks/t2sv_brain_mask_maths.nii.gz 190731-15:35:21,344 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_mid_run_1_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.apply_mask" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_1_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/apply_mask". 190731-15:35:21,346 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_mid_run_2_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_opposite_wf.enhance_and_skullstrip_bold_wf.pre_mask_dilate" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_2_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/enhance_and_skullstrip_bold_wf/pre_mask_dilate". 190731-15:35:21,346 nipype.workflow INFO: [Node] Running "n4_correct" ("nipype.interfaces.ants.segmentation.N4BiasFieldCorrection"), a CommandLine Interface with command: N4BiasFieldCorrection --bspline-fitting [ 200 ] -d 3 --input-image /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/bold_bold_trans_wf/bold_reference_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-02..func..sub-23649_ses-02_task-rest_echo-1_bold.nii.gz/gen_ref/ref_bold.nii.gz --mask-image /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-02..func..sub-23649_ses-02_task-rest_echo-1_bold.nii.gz/check_hdr/tpl-MNI152NLin2009cAsym_res-02_desc-brain_mask_trans_dil_hdr.nii.gz --output ref_bold_corrected.nii.gz 190731-15:35:21,348 nipype.workflow INFO: [Node] Running "apply_mask" ("nipype.interfaces.fsl.maths.ApplyMask"), a CommandLine Interface with command: fslmaths /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_1_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/fixhdr_unifize/uni_xform.nii.gz -mas /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_1_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/combine_masks/ref_bold_corrected_brain_mask_maths.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_1_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/apply_mask/uni_xform_masked.nii.gz 190731-15:35:21,348 nipype.workflow INFO: [Node] Running "pre_mask_dilate" ("nipype.interfaces.fsl.maths.DilateImage"), a CommandLine Interface with command: fslmaths -dt char /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_2_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/enhance_and_skullstrip_bold_wf/map_brainmask/tpl-MNI152NLin2009cAsym_res-02_desc-brain_mask_trans.nii.gz -kernel sphere 3.0000 -dilF /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_2_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/enhance_and_skullstrip_bold_wf/pre_mask_dilate/tpl-MNI152NLin2009cAsym_res-02_desc-brain_mask_trans_dil.nii.gz 190731-15:35:21,466 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.bold_t2smap_wf.skullstrip_t2smap_wf.combine_masks". 190731-15:35:21,542 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_mid_run_1_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.apply_mask". 190731-15:35:21,705 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_mid_run_2_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_opposite_wf.enhance_and_skullstrip_bold_wf.pre_mask_dilate". 190731-15:35:22,187 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_pass". 190731-15:35:22,872 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_mid_run_2_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_matching_wf.enhance_and_skullstrip_bold_wf.init_aff". 190731-15:35:23,225 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_mid_wf.bold_confounds_wf.dvars". 190731-15:35:23,329 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_dilate" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-02..func..sub-23649_ses-02_task-rest_echo-2_bold.nii.gz/skullstrip_first_dilate". 190731-15:35:23,331 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.bold_confounds_wf.dvars" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/bold_confounds_wf/dvars". 190731-15:35:23,331 nipype.workflow INFO: [Node] Running "skullstrip_first_dilate" ("nipype.interfaces.fsl.maths.DilateImage"), a CommandLine Interface with command: fslmaths -dt char /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-02..func..sub-23649_ses-02_task-rest_echo-2_bold.nii.gz/skullstrip_first_pass/ref_bold_corrected_brain_mask.nii.gz -kernel sphere 6.0000 -dilF /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-02..func..sub-23649_ses-02_task-rest_echo-2_bold.nii.gz/skullstrip_first_dilate/ref_bold_corrected_brain_mask_dil.nii.gz 190731-15:35:23,332 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.bold_t2smap_wf.skullstrip_t2smap_wf.mask_reportlet" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/bold_t2smap_wf/skullstrip_t2smap_wf/mask_reportlet". 190731-15:35:23,333 nipype.workflow INFO: [Node] Running "dvars" ("nipype.algorithms.confounds.ComputeDVARS") 190731-15:35:23,334 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.bold_t2smap_wf.skullstrip_t2smap_wf.apply_mask" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/bold_t2smap_wf/skullstrip_t2smap_wf/apply_mask". 190731-15:35:23,335 nipype.workflow INFO: [Node] Running "mask_reportlet" ("niworkflows.interfaces.masks.SimpleShowMaskRPT") 190731-15:35:23,336 nipype.workflow INFO: [Node] Running "apply_mask" ("nipype.interfaces.fsl.maths.ApplyMask"), a CommandLine Interface with command: fslmaths /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/bold_t2smap_wf/t2smap_node/TED.vol0000_xform-00000_merged_masked/t2sv.nii -mas /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/bold_t2smap_wf/skullstrip_t2smap_wf/combine_masks/t2sv_brain_mask_maths.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/bold_t2smap_wf/skullstrip_t2smap_wf/apply_mask/t2sv_masked.nii.gz 190731-15:35:23,355 nipype.interface WARNING: q-forms of reference and mask are substantially different 190731-15:35:23,487 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.bold_t2smap_wf.skullstrip_t2smap_wf.apply_mask". 190731-15:35:23,663 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_dilate". 190731-15:35:23,727 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.n4_correct". 190731-15:35:26,300 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_mask" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-02..func..sub-23649_ses-02_task-rest_echo-2_bold.nii.gz/skullstrip_first_mask". 190731-15:35:26,302 nipype.workflow INFO: [Node] Running "skullstrip_first_mask" ("nipype.interfaces.fsl.maths.ApplyMask"), a CommandLine Interface with command: fslmaths /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-02..func..sub-23649_ses-02_task-rest_echo-2_bold.nii.gz/skullstrip_first_pass/ref_bold_corrected_brain.nii.gz -mas /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-02..func..sub-23649_ses-02_task-rest_echo-2_bold.nii.gz/skullstrip_first_dilate/ref_bold_corrected_brain_mask_dil.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-02..func..sub-23649_ses-02_task-rest_echo-2_bold.nii.gz/skullstrip_first_mask/ref_bold_corrected_brain_masked.nii.gz 190731-15:35:26,459 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_mask". 190731-15:35:26,888 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_pass" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-02..func..sub-23649_ses-02_task-rest_echo-1_bold.nii.gz/skullstrip_first_pass". 190731-15:35:26,890 nipype.workflow INFO: [Node] Running "skullstrip_first_pass" ("nipype.interfaces.fsl.preprocess.BET"), a CommandLine Interface with command: bet /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-02..func..sub-23649_ses-02_task-rest_echo-1_bold.nii.gz/n4_correct/ref_bold_corrected.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-02..func..sub-23649_ses-02_task-rest_echo-1_bold.nii.gz/skullstrip_first_pass/ref_bold_corrected_brain.nii.gz -f 0.20 -m 190731-15:35:26,892 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_mid_run_1_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_matching_wf.fmap2ref_reg" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/fmap2ref_reg". 190731-15:35:26,897 nipype.workflow INFO: [Node] Running "fmap2ref_reg" ("nipype.interfaces.ants.registration.Registration"), a CommandLine Interface with command: antsRegistration --collapse-output-transforms 1 --dimensionality 3 --float 1 --initialize-transforms-per-stage 0 --interpolation LanczosWindowedSinc --output [ transform, transform_Warped.nii.gz ] --transform Translation[ 0.05 ] --metric Mattes[ /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_1_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/apply_mask/uni_xform_masked.nii.gz, /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/enhance_and_skullstrip_bold_wf/apply_mask/uni_xform_masked.nii.gz, 1, 64, Random, 0.5 ] --convergence [ 500, 1e-07, 200 ] --smoothing-sigmas 8.0mm --shrink-factors 2 --use-estimate-learning-rate-once 1 --use-histogram-matching 1 --transform Rigid[ 0.01 ] --metric Mattes[ /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_1_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/apply_mask/uni_xform_masked.nii.gz, /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/enhance_and_skullstrip_bold_wf/apply_mask/uni_xform_masked.nii.gz, 1, 64, Random, 0.5 ] --convergence [ 200, 1e-08, 100 ] --smoothing-sigmas 2.0mm --shrink-factors 1 --use-estimate-learning-rate-once 1 --use-histogram-matching 1 --winsorize-image-intensities [ 0.005, 0.998 ] --write-composite-transform 1 190731-15:35:26,899 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_mid_run_1_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_opposite_wf.fmap2ref_reg" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/fmap2ref_reg". 190731-15:35:26,907 nipype.workflow INFO: [Node] Running "fmap2ref_reg" ("nipype.interfaces.ants.registration.Registration"), a CommandLine Interface with command: antsRegistration --collapse-output-transforms 1 --dimensionality 3 --float 1 --initialize-transforms-per-stage 0 --interpolation LanczosWindowedSinc --output [ transform, transform_Warped.nii.gz ] --transform Translation[ 0.05 ] --metric Mattes[ /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_1_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/apply_mask/uni_xform_masked.nii.gz, /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/enhance_and_skullstrip_bold_wf/apply_mask/uni_xform_masked.nii.gz, 1, 64, Random, 0.5 ] --convergence [ 500, 1e-07, 200 ] --smoothing-sigmas 8.0mm --shrink-factors 2 --use-estimate-learning-rate-once 1 --use-histogram-matching 1 --transform Rigid[ 0.01 ] --metric Mattes[ /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_1_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/apply_mask/uni_xform_masked.nii.gz, /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/enhance_and_skullstrip_bold_wf/apply_mask/uni_xform_masked.nii.gz, 1, 64, Random, 0.5 ] --convergence [ 200, 1e-08, 100 ] --smoothing-sigmas 2.0mm --shrink-factors 1 --use-estimate-learning-rate-once 1 --use-histogram-matching 1 --winsorize-image-intensities [ 0.005, 0.998 ] --write-composite-transform 1 190731-15:35:27,432 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.unifize" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-02..func..sub-23649_ses-02_task-rest_echo-2_bold.nii.gz/unifize". 190731-15:35:27,435 nipype.workflow INFO: [Node] Running "unifize" ("nipype.interfaces.afni.utils.Unifize"), a CommandLine Interface with command: 3dUnifize -clfrac 0.2 -rbt 18.3 65.0 90.0 -prefix uni.nii.gz -T2 -input /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-02..func..sub-23649_ses-02_task-rest_echo-2_bold.nii.gz/unifize/ref_bold_corrected_brain_masked.nii.gz 190731-15:35:28,73 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.bold_t2smap_wf.skullstrip_t2smap_wf.mask_reportlet". 190731-15:35:28,660 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.unifize". 190731-15:35:28,814 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_pass". 190731-15:35:29,436 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.fixhdr_unifize" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-02..func..sub-23649_ses-02_task-rest_echo-2_bold.nii.gz/fixhdr_unifize". 190731-15:35:29,437 nipype.workflow INFO: [Node] Running "fixhdr_unifize" ("niworkflows.interfaces.utils.CopyXForm") 190731-15:35:29,438 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_dilate" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-02..func..sub-23649_ses-02_task-rest_echo-1_bold.nii.gz/skullstrip_first_dilate". 190731-15:35:29,440 nipype.workflow INFO: [Node] Running "skullstrip_first_dilate" ("nipype.interfaces.fsl.maths.DilateImage"), a CommandLine Interface with command: fslmaths -dt char /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-02..func..sub-23649_ses-02_task-rest_echo-1_bold.nii.gz/skullstrip_first_pass/ref_bold_corrected_brain_mask.nii.gz -kernel sphere 6.0000 -dilF /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-02..func..sub-23649_ses-02_task-rest_echo-1_bold.nii.gz/skullstrip_first_dilate/ref_bold_corrected_brain_mask_dil.nii.gz 190731-15:35:29,441 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_mid_run_2_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_opposite_wf.enhance_and_skullstrip_bold_wf.n4_correct" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_2_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/enhance_and_skullstrip_bold_wf/n4_correct". 190731-15:35:29,444 nipype.workflow INFO: [Node] Running "n4_correct" ("nipype.interfaces.ants.segmentation.N4BiasFieldCorrection"), a CommandLine Interface with command: N4BiasFieldCorrection --bspline-fitting [ 200 ] -d 3 --input-image /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_2_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/merge/template.nii.gz --mask-image /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_2_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/enhance_and_skullstrip_bold_wf/check_hdr/tpl-MNI152NLin2009cAsym_res-02_desc-brain_mask_trans_dil_hdr.nii.gz --output template_corrected.nii.gz 190731-15:35:29,472 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.fixhdr_unifize". 190731-15:35:29,775 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_dilate". 190731-15:35:31,427 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.skullstrip_second_pass" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-02..func..sub-23649_ses-02_task-rest_echo-2_bold.nii.gz/skullstrip_second_pass". 190731-15:35:31,428 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_mask" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-02..func..sub-23649_ses-02_task-rest_echo-1_bold.nii.gz/skullstrip_first_mask". 190731-15:35:31,431 nipype.workflow INFO: [Node] Running "skullstrip_first_mask" ("nipype.interfaces.fsl.maths.ApplyMask"), a CommandLine Interface with command: fslmaths /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-02..func..sub-23649_ses-02_task-rest_echo-1_bold.nii.gz/skullstrip_first_pass/ref_bold_corrected_brain.nii.gz -mas /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-02..func..sub-23649_ses-02_task-rest_echo-1_bold.nii.gz/skullstrip_first_dilate/ref_bold_corrected_brain_mask_dil.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-02..func..sub-23649_ses-02_task-rest_echo-1_bold.nii.gz/skullstrip_first_mask/ref_bold_corrected_brain_masked.nii.gz 190731-15:35:31,431 nipype.workflow INFO: [Node] Running "skullstrip_second_pass" ("nipype.interfaces.afni.preprocess.Automask"), a CommandLine Interface with command: 3dAutomask -apply_prefix uni_xform_masked.nii.gz -dilate 1 -prefix uni_xform_mask.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-02..func..sub-23649_ses-02_task-rest_echo-2_bold.nii.gz/skullstrip_second_pass/uni_xform.nii.gz 190731-15:35:31,572 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_mask". 190731-15:35:31,600 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.skullstrip_second_pass". 190731-15:35:31,610 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.bold_confounds_wf.dvars". 190731-15:35:32,476 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_mid_run_2_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_opposite_wf.enhance_and_skullstrip_bold_wf.n4_correct". 190731-15:35:33,418 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.fixhdr_skullstrip2" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-02..func..sub-23649_ses-02_task-rest_echo-2_bold.nii.gz/fixhdr_skullstrip2". 190731-15:35:33,419 nipype.workflow INFO: [Node] Running "fixhdr_skullstrip2" ("niworkflows.interfaces.utils.CopyXForm") 190731-15:35:33,439 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.fixhdr_skullstrip2". 190731-15:35:34,424 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_mid_run_2_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_opposite_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_pass" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_2_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_pass". 190731-15:35:34,426 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.unifize" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-02..func..sub-23649_ses-02_task-rest_echo-1_bold.nii.gz/unifize". 190731-15:35:34,428 nipype.workflow INFO: [Node] Running "skullstrip_first_pass" ("nipype.interfaces.fsl.preprocess.BET"), a CommandLine Interface with command: bet /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_2_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/enhance_and_skullstrip_bold_wf/n4_correct/template_corrected.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_2_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_pass/template_corrected_brain.nii.gz -f 0.20 -m 190731-15:35:34,431 nipype.workflow INFO: [Node] Running "unifize" ("nipype.interfaces.afni.utils.Unifize"), a CommandLine Interface with command: 3dUnifize -clfrac 0.2 -rbt 18.3 65.0 90.0 -prefix uni.nii.gz -T2 -input /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-02..func..sub-23649_ses-02_task-rest_echo-1_bold.nii.gz/unifize/ref_bold_corrected_brain_masked.nii.gz 190731-15:35:35,416 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.combine_masks" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-02..func..sub-23649_ses-02_task-rest_echo-2_bold.nii.gz/combine_masks". 190731-15:35:35,419 nipype.workflow INFO: [Node] Running "combine_masks" ("nipype.interfaces.fsl.maths.BinaryMaths"), a CommandLine Interface with command: fslmaths /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-02..func..sub-23649_ses-02_task-rest_echo-2_bold.nii.gz/skullstrip_first_pass/ref_bold_corrected_brain_mask.nii.gz -mul /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-02..func..sub-23649_ses-02_task-rest_echo-2_bold.nii.gz/fixhdr_skullstrip2/uni_xform_mask_xform.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-02..func..sub-23649_ses-02_task-rest_echo-2_bold.nii.gz/combine_masks/ref_bold_corrected_brain_mask_maths.nii.gz 190731-15:35:35,596 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.combine_masks". 190731-15:35:35,720 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.unifize". 190731-15:35:36,426 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_mid_run_2_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_opposite_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_pass". 190731-15:35:37,962 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.apply_mask" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-02..func..sub-23649_ses-02_task-rest_echo-2_bold.nii.gz/apply_mask". 190731-15:35:37,964 nipype.workflow INFO: [Node] Running "apply_mask" ("nipype.interfaces.fsl.maths.ApplyMask"), a CommandLine Interface with command: fslmaths /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-02..func..sub-23649_ses-02_task-rest_echo-2_bold.nii.gz/fixhdr_unifize/uni_xform.nii.gz -mas /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-02..func..sub-23649_ses-02_task-rest_echo-2_bold.nii.gz/combine_masks/ref_bold_corrected_brain_mask_maths.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-02..func..sub-23649_ses-02_task-rest_echo-2_bold.nii.gz/apply_mask/uni_xform_masked.nii.gz 190731-15:35:37,964 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.fixhdr_unifize" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-02..func..sub-23649_ses-02_task-rest_echo-1_bold.nii.gz/fixhdr_unifize". 190731-15:35:37,966 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_mid_run_2_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_opposite_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_dilate" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_2_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_dilate". 190731-15:35:37,967 nipype.workflow INFO: [Node] Running "fixhdr_unifize" ("niworkflows.interfaces.utils.CopyXForm") 190731-15:35:37,968 nipype.workflow INFO: [Node] Running "skullstrip_first_dilate" ("nipype.interfaces.fsl.maths.DilateImage"), a CommandLine Interface with command: fslmaths -dt char /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_2_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_pass/template_corrected_brain_mask.nii.gz -kernel sphere 6.0000 -dilF /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_2_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_dilate/template_corrected_brain_mask_dil.nii.gz 190731-15:35:38,8 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.fixhdr_unifize". 190731-15:35:38,104 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.apply_mask". 190731-15:35:38,481 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_mid_run_2_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_opposite_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_dilate". 190731-15:35:39,443 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.skullstrip_second_pass" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-02..func..sub-23649_ses-02_task-rest_echo-1_bold.nii.gz/skullstrip_second_pass". 190731-15:35:39,445 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_mid_run_2_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_opposite_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_mask" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_2_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_mask". 190731-15:35:39,446 nipype.workflow INFO: [Node] Running "skullstrip_second_pass" ("nipype.interfaces.afni.preprocess.Automask"), a CommandLine Interface with command: 3dAutomask -apply_prefix uni_xform_masked.nii.gz -dilate 1 -prefix uni_xform_mask.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-02..func..sub-23649_ses-02_task-rest_echo-1_bold.nii.gz/skullstrip_second_pass/uni_xform.nii.gz 190731-15:35:39,447 nipype.workflow INFO: [Node] Running "skullstrip_first_mask" ("nipype.interfaces.fsl.maths.ApplyMask"), a CommandLine Interface with command: fslmaths /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_2_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_pass/template_corrected_brain.nii.gz -mas /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_2_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_dilate/template_corrected_brain_mask_dil.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_2_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_mask/template_corrected_brain_masked.nii.gz 190731-15:35:39,571 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_mid_run_2_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_opposite_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_mask". 190731-15:35:39,621 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.skullstrip_second_pass". 190731-15:35:41,440 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.fixhdr_skullstrip2" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-02..func..sub-23649_ses-02_task-rest_echo-1_bold.nii.gz/fixhdr_skullstrip2". 190731-15:35:41,442 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_mid_run_2_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_opposite_wf.enhance_and_skullstrip_bold_wf.unifize" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_2_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/enhance_and_skullstrip_bold_wf/unifize". 190731-15:35:41,442 nipype.workflow INFO: [Node] Running "fixhdr_skullstrip2" ("niworkflows.interfaces.utils.CopyXForm") 190731-15:35:41,444 nipype.workflow INFO: [Node] Running "unifize" ("nipype.interfaces.afni.utils.Unifize"), a CommandLine Interface with command: 3dUnifize -clfrac 0.2 -rbt 18.3 65.0 90.0 -prefix uni.nii.gz -T2 -input /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_2_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/enhance_and_skullstrip_bold_wf/unifize/template_corrected_brain_masked.nii.gz 190731-15:35:41,465 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.fixhdr_skullstrip2". 190731-15:35:42,713 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_mid_run_2_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_opposite_wf.enhance_and_skullstrip_bold_wf.unifize". 190731-15:35:43,398 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.combine_masks" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-02..func..sub-23649_ses-02_task-rest_echo-1_bold.nii.gz/combine_masks". 190731-15:35:43,400 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_mid_run_2_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_opposite_wf.enhance_and_skullstrip_bold_wf.fixhdr_unifize" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_2_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/enhance_and_skullstrip_bold_wf/fixhdr_unifize". 190731-15:35:43,402 nipype.workflow INFO: [Node] Running "combine_masks" ("nipype.interfaces.fsl.maths.BinaryMaths"), a CommandLine Interface with command: fslmaths /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-02..func..sub-23649_ses-02_task-rest_echo-1_bold.nii.gz/skullstrip_first_pass/ref_bold_corrected_brain_mask.nii.gz -mul /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-02..func..sub-23649_ses-02_task-rest_echo-1_bold.nii.gz/fixhdr_skullstrip2/uni_xform_mask_xform.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-02..func..sub-23649_ses-02_task-rest_echo-1_bold.nii.gz/combine_masks/ref_bold_corrected_brain_mask_maths.nii.gz 190731-15:35:43,402 nipype.workflow INFO: [Node] Running "fixhdr_unifize" ("niworkflows.interfaces.utils.CopyXForm") 190731-15:35:43,461 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_mid_run_2_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_opposite_wf.enhance_and_skullstrip_bold_wf.fixhdr_unifize". 190731-15:35:43,536 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.combine_masks". 190731-15:35:45,925 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.apply_mask" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-02..func..sub-23649_ses-02_task-rest_echo-1_bold.nii.gz/apply_mask". 190731-15:35:45,927 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_mid_run_2_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_opposite_wf.enhance_and_skullstrip_bold_wf.skullstrip_second_pass" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_2_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/enhance_and_skullstrip_bold_wf/skullstrip_second_pass". 190731-15:35:45,928 nipype.workflow INFO: [Node] Running "apply_mask" ("nipype.interfaces.fsl.maths.ApplyMask"), a CommandLine Interface with command: fslmaths /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-02..func..sub-23649_ses-02_task-rest_echo-1_bold.nii.gz/fixhdr_unifize/uni_xform.nii.gz -mas /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-02..func..sub-23649_ses-02_task-rest_echo-1_bold.nii.gz/combine_masks/ref_bold_corrected_brain_mask_maths.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_02_task_rest_echo_1_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/_bold_file_..gs11..users..MBDU..bids..mid_longitudinal_20190717..sub-23649..ses-02..func..sub-23649_ses-02_task-rest_echo-1_bold.nii.gz/apply_mask/uni_xform_masked.nii.gz 190731-15:35:45,931 nipype.workflow INFO: [Node] Running "skullstrip_second_pass" ("nipype.interfaces.afni.preprocess.Automask"), a CommandLine Interface with command: 3dAutomask -apply_prefix uni_xform_masked.nii.gz -dilate 1 -prefix uni_xform_mask.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_2_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/enhance_and_skullstrip_bold_wf/skullstrip_second_pass/uni_xform.nii.gz 190731-15:35:46,41 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_02_task_rest_echo_1_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.apply_mask". 190731-15:35:46,131 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_mid_run_2_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_opposite_wf.enhance_and_skullstrip_bold_wf.skullstrip_second_pass". 190731-15:35:47,454 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_mid_run_2_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_opposite_wf.enhance_and_skullstrip_bold_wf.fixhdr_skullstrip2" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_2_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/enhance_and_skullstrip_bold_wf/fixhdr_skullstrip2". 190731-15:35:47,456 nipype.workflow INFO: [Node] Running "fixhdr_skullstrip2" ("niworkflows.interfaces.utils.CopyXForm") 190731-15:35:47,481 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_mid_run_2_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_opposite_wf.enhance_and_skullstrip_bold_wf.fixhdr_skullstrip2". 190731-15:35:49,446 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_mid_run_2_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_opposite_wf.enhance_and_skullstrip_bold_wf.combine_masks" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_2_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/enhance_and_skullstrip_bold_wf/combine_masks". 190731-15:35:49,449 nipype.workflow INFO: [Node] Running "combine_masks" ("nipype.interfaces.fsl.maths.BinaryMaths"), a CommandLine Interface with command: fslmaths /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_2_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_pass/template_corrected_brain_mask.nii.gz -mul /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_2_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/enhance_and_skullstrip_bold_wf/fixhdr_skullstrip2/uni_xform_mask_xform.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_2_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/enhance_and_skullstrip_bold_wf/combine_masks/template_corrected_brain_mask_maths.nii.gz 190731-15:35:49,558 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_mid_run_2_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_opposite_wf.enhance_and_skullstrip_bold_wf.combine_masks". 190731-15:35:51,469 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_mid_run_2_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_opposite_wf.enhance_and_skullstrip_bold_wf.apply_mask" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_2_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/enhance_and_skullstrip_bold_wf/apply_mask". 190731-15:35:51,471 nipype.workflow INFO: [Node] Running "apply_mask" ("nipype.interfaces.fsl.maths.ApplyMask"), a CommandLine Interface with command: fslmaths /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_2_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/enhance_and_skullstrip_bold_wf/fixhdr_unifize/uni_xform.nii.gz -mas /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_2_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/enhance_and_skullstrip_bold_wf/combine_masks/template_corrected_brain_mask_maths.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_2_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/enhance_and_skullstrip_bold_wf/apply_mask/uni_xform_masked.nii.gz 190731-15:35:51,595 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_mid_run_2_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_opposite_wf.enhance_and_skullstrip_bold_wf.apply_mask". 190731-15:35:54,350 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_mid_run_1_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_opposite_wf.fmap2ref_reg". 190731-15:35:55,411 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_mid_run_1_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_matching_wf.fmap2ref_reg". 190731-15:35:55,416 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_mid_run_2_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_matching_wf.enhance_and_skullstrip_bold_wf.norm" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_2_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/enhance_and_skullstrip_bold_wf/norm". 190731-15:35:55,420 nipype.workflow INFO: [Node] Running "norm" ("niworkflows.interfaces.fixes.FixHeaderRegistration"), a CommandLine Interface with command: antsRegistration --collapse-output-transforms 1 --dimensionality 3 --float 1 --initial-moving-transform [ /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_2_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/enhance_and_skullstrip_bold_wf/init_aff/initialization.mat, 0 ] --initialize-transforms-per-stage 0 --interpolation Linear --output transform --transform Affine[ 0.1 ] --metric Mattes[ /home/sahad3/.cache/templateflow/tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_res-02_desc-fMRIPrep_boldref.nii.gz, /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_2_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/merge/template.nii.gz, 1, 64, Random, 0.2 ] --convergence [ 200, 1e-09, 10 ] --smoothing-sigmas 2.0mm --shrink-factors 2 --use-estimate-learning-rate-once 1 --use-histogram-matching 1 --winsorize-image-intensities [ 0.05, 0.98 ] --write-composite-transform 0 190731-15:35:57,415 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_mid_run_1_wf.sdc_wf.pepolar_unwarp_wf.qwarp" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_1_wf/sdc_wf/pepolar_unwarp_wf/qwarp". 190731-15:35:57,419 nipype.workflow INFO: [Node] Running "qwarp" ("nipype.interfaces.afni.preprocess.QwarpPlusMinus"), a CommandLine Interface with command: 3dQwarp -prefix Qwarp.nii.gz -plusminus -noXdis -noZdis -base /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_1_wf/sdc_wf/pepolar_unwarp_wf/qwarp/transform_Warped.nii.gz -blur -1.0 -1.0 -source /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_1_wf/sdc_wf/pepolar_unwarp_wf/qwarp/transform_Warped_c0000.nii.gz -minpatch 9 -nopadWARP -noweight -pblur 0.05 0.05 190731-15:36:03,456 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_mid_run_2_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_matching_wf.enhance_and_skullstrip_bold_wf.norm". 190731-15:36:05,417 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_mid_run_2_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_matching_wf.enhance_and_skullstrip_bold_wf.map_brainmask" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_2_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/enhance_and_skullstrip_bold_wf/map_brainmask". 190731-15:36:05,419 nipype.workflow INFO: [Node] Running "map_brainmask" ("niworkflows.interfaces.fixes.FixHeaderApplyTransforms"), a CommandLine Interface with command: antsApplyTransforms --default-value 0 --float 1 --input /home/sahad3/.cache/templateflow/tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_res-02_desc-brain_mask.nii.gz --interpolation MultiLabel --output tpl-MNI152NLin2009cAsym_res-02_desc-brain_mask_trans.nii.gz --reference-image /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_2_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/merge/template.nii.gz --transform [ /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_2_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/enhance_and_skullstrip_bold_wf/norm/transform0GenericAffine.mat, 1 ] 190731-15:36:05,445 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_mid_run_2_wf.bold_hmc_wf.fsl2itk" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_2_wf/bold_hmc_wf/fsl2itk". 190731-15:36:05,459 nipype.workflow INFO: [Node] Running "fsl2itk" ("niworkflows.interfaces.itk.MCFLIRT2ITK") 190731-15:36:07,453 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_mid_run_2_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_matching_wf.enhance_and_skullstrip_bold_wf.map_brainmask". 190731-15:36:09,444 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_mid_run_2_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_matching_wf.enhance_and_skullstrip_bold_wf.pre_mask_dilate" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_2_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/enhance_and_skullstrip_bold_wf/pre_mask_dilate". 190731-15:36:09,446 nipype.workflow INFO: [Node] Running "pre_mask_dilate" ("nipype.interfaces.fsl.maths.DilateImage"), a CommandLine Interface with command: fslmaths -dt char /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_2_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/enhance_and_skullstrip_bold_wf/map_brainmask/tpl-MNI152NLin2009cAsym_res-02_desc-brain_mask_trans.nii.gz -kernel sphere 3.0000 -dilF /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_2_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/enhance_and_skullstrip_bold_wf/pre_mask_dilate/tpl-MNI152NLin2009cAsym_res-02_desc-brain_mask_trans_dil.nii.gz 190731-15:36:09,802 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_mid_run_2_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_matching_wf.enhance_and_skullstrip_bold_wf.pre_mask_dilate". 190731-15:36:11,489 nipype.interface WARNING: q-forms of reference and mask are substantially different 190731-15:36:13,438 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_mid_run_2_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_matching_wf.enhance_and_skullstrip_bold_wf.n4_correct" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_2_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/enhance_and_skullstrip_bold_wf/n4_correct". 190731-15:36:13,440 nipype.workflow INFO: [Node] Running "n4_correct" ("nipype.interfaces.ants.segmentation.N4BiasFieldCorrection"), a CommandLine Interface with command: N4BiasFieldCorrection --bspline-fitting [ 200 ] -d 3 --input-image /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_2_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/merge/template.nii.gz --mask-image /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_2_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/enhance_and_skullstrip_bold_wf/check_hdr/tpl-MNI152NLin2009cAsym_res-02_desc-brain_mask_trans_dil_hdr.nii.gz --output template_corrected.nii.gz 190731-15:36:15,914 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_mid_run_2_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_matching_wf.enhance_and_skullstrip_bold_wf.n4_correct". 190731-15:36:17,461 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_mid_run_2_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_matching_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_pass" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_2_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_pass". 190731-15:36:17,463 nipype.workflow INFO: [Node] Running "skullstrip_first_pass" ("nipype.interfaces.fsl.preprocess.BET"), a CommandLine Interface with command: bet /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_2_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/enhance_and_skullstrip_bold_wf/n4_correct/template_corrected.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_2_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_pass/template_corrected_brain.nii.gz -f 0.20 -m 190731-15:36:19,841 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_mid_run_2_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_matching_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_pass". 190731-15:36:21,763 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_mid_run_2_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_matching_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_dilate" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_2_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_dilate". 190731-15:36:21,765 nipype.workflow INFO: [Node] Running "skullstrip_first_dilate" ("nipype.interfaces.fsl.maths.DilateImage"), a CommandLine Interface with command: fslmaths -dt char /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_2_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_pass/template_corrected_brain_mask.nii.gz -kernel sphere 6.0000 -dilF /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_2_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_dilate/template_corrected_brain_mask_dil.nii.gz 190731-15:36:22,318 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_mid_run_2_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_matching_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_dilate". 190731-15:36:23,450 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_mid_run_2_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_matching_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_mask" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_2_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_mask". 190731-15:36:23,453 nipype.workflow INFO: [Node] Running "skullstrip_first_mask" ("nipype.interfaces.fsl.maths.ApplyMask"), a CommandLine Interface with command: fslmaths /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_2_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_pass/template_corrected_brain.nii.gz -mas /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_2_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_dilate/template_corrected_brain_mask_dil.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_2_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_mask/template_corrected_brain_masked.nii.gz 190731-15:36:23,610 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_mid_run_2_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_matching_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_mask". 190731-15:36:25,557 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_mid_run_2_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_matching_wf.enhance_and_skullstrip_bold_wf.unifize" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_2_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/enhance_and_skullstrip_bold_wf/unifize". 190731-15:36:25,560 nipype.workflow INFO: [Node] Running "unifize" ("nipype.interfaces.afni.utils.Unifize"), a CommandLine Interface with command: 3dUnifize -clfrac 0.2 -rbt 18.3 65.0 90.0 -prefix uni.nii.gz -T2 -input /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_2_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/enhance_and_skullstrip_bold_wf/unifize/template_corrected_brain_masked.nii.gz 190731-15:36:26,896 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_mid_run_2_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_matching_wf.enhance_and_skullstrip_bold_wf.unifize". 190731-15:36:27,469 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_mid_run_2_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_matching_wf.enhance_and_skullstrip_bold_wf.fixhdr_unifize" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_2_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/enhance_and_skullstrip_bold_wf/fixhdr_unifize". 190731-15:36:27,472 nipype.workflow INFO: [Node] Running "fixhdr_unifize" ("niworkflows.interfaces.utils.CopyXForm") 190731-15:36:27,520 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_mid_run_2_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_matching_wf.enhance_and_skullstrip_bold_wf.fixhdr_unifize". 190731-15:36:29,474 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_mid_run_2_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_matching_wf.enhance_and_skullstrip_bold_wf.skullstrip_second_pass" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_2_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/enhance_and_skullstrip_bold_wf/skullstrip_second_pass". 190731-15:36:29,476 nipype.workflow INFO: [Node] Running "skullstrip_second_pass" ("nipype.interfaces.afni.preprocess.Automask"), a CommandLine Interface with command: 3dAutomask -apply_prefix uni_xform_masked.nii.gz -dilate 1 -prefix uni_xform_mask.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_2_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/enhance_and_skullstrip_bold_wf/skullstrip_second_pass/uni_xform.nii.gz 190731-15:36:29,734 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_mid_run_2_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_matching_wf.enhance_and_skullstrip_bold_wf.skullstrip_second_pass". 190731-15:36:31,697 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_mid_run_2_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_matching_wf.enhance_and_skullstrip_bold_wf.fixhdr_skullstrip2" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_2_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/enhance_and_skullstrip_bold_wf/fixhdr_skullstrip2". 190731-15:36:31,699 nipype.workflow INFO: [Node] Running "fixhdr_skullstrip2" ("niworkflows.interfaces.utils.CopyXForm") 190731-15:36:31,731 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_mid_run_2_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_matching_wf.enhance_and_skullstrip_bold_wf.fixhdr_skullstrip2". 190731-15:36:33,710 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_mid_run_2_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_matching_wf.enhance_and_skullstrip_bold_wf.combine_masks" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_2_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/enhance_and_skullstrip_bold_wf/combine_masks". 190731-15:36:33,712 nipype.workflow INFO: [Node] Running "combine_masks" ("nipype.interfaces.fsl.maths.BinaryMaths"), a CommandLine Interface with command: fslmaths /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_2_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_pass/template_corrected_brain_mask.nii.gz -mul /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_2_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/enhance_and_skullstrip_bold_wf/fixhdr_skullstrip2/uni_xform_mask_xform.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_2_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/enhance_and_skullstrip_bold_wf/combine_masks/template_corrected_brain_mask_maths.nii.gz 190731-15:36:33,827 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_mid_run_2_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_matching_wf.enhance_and_skullstrip_bold_wf.combine_masks". 190731-15:36:35,514 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_mid_run_2_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_matching_wf.enhance_and_skullstrip_bold_wf.apply_mask" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_2_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/enhance_and_skullstrip_bold_wf/apply_mask". 190731-15:36:35,516 nipype.workflow INFO: [Node] Running "apply_mask" ("nipype.interfaces.fsl.maths.ApplyMask"), a CommandLine Interface with command: fslmaths /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_2_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/enhance_and_skullstrip_bold_wf/fixhdr_unifize/uni_xform.nii.gz -mas /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_2_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/enhance_and_skullstrip_bold_wf/combine_masks/template_corrected_brain_mask_maths.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_2_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/enhance_and_skullstrip_bold_wf/apply_mask/uni_xform_masked.nii.gz 190731-15:36:35,670 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_mid_run_2_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_matching_wf.enhance_and_skullstrip_bold_wf.apply_mask". 190731-15:36:42,571 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_mid_run_2_wf.bold_hmc_wf.fsl2itk". 190731-15:36:43,465 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_mid_run_2_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.init_aff" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_2_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/init_aff". 190731-15:36:43,468 nipype.workflow INFO: [Node] Running "init_aff" ("niworkflows.interfaces.ants.AI"), a CommandLine Interface with command: antsAI -c [10,0.000001,10] -d 3 -x /home/sahad3/.cache/templateflow/tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_res-02_desc-brain_mask.nii.gz -m Mattes[/home/sahad3/.cache/templateflow/tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_res-02_desc-fMRIPrep_boldref.nii.gz,/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_2_wf/bold_reference_wf/gen_ref/ref_bold.nii.gz,32,Regular,0.200000] -o initialization.mat -p 0 -s [20.000000,0.120000] -t Affine[0.100000] -v 1 190731-15:36:50,453 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_mid_run_2_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.init_aff". 190731-15:36:51,577 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_mid_run_2_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.norm" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_2_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/norm". 190731-15:36:51,581 nipype.workflow INFO: [Node] Running "norm" ("niworkflows.interfaces.fixes.FixHeaderRegistration"), a CommandLine Interface with command: antsRegistration --collapse-output-transforms 1 --dimensionality 3 --float 1 --initial-moving-transform [ /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_2_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/init_aff/initialization.mat, 0 ] --initialize-transforms-per-stage 0 --interpolation Linear --output transform --transform Affine[ 0.1 ] --metric Mattes[ /home/sahad3/.cache/templateflow/tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_res-02_desc-fMRIPrep_boldref.nii.gz, /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_2_wf/bold_reference_wf/gen_ref/ref_bold.nii.gz, 1, 64, Random, 0.2 ] --convergence [ 200, 1e-09, 10 ] --smoothing-sigmas 2.0mm --shrink-factors 2 --use-estimate-learning-rate-once 1 --use-histogram-matching 1 --winsorize-image-intensities [ 0.05, 0.98 ] --write-composite-transform 0 190731-15:36:54,157 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_mid_run_2_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.norm". 190731-15:36:55,521 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_mid_run_2_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.map_brainmask" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_2_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/map_brainmask". 190731-15:36:55,524 nipype.workflow INFO: [Node] Running "map_brainmask" ("niworkflows.interfaces.fixes.FixHeaderApplyTransforms"), a CommandLine Interface with command: antsApplyTransforms --default-value 0 --float 1 --input /home/sahad3/.cache/templateflow/tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_res-02_desc-brain_mask.nii.gz --interpolation MultiLabel --output tpl-MNI152NLin2009cAsym_res-02_desc-brain_mask_trans.nii.gz --reference-image /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_2_wf/bold_reference_wf/gen_ref/ref_bold.nii.gz --transform [ /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_2_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/norm/transform0GenericAffine.mat, 1 ] 190731-15:36:55,537 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_rest_echo_1_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_opposite_wf.enhance_and_skullstrip_bold_wf.init_aff" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/enhance_and_skullstrip_bold_wf/init_aff". 190731-15:36:55,541 nipype.workflow INFO: [Node] Running "init_aff" ("niworkflows.interfaces.ants.AI"), a CommandLine Interface with command: antsAI -c [10,0.000001,10] -d 3 -x /home/sahad3/.cache/templateflow/tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_res-02_desc-brain_mask.nii.gz -m Mattes[/home/sahad3/.cache/templateflow/tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_res-02_desc-fMRIPrep_boldref.nii.gz,/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/merge/template.nii.gz,32,Regular,0.200000] -o initialization.mat -p 0 -s [20.000000,0.120000] -t Affine[0.100000] -v 1 190731-15:36:58,110 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_mid_run_2_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.map_brainmask". 190731-15:36:59,493 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_mid_run_2_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.pre_mask_dilate" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_2_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/pre_mask_dilate". 190731-15:36:59,496 nipype.workflow INFO: [Node] Running "pre_mask_dilate" ("nipype.interfaces.fsl.maths.DilateImage"), a CommandLine Interface with command: fslmaths -dt char /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_2_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/map_brainmask/tpl-MNI152NLin2009cAsym_res-02_desc-brain_mask_trans.nii.gz -kernel sphere 3.0000 -dilF /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_2_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/pre_mask_dilate/tpl-MNI152NLin2009cAsym_res-02_desc-brain_mask_trans_dil.nii.gz 190731-15:36:59,793 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_mid_run_2_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.pre_mask_dilate". 190731-15:37:02,991 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_mid_run_1_wf.sdc_wf.pepolar_unwarp_wf.qwarp". 190731-15:37:03,217 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_rest_echo_1_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_opposite_wf.enhance_and_skullstrip_bold_wf.init_aff". 190731-15:37:03,478 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_mid_run_2_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.n4_correct" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_2_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/n4_correct". 190731-15:37:03,480 nipype.workflow INFO: [Node] Running "n4_correct" ("nipype.interfaces.ants.segmentation.N4BiasFieldCorrection"), a CommandLine Interface with command: N4BiasFieldCorrection --bspline-fitting [ 200 ] -d 3 --input-image /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_2_wf/bold_reference_wf/gen_ref/ref_bold.nii.gz --mask-image /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_2_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/check_hdr/tpl-MNI152NLin2009cAsym_res-02_desc-brain_mask_trans_dil_hdr.nii.gz --output ref_bold_corrected.nii.gz 190731-15:37:05,537 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_mid_run_1_wf.sdc_wf.pepolar_unwarp_wf.cphdr_warp" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_1_wf/sdc_wf/pepolar_unwarp_wf/cphdr_warp". 190731-15:37:05,539 nipype.workflow INFO: [Node] Running "cphdr_warp" ("niworkflows.interfaces.utils.CopyHeader") 190731-15:37:05,541 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_rest_echo_1_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_opposite_wf.enhance_and_skullstrip_bold_wf.norm" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/enhance_and_skullstrip_bold_wf/norm". 190731-15:37:05,543 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_rest_echo_1_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_matching_wf.enhance_and_skullstrip_bold_wf.init_aff" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/enhance_and_skullstrip_bold_wf/init_aff". 190731-15:37:05,545 nipype.workflow INFO: [Node] Running "norm" ("niworkflows.interfaces.fixes.FixHeaderRegistration"), a CommandLine Interface with command: antsRegistration --collapse-output-transforms 1 --dimensionality 3 --float 1 --initial-moving-transform [ /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/enhance_and_skullstrip_bold_wf/init_aff/initialization.mat, 0 ] --initialize-transforms-per-stage 0 --interpolation Linear --output transform --transform Affine[ 0.1 ] --metric Mattes[ /home/sahad3/.cache/templateflow/tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_res-02_desc-fMRIPrep_boldref.nii.gz, /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/merge/template.nii.gz, 1, 64, Random, 0.2 ] --convergence [ 200, 1e-09, 10 ] --smoothing-sigmas 2.0mm --shrink-factors 2 --use-estimate-learning-rate-once 1 --use-histogram-matching 1 --winsorize-image-intensities [ 0.05, 0.98 ] --write-composite-transform 0 190731-15:37:05,546 nipype.workflow INFO: [Node] Running "init_aff" ("niworkflows.interfaces.ants.AI"), a CommandLine Interface with command: antsAI -c [10,0.000001,10] -d 3 -x /home/sahad3/.cache/templateflow/tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_res-02_desc-brain_mask.nii.gz -m Mattes[/home/sahad3/.cache/templateflow/tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_res-02_desc-fMRIPrep_boldref.nii.gz,/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/merge/template.nii.gz,32,Regular,0.200000] -o initialization.mat -p 0 -s [20.000000,0.120000] -t Affine[0.100000] -v 1 190731-15:37:05,660 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_mid_run_1_wf.sdc_wf.pepolar_unwarp_wf.cphdr_warp". 190731-15:37:05,994 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_mid_run_2_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.n4_correct". 190731-15:37:06,635 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_rest_echo_1_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_opposite_wf.enhance_and_skullstrip_bold_wf.norm". 190731-15:37:07,476 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_mid_run_1_wf.sdc_wf.pepolar_unwarp_wf.to_ants" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_1_wf/sdc_wf/pepolar_unwarp_wf/to_ants". 190731-15:37:07,478 nipype.workflow INFO: [Node] Running "to_ants" ("nipype.interfaces.utility.wrappers.Function") 190731-15:37:07,478 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_mid_run_2_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_pass" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_2_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_pass". 190731-15:37:07,481 nipype.workflow INFO: [Node] Running "skullstrip_first_pass" ("nipype.interfaces.fsl.preprocess.BET"), a CommandLine Interface with command: bet /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_2_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/n4_correct/ref_bold_corrected.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_2_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_pass/ref_bold_corrected_brain.nii.gz -f 0.20 -m 190731-15:37:07,483 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_rest_echo_1_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_opposite_wf.enhance_and_skullstrip_bold_wf.map_brainmask" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/enhance_and_skullstrip_bold_wf/map_brainmask". 190731-15:37:07,486 nipype.workflow INFO: [Node] Running "map_brainmask" ("niworkflows.interfaces.fixes.FixHeaderApplyTransforms"), a CommandLine Interface with command: antsApplyTransforms --default-value 0 --float 1 --input /home/sahad3/.cache/templateflow/tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_res-02_desc-brain_mask.nii.gz --interpolation MultiLabel --output tpl-MNI152NLin2009cAsym_res-02_desc-brain_mask_trans.nii.gz --reference-image /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/merge/template.nii.gz --transform [ /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/enhance_and_skullstrip_bold_wf/norm/transform0GenericAffine.mat, 1 ] 190731-15:37:07,499 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_rest_echo_1_wf.bold_hmc_wf.fsl2itk" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_rest_echo_1_wf/bold_hmc_wf/fsl2itk". 190731-15:37:07,508 nipype.workflow INFO: [Node] Running "fsl2itk" ("niworkflows.interfaces.itk.MCFLIRT2ITK") 190731-15:37:07,556 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_mid_run_1_wf.sdc_wf.pepolar_unwarp_wf.to_ants". 190731-15:37:09,336 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_rest_echo_1_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_opposite_wf.enhance_and_skullstrip_bold_wf.map_brainmask". 190731-15:37:09,359 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_rest_echo_1_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_matching_wf.enhance_and_skullstrip_bold_wf.init_aff". 190731-15:37:09,365 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_mid_run_2_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_pass". 190731-15:37:10,5 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_mid_run_1_wf.sdc_wf.pepolar_unwarp_wf.unwarp_reference" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_1_wf/sdc_wf/pepolar_unwarp_wf/unwarp_reference". 190731-15:37:10,8 nipype.workflow INFO: [Node] Running "unwarp_reference" ("niworkflows.interfaces.registration.ANTSApplyTransformsRPT"), a CommandLine Interface with command: antsApplyTransforms --default-value 0 --dimensionality 3 --float 1 --input /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_1_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/n4_correct/ref_bold_corrected.nii.gz --interpolation LanczosWindowedSinc --output ref_bold_corrected_trans.nii.gz --reference-image /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_1_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/n4_correct/ref_bold_corrected.nii.gz --transform /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_1_wf/sdc_wf/pepolar_unwarp_wf/cphdr_warp/_warpfieldQwarp_PLUS_WARP_fixhdr.nii.gz 190731-15:37:11,534 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_mid_run_1_wf.bold_bold_trans_wf.bold_transform" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_1_wf/bold_bold_trans_wf/bold_transform". 190731-15:37:11,534 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_mid_run_2_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_dilate" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_2_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_dilate". 190731-15:37:11,536 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_rest_echo_1_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_opposite_wf.enhance_and_skullstrip_bold_wf.pre_mask_dilate" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/enhance_and_skullstrip_bold_wf/pre_mask_dilate". 190731-15:37:11,537 nipype.workflow INFO: [Node] Running "skullstrip_first_dilate" ("nipype.interfaces.fsl.maths.DilateImage"), a CommandLine Interface with command: fslmaths -dt char /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_2_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_pass/ref_bold_corrected_brain_mask.nii.gz -kernel sphere 6.0000 -dilF /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_2_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_dilate/ref_bold_corrected_brain_mask_dil.nii.gz 190731-15:37:11,538 nipype.workflow INFO: [Node] Running "pre_mask_dilate" ("nipype.interfaces.fsl.maths.DilateImage"), a CommandLine Interface with command: fslmaths -dt char /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/enhance_and_skullstrip_bold_wf/map_brainmask/tpl-MNI152NLin2009cAsym_res-02_desc-brain_mask_trans.nii.gz -kernel sphere 3.0000 -dilF /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/enhance_and_skullstrip_bold_wf/pre_mask_dilate/tpl-MNI152NLin2009cAsym_res-02_desc-brain_mask_trans_dil.nii.gz 190731-15:37:11,543 nipype.workflow INFO: [Node] Running "bold_transform" ("niworkflows.interfaces.itk.MultiApplyTransforms") 190731-15:37:11,660 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_mid_run_1_wf.sdc_wf.pepolar_unwarp_wf.unwarp_reference". 190731-15:37:11,702 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_rest_echo_1_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_opposite_wf.enhance_and_skullstrip_bold_wf.pre_mask_dilate". 190731-15:37:11,958 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_mid_run_2_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_dilate". 190731-15:37:13,521 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_mid_run_2_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_mask" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_2_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_mask". 190731-15:37:13,524 nipype.workflow INFO: [Node] Running "skullstrip_first_mask" ("nipype.interfaces.fsl.maths.ApplyMask"), a CommandLine Interface with command: fslmaths /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_2_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_pass/ref_bold_corrected_brain.nii.gz -mas /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_2_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_dilate/ref_bold_corrected_brain_mask_dil.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_2_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_mask/ref_bold_corrected_brain_masked.nii.gz 190731-15:37:13,657 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_mid_run_2_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_mask". 190731-15:37:15,473 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_mid_run_2_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.unifize" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_2_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/unifize". 190731-15:37:15,476 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_rest_echo_1_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_opposite_wf.enhance_and_skullstrip_bold_wf.n4_correct" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/enhance_and_skullstrip_bold_wf/n4_correct". 190731-15:37:15,476 nipype.workflow INFO: [Node] Running "unifize" ("nipype.interfaces.afni.utils.Unifize"), a CommandLine Interface with command: 3dUnifize -clfrac 0.2 -rbt 18.3 65.0 90.0 -prefix uni.nii.gz -T2 -input /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_2_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/unifize/ref_bold_corrected_brain_masked.nii.gz 190731-15:37:15,478 nipype.workflow INFO: [Node] Running "n4_correct" ("nipype.interfaces.ants.segmentation.N4BiasFieldCorrection"), a CommandLine Interface with command: N4BiasFieldCorrection --bspline-fitting [ 200 ] -d 3 --input-image /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/merge/template.nii.gz --mask-image /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/enhance_and_skullstrip_bold_wf/check_hdr/tpl-MNI152NLin2009cAsym_res-02_desc-brain_mask_trans_dil_hdr.nii.gz --output template_corrected.nii.gz 190731-15:37:16,780 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_mid_run_2_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.unifize". 190731-15:37:17,513 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_mid_run_2_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.fixhdr_unifize" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_2_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/fixhdr_unifize". 190731-15:37:17,514 nipype.workflow INFO: [Node] Running "fixhdr_unifize" ("niworkflows.interfaces.utils.CopyXForm") 190731-15:37:17,554 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_mid_run_2_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.fixhdr_unifize". 190731-15:37:17,746 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_rest_echo_1_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_opposite_wf.enhance_and_skullstrip_bold_wf.n4_correct". 190731-15:37:19,528 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_mid_run_2_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.skullstrip_second_pass" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_2_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_second_pass". 190731-15:37:19,529 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_rest_echo_1_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_opposite_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_pass" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_pass". 190731-15:37:19,531 nipype.workflow INFO: [Node] Running "skullstrip_first_pass" ("nipype.interfaces.fsl.preprocess.BET"), a CommandLine Interface with command: bet /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/enhance_and_skullstrip_bold_wf/n4_correct/template_corrected.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_pass/template_corrected_brain.nii.gz -f 0.20 -m 190731-15:37:19,531 nipype.workflow INFO: [Node] Running "skullstrip_second_pass" ("nipype.interfaces.afni.preprocess.Automask"), a CommandLine Interface with command: 3dAutomask -apply_prefix uni_xform_masked.nii.gz -dilate 1 -prefix uni_xform_mask.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_2_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_second_pass/uni_xform.nii.gz 190731-15:37:19,769 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_mid_run_2_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.skullstrip_second_pass". 190731-15:37:21,511 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_mid_run_2_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.fixhdr_skullstrip2" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_2_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/fixhdr_skullstrip2". 190731-15:37:21,513 nipype.workflow INFO: [Node] Running "fixhdr_skullstrip2" ("niworkflows.interfaces.utils.CopyXForm") 190731-15:37:21,534 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_mid_run_2_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.fixhdr_skullstrip2". 190731-15:37:21,948 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_rest_echo_1_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_opposite_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_pass". 190731-15:37:23,492 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_mid_run_2_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.combine_masks" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_2_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/combine_masks". 190731-15:37:23,494 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_rest_echo_1_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_opposite_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_dilate" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_dilate". 190731-15:37:23,496 nipype.workflow INFO: [Node] Running "combine_masks" ("nipype.interfaces.fsl.maths.BinaryMaths"), a CommandLine Interface with command: fslmaths /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_2_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_pass/ref_bold_corrected_brain_mask.nii.gz -mul /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_2_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/fixhdr_skullstrip2/uni_xform_mask_xform.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_2_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/combine_masks/ref_bold_corrected_brain_mask_maths.nii.gz 190731-15:37:23,498 nipype.workflow INFO: [Node] Running "skullstrip_first_dilate" ("nipype.interfaces.fsl.maths.DilateImage"), a CommandLine Interface with command: fslmaths -dt char /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_pass/template_corrected_brain_mask.nii.gz -kernel sphere 6.0000 -dilF /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_dilate/template_corrected_brain_mask_dil.nii.gz 190731-15:37:23,631 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_mid_run_2_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.combine_masks". 190731-15:37:23,831 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_rest_echo_1_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_opposite_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_dilate". 190731-15:37:25,496 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_mid_run_2_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.apply_mask" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_2_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/apply_mask". 190731-15:37:25,498 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_rest_echo_1_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_opposite_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_mask" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_mask". 190731-15:37:25,499 nipype.workflow INFO: [Node] Running "apply_mask" ("nipype.interfaces.fsl.maths.ApplyMask"), a CommandLine Interface with command: fslmaths /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_2_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/fixhdr_unifize/uni_xform.nii.gz -mas /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_2_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/combine_masks/ref_bold_corrected_brain_mask_maths.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_2_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/apply_mask/uni_xform_masked.nii.gz 190731-15:37:25,500 nipype.workflow INFO: [Node] Running "skullstrip_first_mask" ("nipype.interfaces.fsl.maths.ApplyMask"), a CommandLine Interface with command: fslmaths /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_pass/template_corrected_brain.nii.gz -mas /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_dilate/template_corrected_brain_mask_dil.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_mask/template_corrected_brain_masked.nii.gz 190731-15:37:25,625 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_rest_echo_1_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_opposite_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_mask". 190731-15:37:25,625 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_mid_run_2_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.apply_mask". 190731-15:37:26,689 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_rest_echo_1_wf.bold_hmc_wf.fsl2itk". 190731-15:37:27,535 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_rest_echo_1_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_opposite_wf.enhance_and_skullstrip_bold_wf.unifize" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/enhance_and_skullstrip_bold_wf/unifize". 190731-15:37:27,538 nipype.workflow INFO: [Node] Running "unifize" ("nipype.interfaces.afni.utils.Unifize"), a CommandLine Interface with command: 3dUnifize -clfrac 0.2 -rbt 18.3 65.0 90.0 -prefix uni.nii.gz -T2 -input /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/enhance_and_skullstrip_bold_wf/unifize/template_corrected_brain_masked.nii.gz 190731-15:37:27,544 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_mid_run_1_wf.sdc_wf.pepolar_unwarp_wf.enhance_and_skullstrip_bold_wf.init_aff" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_1_wf/sdc_wf/pepolar_unwarp_wf/enhance_and_skullstrip_bold_wf/init_aff". 190731-15:37:27,547 nipype.workflow INFO: [Node] Running "init_aff" ("niworkflows.interfaces.ants.AI"), a CommandLine Interface with command: antsAI -c [10,0.000001,10] -d 3 -x /home/sahad3/.cache/templateflow/tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_res-02_desc-brain_mask.nii.gz -m Mattes[/home/sahad3/.cache/templateflow/tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_res-02_desc-fMRIPrep_boldref.nii.gz,/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_1_wf/sdc_wf/pepolar_unwarp_wf/unwarp_reference/ref_bold_corrected_trans.nii.gz,32,Regular,0.200000] -o initialization.mat -p 0 -s [20.000000,0.120000] -t Affine[0.100000] -v 1 190731-15:37:28,778 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_rest_echo_1_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_opposite_wf.enhance_and_skullstrip_bold_wf.unifize". 190731-15:37:29,604 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_rest_echo_1_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_opposite_wf.enhance_and_skullstrip_bold_wf.fixhdr_unifize" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/enhance_and_skullstrip_bold_wf/fixhdr_unifize". 190731-15:37:29,606 nipype.workflow INFO: [Node] Running "fixhdr_unifize" ("niworkflows.interfaces.utils.CopyXForm") 190731-15:37:29,644 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_rest_echo_1_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_opposite_wf.enhance_and_skullstrip_bold_wf.fixhdr_unifize". 190731-15:37:31,481 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_rest_echo_1_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_opposite_wf.enhance_and_skullstrip_bold_wf.skullstrip_second_pass" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/enhance_and_skullstrip_bold_wf/skullstrip_second_pass". 190731-15:37:31,485 nipype.workflow INFO: [Node] Running "skullstrip_second_pass" ("nipype.interfaces.afni.preprocess.Automask"), a CommandLine Interface with command: 3dAutomask -apply_prefix uni_xform_masked.nii.gz -dilate 1 -prefix uni_xform_mask.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/enhance_and_skullstrip_bold_wf/skullstrip_second_pass/uni_xform.nii.gz 190731-15:37:31,694 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_rest_echo_1_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_opposite_wf.enhance_and_skullstrip_bold_wf.skullstrip_second_pass". 190731-15:37:33,533 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_rest_echo_1_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_opposite_wf.enhance_and_skullstrip_bold_wf.fixhdr_skullstrip2" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/enhance_and_skullstrip_bold_wf/fixhdr_skullstrip2". 190731-15:37:33,535 nipype.workflow INFO: [Node] Running "fixhdr_skullstrip2" ("niworkflows.interfaces.utils.CopyXForm") 190731-15:37:33,557 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_rest_echo_1_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_opposite_wf.enhance_and_skullstrip_bold_wf.fixhdr_skullstrip2". 190731-15:37:34,25 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_mid_run_1_wf.sdc_wf.pepolar_unwarp_wf.enhance_and_skullstrip_bold_wf.init_aff". 190731-15:37:35,486 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_mid_run_1_wf.sdc_wf.pepolar_unwarp_wf.enhance_and_skullstrip_bold_wf.norm" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_1_wf/sdc_wf/pepolar_unwarp_wf/enhance_and_skullstrip_bold_wf/norm". 190731-15:37:35,488 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_rest_echo_1_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_opposite_wf.enhance_and_skullstrip_bold_wf.combine_masks" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/enhance_and_skullstrip_bold_wf/combine_masks". 190731-15:37:35,490 nipype.workflow INFO: [Node] Running "norm" ("niworkflows.interfaces.fixes.FixHeaderRegistration"), a CommandLine Interface with command: antsRegistration --collapse-output-transforms 1 --dimensionality 3 --float 1 --initial-moving-transform [ /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_1_wf/sdc_wf/pepolar_unwarp_wf/enhance_and_skullstrip_bold_wf/init_aff/initialization.mat, 0 ] --initialize-transforms-per-stage 0 --interpolation Linear --output transform --transform Affine[ 0.1 ] --metric Mattes[ /home/sahad3/.cache/templateflow/tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_res-02_desc-fMRIPrep_boldref.nii.gz, /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_1_wf/sdc_wf/pepolar_unwarp_wf/unwarp_reference/ref_bold_corrected_trans.nii.gz, 1, 64, Random, 0.2 ] --convergence [ 200, 1e-09, 10 ] --smoothing-sigmas 2.0mm --shrink-factors 2 --use-estimate-learning-rate-once 1 --use-histogram-matching 1 --winsorize-image-intensities [ 0.05, 0.98 ] --write-composite-transform 0 190731-15:37:35,491 nipype.workflow INFO: [Node] Running "combine_masks" ("nipype.interfaces.fsl.maths.BinaryMaths"), a CommandLine Interface with command: fslmaths /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_pass/template_corrected_brain_mask.nii.gz -mul /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/enhance_and_skullstrip_bold_wf/fixhdr_skullstrip2/uni_xform_mask_xform.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/enhance_and_skullstrip_bold_wf/combine_masks/template_corrected_brain_mask_maths.nii.gz 190731-15:37:35,611 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_rest_echo_1_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_opposite_wf.enhance_and_skullstrip_bold_wf.combine_masks". 190731-15:37:37,379 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_mid_run_1_wf.sdc_wf.pepolar_unwarp_wf.enhance_and_skullstrip_bold_wf.norm". 190731-15:37:37,534 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_rest_echo_1_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_opposite_wf.enhance_and_skullstrip_bold_wf.apply_mask" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/enhance_and_skullstrip_bold_wf/apply_mask". 190731-15:37:37,538 nipype.workflow INFO: [Node] Running "apply_mask" ("nipype.interfaces.fsl.maths.ApplyMask"), a CommandLine Interface with command: fslmaths /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/enhance_and_skullstrip_bold_wf/fixhdr_unifize/uni_xform.nii.gz -mas /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/enhance_and_skullstrip_bold_wf/combine_masks/template_corrected_brain_mask_maths.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/enhance_and_skullstrip_bold_wf/apply_mask/uni_xform_masked.nii.gz 190731-15:37:37,699 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_rest_echo_1_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_opposite_wf.enhance_and_skullstrip_bold_wf.apply_mask". 190731-15:37:39,489 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_mid_run_1_wf.sdc_wf.pepolar_unwarp_wf.enhance_and_skullstrip_bold_wf.map_brainmask" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_1_wf/sdc_wf/pepolar_unwarp_wf/enhance_and_skullstrip_bold_wf/map_brainmask". 190731-15:37:39,492 nipype.workflow INFO: [Node] Running "map_brainmask" ("niworkflows.interfaces.fixes.FixHeaderApplyTransforms"), a CommandLine Interface with command: antsApplyTransforms --default-value 0 --float 1 --input /home/sahad3/.cache/templateflow/tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_res-02_desc-brain_mask.nii.gz --interpolation MultiLabel --output tpl-MNI152NLin2009cAsym_res-02_desc-brain_mask_trans.nii.gz --reference-image /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_1_wf/sdc_wf/pepolar_unwarp_wf/unwarp_reference/ref_bold_corrected_trans.nii.gz --transform [ /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_1_wf/sdc_wf/pepolar_unwarp_wf/enhance_and_skullstrip_bold_wf/norm/transform0GenericAffine.mat, 1 ] 190731-15:37:39,494 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_mid_run_2_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_matching_wf.fmap2ref_reg" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_2_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/fmap2ref_reg". 190731-15:37:39,501 nipype.workflow INFO: [Node] Running "fmap2ref_reg" ("nipype.interfaces.ants.registration.Registration"), a CommandLine Interface with command: antsRegistration --collapse-output-transforms 1 --dimensionality 3 --float 1 --initialize-transforms-per-stage 0 --interpolation LanczosWindowedSinc --output [ transform, transform_Warped.nii.gz ] --transform Translation[ 0.05 ] --metric Mattes[ /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_2_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/apply_mask/uni_xform_masked.nii.gz, /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_2_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/enhance_and_skullstrip_bold_wf/apply_mask/uni_xform_masked.nii.gz, 1, 64, Random, 0.5 ] --convergence [ 500, 1e-07, 200 ] --smoothing-sigmas 8.0mm --shrink-factors 2 --use-estimate-learning-rate-once 1 --use-histogram-matching 1 --transform Rigid[ 0.01 ] --metric Mattes[ /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_2_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/apply_mask/uni_xform_masked.nii.gz, /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_2_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/enhance_and_skullstrip_bold_wf/apply_mask/uni_xform_masked.nii.gz, 1, 64, Random, 0.5 ] --convergence [ 200, 1e-08, 100 ] --smoothing-sigmas 2.0mm --shrink-factors 1 --use-estimate-learning-rate-once 1 --use-histogram-matching 1 --winsorize-image-intensities [ 0.005, 0.998 ] --write-composite-transform 1 190731-15:37:41,702 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_mid_run_1_wf.sdc_wf.pepolar_unwarp_wf.enhance_and_skullstrip_bold_wf.map_brainmask". 190731-15:37:43,504 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_mid_run_1_wf.sdc_wf.pepolar_unwarp_wf.enhance_and_skullstrip_bold_wf.pre_mask_dilate" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_1_wf/sdc_wf/pepolar_unwarp_wf/enhance_and_skullstrip_bold_wf/pre_mask_dilate". 190731-15:37:43,507 nipype.workflow INFO: [Node] Running "pre_mask_dilate" ("nipype.interfaces.fsl.maths.DilateImage"), a CommandLine Interface with command: fslmaths -dt char /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_1_wf/sdc_wf/pepolar_unwarp_wf/enhance_and_skullstrip_bold_wf/map_brainmask/tpl-MNI152NLin2009cAsym_res-02_desc-brain_mask_trans.nii.gz -kernel sphere 3.0000 -dilF /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_1_wf/sdc_wf/pepolar_unwarp_wf/enhance_and_skullstrip_bold_wf/pre_mask_dilate/tpl-MNI152NLin2009cAsym_res-02_desc-brain_mask_trans_dil.nii.gz 190731-15:37:43,789 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_mid_run_1_wf.sdc_wf.pepolar_unwarp_wf.enhance_and_skullstrip_bold_wf.pre_mask_dilate". 190731-15:37:45,551 nipype.interface WARNING: q-forms of reference and mask are substantially different 190731-15:37:47,498 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_mid_run_1_wf.sdc_wf.pepolar_unwarp_wf.enhance_and_skullstrip_bold_wf.n4_correct" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_1_wf/sdc_wf/pepolar_unwarp_wf/enhance_and_skullstrip_bold_wf/n4_correct". 190731-15:37:47,502 nipype.workflow INFO: [Node] Running "n4_correct" ("nipype.interfaces.ants.segmentation.N4BiasFieldCorrection"), a CommandLine Interface with command: N4BiasFieldCorrection --bspline-fitting [ 200 ] -d 3 --input-image /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_1_wf/sdc_wf/pepolar_unwarp_wf/unwarp_reference/ref_bold_corrected_trans.nii.gz --mask-image /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_1_wf/sdc_wf/pepolar_unwarp_wf/enhance_and_skullstrip_bold_wf/check_hdr/tpl-MNI152NLin2009cAsym_res-02_desc-brain_mask_trans_dil_hdr.nii.gz --output ref_bold_corrected_trans_corrected.nii.gz 190731-15:37:50,155 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_mid_run_1_wf.sdc_wf.pepolar_unwarp_wf.enhance_and_skullstrip_bold_wf.n4_correct". 190731-15:37:51,498 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_mid_run_1_wf.sdc_wf.pepolar_unwarp_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_pass" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_1_wf/sdc_wf/pepolar_unwarp_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_pass". 190731-15:37:51,502 nipype.workflow INFO: [Node] Running "skullstrip_first_pass" ("nipype.interfaces.fsl.preprocess.BET"), a CommandLine Interface with command: bet /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_1_wf/sdc_wf/pepolar_unwarp_wf/enhance_and_skullstrip_bold_wf/n4_correct/ref_bold_corrected_trans_corrected.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_1_wf/sdc_wf/pepolar_unwarp_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_pass/ref_bold_corrected_trans_corrected_brain.nii.gz -f 0.20 -m 190731-15:37:53,702 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_mid_run_1_wf.sdc_wf.pepolar_unwarp_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_pass". 190731-15:37:55,518 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_mid_run_1_wf.sdc_wf.pepolar_unwarp_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_dilate" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_1_wf/sdc_wf/pepolar_unwarp_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_dilate". 190731-15:37:55,521 nipype.workflow INFO: [Node] Running "skullstrip_first_dilate" ("nipype.interfaces.fsl.maths.DilateImage"), a CommandLine Interface with command: fslmaths -dt char /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_1_wf/sdc_wf/pepolar_unwarp_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_pass/ref_bold_corrected_trans_corrected_brain_mask.nii.gz -kernel sphere 6.0000 -dilF /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_1_wf/sdc_wf/pepolar_unwarp_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_dilate/ref_bold_corrected_trans_corrected_brain_mask_dil.nii.gz 190731-15:37:55,967 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_mid_run_1_wf.sdc_wf.pepolar_unwarp_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_dilate". 190731-15:37:57,500 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_mid_run_1_wf.sdc_wf.pepolar_unwarp_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_mask" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_1_wf/sdc_wf/pepolar_unwarp_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_mask". 190731-15:37:57,504 nipype.workflow INFO: [Node] Running "skullstrip_first_mask" ("nipype.interfaces.fsl.maths.ApplyMask"), a CommandLine Interface with command: fslmaths /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_1_wf/sdc_wf/pepolar_unwarp_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_pass/ref_bold_corrected_trans_corrected_brain.nii.gz -mas /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_1_wf/sdc_wf/pepolar_unwarp_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_dilate/ref_bold_corrected_trans_corrected_brain_mask_dil.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_1_wf/sdc_wf/pepolar_unwarp_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_mask/ref_bold_corrected_trans_corrected_brain_masked.nii.gz 190731-15:37:57,676 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_mid_run_1_wf.sdc_wf.pepolar_unwarp_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_mask". 190731-15:37:59,525 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_mid_run_1_wf.sdc_wf.pepolar_unwarp_wf.enhance_and_skullstrip_bold_wf.unifize" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_1_wf/sdc_wf/pepolar_unwarp_wf/enhance_and_skullstrip_bold_wf/unifize". 190731-15:37:59,529 nipype.workflow INFO: [Node] Running "unifize" ("nipype.interfaces.afni.utils.Unifize"), a CommandLine Interface with command: 3dUnifize -clfrac 0.2 -rbt 18.3 65.0 90.0 -prefix uni.nii.gz -T2 -input /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_1_wf/sdc_wf/pepolar_unwarp_wf/enhance_and_skullstrip_bold_wf/unifize/ref_bold_corrected_trans_corrected_brain_masked.nii.gz 190731-15:38:00,836 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_mid_run_1_wf.sdc_wf.pepolar_unwarp_wf.enhance_and_skullstrip_bold_wf.unifize". 190731-15:38:01,3 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_mid_run_2_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_matching_wf.fmap2ref_reg". 190731-15:38:01,498 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_mid_run_1_wf.sdc_wf.pepolar_unwarp_wf.enhance_and_skullstrip_bold_wf.fixhdr_unifize" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_1_wf/sdc_wf/pepolar_unwarp_wf/enhance_and_skullstrip_bold_wf/fixhdr_unifize". 190731-15:38:01,500 nipype.workflow INFO: [Node] Running "fixhdr_unifize" ("niworkflows.interfaces.utils.CopyXForm") 190731-15:38:01,503 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_mid_run_2_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_opposite_wf.fmap2ref_reg" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_2_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/fmap2ref_reg". 190731-15:38:01,508 nipype.workflow INFO: [Node] Running "fmap2ref_reg" ("nipype.interfaces.ants.registration.Registration"), a CommandLine Interface with command: antsRegistration --collapse-output-transforms 1 --dimensionality 3 --float 1 --initialize-transforms-per-stage 0 --interpolation LanczosWindowedSinc --output [ transform, transform_Warped.nii.gz ] --transform Translation[ 0.05 ] --metric Mattes[ /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_2_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/apply_mask/uni_xform_masked.nii.gz, /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_2_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/enhance_and_skullstrip_bold_wf/apply_mask/uni_xform_masked.nii.gz, 1, 64, Random, 0.5 ] --convergence [ 500, 1e-07, 200 ] --smoothing-sigmas 8.0mm --shrink-factors 2 --use-estimate-learning-rate-once 1 --use-histogram-matching 1 --transform Rigid[ 0.01 ] --metric Mattes[ /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_2_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/apply_mask/uni_xform_masked.nii.gz, /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_2_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/enhance_and_skullstrip_bold_wf/apply_mask/uni_xform_masked.nii.gz, 1, 64, Random, 0.5 ] --convergence [ 200, 1e-08, 100 ] --smoothing-sigmas 2.0mm --shrink-factors 1 --use-estimate-learning-rate-once 1 --use-histogram-matching 1 --winsorize-image-intensities [ 0.005, 0.998 ] --write-composite-transform 1 190731-15:38:01,545 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_mid_run_1_wf.sdc_wf.pepolar_unwarp_wf.enhance_and_skullstrip_bold_wf.fixhdr_unifize". 190731-15:38:03,515 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_mid_run_1_wf.sdc_wf.pepolar_unwarp_wf.enhance_and_skullstrip_bold_wf.skullstrip_second_pass" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_1_wf/sdc_wf/pepolar_unwarp_wf/enhance_and_skullstrip_bold_wf/skullstrip_second_pass". 190731-15:38:03,519 nipype.workflow INFO: [Node] Running "skullstrip_second_pass" ("nipype.interfaces.afni.preprocess.Automask"), a CommandLine Interface with command: 3dAutomask -apply_prefix uni_xform_masked.nii.gz -dilate 1 -prefix uni_xform_mask.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_1_wf/sdc_wf/pepolar_unwarp_wf/enhance_and_skullstrip_bold_wf/skullstrip_second_pass/uni_xform.nii.gz 190731-15:38:03,685 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_mid_run_1_wf.sdc_wf.pepolar_unwarp_wf.enhance_and_skullstrip_bold_wf.skullstrip_second_pass". 190731-15:38:05,583 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_mid_run_1_wf.sdc_wf.pepolar_unwarp_wf.enhance_and_skullstrip_bold_wf.fixhdr_skullstrip2" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_1_wf/sdc_wf/pepolar_unwarp_wf/enhance_and_skullstrip_bold_wf/fixhdr_skullstrip2". 190731-15:38:05,585 nipype.workflow INFO: [Node] Running "fixhdr_skullstrip2" ("niworkflows.interfaces.utils.CopyXForm") 190731-15:38:05,620 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_mid_run_1_wf.sdc_wf.pepolar_unwarp_wf.enhance_and_skullstrip_bold_wf.fixhdr_skullstrip2". 190731-15:38:07,525 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_mid_run_1_wf.sdc_wf.pepolar_unwarp_wf.enhance_and_skullstrip_bold_wf.combine_masks" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_1_wf/sdc_wf/pepolar_unwarp_wf/enhance_and_skullstrip_bold_wf/combine_masks". 190731-15:38:07,528 nipype.workflow INFO: [Node] Running "combine_masks" ("nipype.interfaces.fsl.maths.BinaryMaths"), a CommandLine Interface with command: fslmaths /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_1_wf/sdc_wf/pepolar_unwarp_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_pass/ref_bold_corrected_trans_corrected_brain_mask.nii.gz -mul /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_1_wf/sdc_wf/pepolar_unwarp_wf/enhance_and_skullstrip_bold_wf/fixhdr_skullstrip2/uni_xform_mask_xform.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_1_wf/sdc_wf/pepolar_unwarp_wf/enhance_and_skullstrip_bold_wf/combine_masks/ref_bold_corrected_trans_corrected_brain_mask_maths.nii.gz 190731-15:38:07,649 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_mid_run_1_wf.sdc_wf.pepolar_unwarp_wf.enhance_and_skullstrip_bold_wf.combine_masks". 190731-15:38:09,554 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_mid_run_1_wf.sdc_wf.pepolar_unwarp_wf.enhance_and_skullstrip_bold_wf.apply_mask" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_1_wf/sdc_wf/pepolar_unwarp_wf/enhance_and_skullstrip_bold_wf/apply_mask". 190731-15:38:09,557 nipype.workflow INFO: [Node] Running "apply_mask" ("nipype.interfaces.fsl.maths.ApplyMask"), a CommandLine Interface with command: fslmaths /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_1_wf/sdc_wf/pepolar_unwarp_wf/enhance_and_skullstrip_bold_wf/fixhdr_unifize/uni_xform.nii.gz -mas /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_1_wf/sdc_wf/pepolar_unwarp_wf/enhance_and_skullstrip_bold_wf/combine_masks/ref_bold_corrected_trans_corrected_brain_mask_maths.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_1_wf/sdc_wf/pepolar_unwarp_wf/enhance_and_skullstrip_bold_wf/apply_mask/uni_xform_masked.nii.gz 190731-15:38:09,715 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_mid_run_1_wf.sdc_wf.pepolar_unwarp_wf.enhance_and_skullstrip_bold_wf.apply_mask". 190731-15:38:11,664 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_mid_run_1_wf.bold_bold_trans_wf.bold_transform". 190731-15:38:13,533 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_rest_echo_1_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_matching_wf.enhance_and_skullstrip_bold_wf.norm" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/enhance_and_skullstrip_bold_wf/norm". 190731-15:38:13,537 nipype.workflow INFO: [Node] Running "norm" ("niworkflows.interfaces.fixes.FixHeaderRegistration"), a CommandLine Interface with command: antsRegistration --collapse-output-transforms 1 --dimensionality 3 --float 1 --initial-moving-transform [ /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/enhance_and_skullstrip_bold_wf/init_aff/initialization.mat, 0 ] --initialize-transforms-per-stage 0 --interpolation Linear --output transform --transform Affine[ 0.1 ] --metric Mattes[ /home/sahad3/.cache/templateflow/tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_res-02_desc-fMRIPrep_boldref.nii.gz, /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/merge/template.nii.gz, 1, 64, Random, 0.2 ] --convergence [ 200, 1e-09, 10 ] --smoothing-sigmas 2.0mm --shrink-factors 2 --use-estimate-learning-rate-once 1 --use-histogram-matching 1 --winsorize-image-intensities [ 0.05, 0.98 ] --write-composite-transform 0 190731-15:38:13,576 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_mid_run_1_wf.bold_bold_trans_wf.merge" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_1_wf/bold_bold_trans_wf/merge". 190731-15:38:13,585 nipype.workflow INFO: [Node] Running "merge" ("fmriprep.interfaces.nilearn.Merge") 190731-15:38:15,301 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_rest_echo_1_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_matching_wf.enhance_and_skullstrip_bold_wf.norm". 190731-15:38:17,536 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_rest_echo_1_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_matching_wf.enhance_and_skullstrip_bold_wf.map_brainmask" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/enhance_and_skullstrip_bold_wf/map_brainmask". 190731-15:38:17,538 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_rest_echo_1_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.init_aff" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_rest_echo_1_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/init_aff". 190731-15:38:17,539 nipype.workflow INFO: [Node] Running "map_brainmask" ("niworkflows.interfaces.fixes.FixHeaderApplyTransforms"), a CommandLine Interface with command: antsApplyTransforms --default-value 0 --float 1 --input /home/sahad3/.cache/templateflow/tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_res-02_desc-brain_mask.nii.gz --interpolation MultiLabel --output tpl-MNI152NLin2009cAsym_res-02_desc-brain_mask_trans.nii.gz --reference-image /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/merge/template.nii.gz --transform [ /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/enhance_and_skullstrip_bold_wf/norm/transform0GenericAffine.mat, 1 ] 190731-15:38:17,541 nipype.workflow INFO: [Node] Running "init_aff" ("niworkflows.interfaces.ants.AI"), a CommandLine Interface with command: antsAI -c [10,0.000001,10] -d 3 -x /home/sahad3/.cache/templateflow/tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_res-02_desc-brain_mask.nii.gz -m Mattes[/home/sahad3/.cache/templateflow/tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_res-02_desc-fMRIPrep_boldref.nii.gz,/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_rest_echo_1_wf/bold_reference_wf/gen_ref/ref_bold.nii.gz,32,Regular,0.200000] -o initialization.mat -p 0 -s [20.000000,0.120000] -t Affine[0.100000] -v 1 190731-15:38:17,861 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_mid_run_2_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_opposite_wf.fmap2ref_reg". 190731-15:38:19,424 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_rest_echo_1_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_matching_wf.enhance_and_skullstrip_bold_wf.map_brainmask". 190731-15:38:19,526 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_mid_run_2_wf.sdc_wf.pepolar_unwarp_wf.qwarp" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_2_wf/sdc_wf/pepolar_unwarp_wf/qwarp". 190731-15:38:19,531 nipype.workflow INFO: [Node] Running "qwarp" ("nipype.interfaces.afni.preprocess.QwarpPlusMinus"), a CommandLine Interface with command: 3dQwarp -prefix Qwarp.nii.gz -plusminus -noXdis -noZdis -base /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_2_wf/sdc_wf/pepolar_unwarp_wf/qwarp/transform_Warped.nii.gz -blur -1.0 -1.0 -source /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_2_wf/sdc_wf/pepolar_unwarp_wf/qwarp/transform_Warped_c0000.nii.gz -minpatch 9 -nopadWARP -noweight -pblur 0.05 0.05 190731-15:38:21,532 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_rest_echo_1_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_matching_wf.enhance_and_skullstrip_bold_wf.pre_mask_dilate" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/enhance_and_skullstrip_bold_wf/pre_mask_dilate". 190731-15:38:21,535 nipype.workflow INFO: [Node] Running "pre_mask_dilate" ("nipype.interfaces.fsl.maths.DilateImage"), a CommandLine Interface with command: fslmaths -dt char /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/enhance_and_skullstrip_bold_wf/map_brainmask/tpl-MNI152NLin2009cAsym_res-02_desc-brain_mask_trans.nii.gz -kernel sphere 3.0000 -dilF /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/enhance_and_skullstrip_bold_wf/pre_mask_dilate/tpl-MNI152NLin2009cAsym_res-02_desc-brain_mask_trans_dil.nii.gz 190731-15:38:21,751 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_rest_echo_1_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_matching_wf.enhance_and_skullstrip_bold_wf.pre_mask_dilate". 190731-15:38:22,539 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_rest_echo_1_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.init_aff". 190731-15:38:24,90 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_rest_echo_1_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.norm" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_rest_echo_1_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/norm". 190731-15:38:24,97 nipype.workflow INFO: [Node] Running "norm" ("niworkflows.interfaces.fixes.FixHeaderRegistration"), a CommandLine Interface with command: antsRegistration --collapse-output-transforms 1 --dimensionality 3 --float 1 --initial-moving-transform [ /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_rest_echo_1_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/init_aff/initialization.mat, 0 ] --initialize-transforms-per-stage 0 --interpolation Linear --output transform --transform Affine[ 0.1 ] --metric Mattes[ /home/sahad3/.cache/templateflow/tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_res-02_desc-fMRIPrep_boldref.nii.gz, /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_rest_echo_1_wf/bold_reference_wf/gen_ref/ref_bold.nii.gz, 1, 64, Random, 0.2 ] --convergence [ 200, 1e-09, 10 ] --smoothing-sigmas 2.0mm --shrink-factors 2 --use-estimate-learning-rate-once 1 --use-histogram-matching 1 --winsorize-image-intensities [ 0.05, 0.98 ] --write-composite-transform 0 190731-15:38:25,526 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_rest_echo_1_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_matching_wf.enhance_and_skullstrip_bold_wf.n4_correct" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/enhance_and_skullstrip_bold_wf/n4_correct". 190731-15:38:25,529 nipype.workflow INFO: [Node] Running "n4_correct" ("nipype.interfaces.ants.segmentation.N4BiasFieldCorrection"), a CommandLine Interface with command: N4BiasFieldCorrection --bspline-fitting [ 200 ] -d 3 --input-image /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/merge/template.nii.gz --mask-image /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/enhance_and_skullstrip_bold_wf/check_hdr/tpl-MNI152NLin2009cAsym_res-02_desc-brain_mask_trans_dil_hdr.nii.gz --output template_corrected.nii.gz 190731-15:38:26,356 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_rest_echo_1_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.norm". 190731-15:38:27,535 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_rest_echo_1_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.map_brainmask" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_rest_echo_1_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/map_brainmask". 190731-15:38:27,538 nipype.workflow INFO: [Node] Running "map_brainmask" ("niworkflows.interfaces.fixes.FixHeaderApplyTransforms"), a CommandLine Interface with command: antsApplyTransforms --default-value 0 --float 1 --input /home/sahad3/.cache/templateflow/tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_res-02_desc-brain_mask.nii.gz --interpolation MultiLabel --output tpl-MNI152NLin2009cAsym_res-02_desc-brain_mask_trans.nii.gz --reference-image /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_rest_echo_1_wf/bold_reference_wf/gen_ref/ref_bold.nii.gz --transform [ /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_rest_echo_1_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/norm/transform0GenericAffine.mat, 1 ] 190731-15:38:27,547 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_04_task_mid_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_opposite_wf.enhance_and_skullstrip_bold_wf.init_aff" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_04_task_mid_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/enhance_and_skullstrip_bold_wf/init_aff". 190731-15:38:27,549 nipype.workflow INFO: [Node] Running "init_aff" ("niworkflows.interfaces.ants.AI"), a CommandLine Interface with command: antsAI -c [10,0.000001,10] -d 3 -x /home/sahad3/.cache/templateflow/tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_res-02_desc-brain_mask.nii.gz -m Mattes[/home/sahad3/.cache/templateflow/tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_res-02_desc-fMRIPrep_boldref.nii.gz,/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_04_task_mid_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/merge/template.nii.gz,32,Regular,0.200000] -o initialization.mat -p 0 -s [20.000000,0.120000] -t Affine[0.100000] -v 1 190731-15:38:27,881 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_rest_echo_1_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_matching_wf.enhance_and_skullstrip_bold_wf.n4_correct". 190731-15:38:28,668 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_mid_run_1_wf.bold_bold_trans_wf.merge". 190731-15:38:29,903 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_rest_echo_1_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.map_brainmask". 190731-15:38:33,18 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_04_task_mid_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_opposite_wf.enhance_and_skullstrip_bold_wf.init_aff". 190731-15:38:43,353 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_rest_echo_1_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_matching_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_pass" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_pass". 190731-15:38:43,356 nipype.workflow INFO: [Node] Running "skullstrip_first_pass" ("nipype.interfaces.fsl.preprocess.BET"), a CommandLine Interface with command: bet /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/enhance_and_skullstrip_bold_wf/n4_correct/template_corrected.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_pass/template_corrected_brain.nii.gz -f 0.20 -m 190731-15:38:43,359 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_mid_run_1_wf.bold_bold_trans_wf.bold_reference_wf.validate" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_1_wf/bold_bold_trans_wf/bold_reference_wf/validate". 190731-15:38:43,360 nipype.workflow INFO: [Node] Running "validate" ("niworkflows.interfaces.images.ValidateImage") 190731-15:38:43,870 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_rest_echo_1_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.pre_mask_dilate" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_rest_echo_1_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/pre_mask_dilate". 190731-15:38:43,872 nipype.workflow INFO: [Node] Running "pre_mask_dilate" ("nipype.interfaces.fsl.maths.DilateImage"), a CommandLine Interface with command: fslmaths -dt char /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_rest_echo_1_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/map_brainmask/tpl-MNI152NLin2009cAsym_res-02_desc-brain_mask_trans.nii.gz -kernel sphere 3.0000 -dilF /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_rest_echo_1_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/pre_mask_dilate/tpl-MNI152NLin2009cAsym_res-02_desc-brain_mask_trans_dil.nii.gz 190731-15:38:43,876 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_04_task_mid_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_opposite_wf.enhance_and_skullstrip_bold_wf.norm" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_04_task_mid_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/enhance_and_skullstrip_bold_wf/norm". 190731-15:38:43,882 nipype.workflow INFO: [Node] Running "norm" ("niworkflows.interfaces.fixes.FixHeaderRegistration"), a CommandLine Interface with command: antsRegistration --collapse-output-transforms 1 --dimensionality 3 --float 1 --initial-moving-transform [ /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_04_task_mid_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/enhance_and_skullstrip_bold_wf/init_aff/initialization.mat, 0 ] --initialize-transforms-per-stage 0 --interpolation Linear --output transform --transform Affine[ 0.1 ] --metric Mattes[ /home/sahad3/.cache/templateflow/tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_res-02_desc-fMRIPrep_boldref.nii.gz, /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_04_task_mid_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/merge/template.nii.gz, 1, 64, Random, 0.2 ] --convergence [ 200, 1e-09, 10 ] --smoothing-sigmas 2.0mm --shrink-factors 2 --use-estimate-learning-rate-once 1 --use-histogram-matching 1 --winsorize-image-intensities [ 0.05, 0.98 ] --write-composite-transform 0 190731-15:38:44,57 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_rest_echo_1_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.pre_mask_dilate". 190731-15:38:45,786 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_04_task_mid_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_opposite_wf.enhance_and_skullstrip_bold_wf.norm". 190731-15:38:47,561 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_rest_echo_1_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_matching_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_pass". 190731-15:38:47,674 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_mid_run_1_wf.bold_bold_trans_wf.bold_reference_wf.validate". 190731-15:38:47,891 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_rest_echo_1_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.n4_correct" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_rest_echo_1_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/n4_correct". 190731-15:38:47,893 nipype.workflow INFO: [Node] Running "n4_correct" ("nipype.interfaces.ants.segmentation.N4BiasFieldCorrection"), a CommandLine Interface with command: N4BiasFieldCorrection --bspline-fitting [ 200 ] -d 3 --input-image /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_rest_echo_1_wf/bold_reference_wf/gen_ref/ref_bold.nii.gz --mask-image /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_rest_echo_1_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/check_hdr/tpl-MNI152NLin2009cAsym_res-02_desc-brain_mask_trans_dil_hdr.nii.gz --output ref_bold_corrected.nii.gz 190731-15:38:47,894 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_04_task_mid_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_opposite_wf.enhance_and_skullstrip_bold_wf.map_brainmask" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_04_task_mid_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/enhance_and_skullstrip_bold_wf/map_brainmask". 190731-15:38:47,897 nipype.workflow INFO: [Node] Running "map_brainmask" ("niworkflows.interfaces.fixes.FixHeaderApplyTransforms"), a CommandLine Interface with command: antsApplyTransforms --default-value 0 --float 1 --input /home/sahad3/.cache/templateflow/tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_res-02_desc-brain_mask.nii.gz --interpolation MultiLabel --output tpl-MNI152NLin2009cAsym_res-02_desc-brain_mask_trans.nii.gz --reference-image /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_04_task_mid_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/merge/template.nii.gz --transform [ /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_04_task_mid_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/enhance_and_skullstrip_bold_wf/norm/transform0GenericAffine.mat, 1 ] 190731-15:38:47,897 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_04_task_mid_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_matching_wf.enhance_and_skullstrip_bold_wf.init_aff" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_04_task_mid_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/enhance_and_skullstrip_bold_wf/init_aff". 190731-15:38:47,900 nipype.workflow INFO: [Node] Running "init_aff" ("niworkflows.interfaces.ants.AI"), a CommandLine Interface with command: antsAI -c [10,0.000001,10] -d 3 -x /home/sahad3/.cache/templateflow/tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_res-02_desc-brain_mask.nii.gz -m Mattes[/home/sahad3/.cache/templateflow/tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_res-02_desc-fMRIPrep_boldref.nii.gz,/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_04_task_mid_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/merge/template.nii.gz,32,Regular,0.200000] -o initialization.mat -p 0 -s [20.000000,0.120000] -t Affine[0.100000] -v 1 190731-15:38:49,961 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_mid_run_1_wf.bold_bold_trans_wf.bold_reference_wf.gen_ref" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_1_wf/bold_bold_trans_wf/bold_reference_wf/gen_ref". 190731-15:38:49,964 nipype.workflow INFO: [Node] Running "gen_ref" ("niworkflows.interfaces.registration.EstimateReferenceImage") 190731-15:38:49,964 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_rest_echo_1_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_matching_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_dilate" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_dilate". 190731-15:38:49,967 nipype.workflow INFO: [Node] Running "skullstrip_first_dilate" ("nipype.interfaces.fsl.maths.DilateImage"), a CommandLine Interface with command: fslmaths -dt char /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_pass/template_corrected_brain_mask.nii.gz -kernel sphere 6.0000 -dilF /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_dilate/template_corrected_brain_mask_dil.nii.gz 190731-15:38:50,293 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_rest_echo_1_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.n4_correct". 190731-15:38:50,351 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_04_task_mid_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_opposite_wf.enhance_and_skullstrip_bold_wf.map_brainmask". 190731-15:38:50,461 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_rest_echo_1_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_matching_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_dilate". 190731-15:38:50,522 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_mid_run_1_wf.bold_bold_trans_wf.bold_reference_wf.gen_ref". 190731-15:38:52,402 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_rest_echo_1_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_matching_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_mask" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_mask". 190731-15:38:52,404 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_rest_echo_1_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_pass" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_rest_echo_1_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_pass". 190731-15:38:52,405 nipype.workflow INFO: [Node] Running "skullstrip_first_mask" ("nipype.interfaces.fsl.maths.ApplyMask"), a CommandLine Interface with command: fslmaths /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_pass/template_corrected_brain.nii.gz -mas /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_dilate/template_corrected_brain_mask_dil.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_mask/template_corrected_brain_masked.nii.gz 190731-15:38:52,406 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_04_task_mid_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_opposite_wf.enhance_and_skullstrip_bold_wf.pre_mask_dilate" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_04_task_mid_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/enhance_and_skullstrip_bold_wf/pre_mask_dilate". 190731-15:38:52,407 nipype.workflow INFO: [Node] Running "skullstrip_first_pass" ("nipype.interfaces.fsl.preprocess.BET"), a CommandLine Interface with command: bet /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_rest_echo_1_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/n4_correct/ref_bold_corrected.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_rest_echo_1_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_pass/ref_bold_corrected_brain.nii.gz -f 0.20 -m 190731-15:38:52,410 nipype.workflow INFO: [Node] Running "pre_mask_dilate" ("nipype.interfaces.fsl.maths.DilateImage"), a CommandLine Interface with command: fslmaths -dt char /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_04_task_mid_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/enhance_and_skullstrip_bold_wf/map_brainmask/tpl-MNI152NLin2009cAsym_res-02_desc-brain_mask_trans.nii.gz -kernel sphere 3.0000 -dilF /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_04_task_mid_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/enhance_and_skullstrip_bold_wf/pre_mask_dilate/tpl-MNI152NLin2009cAsym_res-02_desc-brain_mask_trans_dil.nii.gz 190731-15:38:52,529 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_rest_echo_1_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_matching_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_mask". 190731-15:38:52,702 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_04_task_mid_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_opposite_wf.enhance_and_skullstrip_bold_wf.pre_mask_dilate". 190731-15:38:53,405 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_04_task_mid_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_matching_wf.enhance_and_skullstrip_bold_wf.init_aff". 190731-15:38:53,901 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_rest_echo_1_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_matching_wf.enhance_and_skullstrip_bold_wf.unifize" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/enhance_and_skullstrip_bold_wf/unifize". 190731-15:38:53,905 nipype.workflow INFO: [Node] Running "unifize" ("nipype.interfaces.afni.utils.Unifize"), a CommandLine Interface with command: 3dUnifize -clfrac 0.2 -rbt 18.3 65.0 90.0 -prefix uni.nii.gz -T2 -input /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/enhance_and_skullstrip_bold_wf/unifize/template_corrected_brain_masked.nii.gz 190731-15:38:54,459 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_rest_echo_1_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_pass". 190731-15:38:55,142 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_rest_echo_1_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_matching_wf.enhance_and_skullstrip_bold_wf.unifize". 190731-15:38:55,863 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_mid_run_1_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.init_aff" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_1_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/init_aff". 190731-15:38:55,865 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_rest_echo_1_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_matching_wf.enhance_and_skullstrip_bold_wf.fixhdr_unifize" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/enhance_and_skullstrip_bold_wf/fixhdr_unifize". 190731-15:38:55,866 nipype.workflow INFO: [Node] Running "init_aff" ("niworkflows.interfaces.ants.AI"), a CommandLine Interface with command: antsAI -c [10,0.000001,10] -d 3 -x /home/sahad3/.cache/templateflow/tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_res-02_desc-brain_mask.nii.gz -m Mattes[/home/sahad3/.cache/templateflow/tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_res-02_desc-fMRIPrep_boldref.nii.gz,/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_1_wf/bold_bold_trans_wf/bold_reference_wf/gen_ref/ref_bold.nii.gz,32,Regular,0.200000] -o initialization.mat -p 0 -s [20.000000,0.120000] -t Affine[0.100000] -v 1 190731-15:38:55,867 nipype.workflow INFO: [Node] Running "fixhdr_unifize" ("niworkflows.interfaces.utils.CopyXForm") 190731-15:38:55,867 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_rest_echo_1_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_dilate" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_rest_echo_1_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_dilate". 190731-15:38:55,870 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_04_task_mid_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_opposite_wf.enhance_and_skullstrip_bold_wf.n4_correct" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_04_task_mid_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/enhance_and_skullstrip_bold_wf/n4_correct". 190731-15:38:55,871 nipype.workflow INFO: [Node] Running "skullstrip_first_dilate" ("nipype.interfaces.fsl.maths.DilateImage"), a CommandLine Interface with command: fslmaths -dt char /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_rest_echo_1_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_pass/ref_bold_corrected_brain_mask.nii.gz -kernel sphere 6.0000 -dilF /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_rest_echo_1_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_dilate/ref_bold_corrected_brain_mask_dil.nii.gz 190731-15:38:55,873 nipype.workflow INFO: [Node] Running "n4_correct" ("nipype.interfaces.ants.segmentation.N4BiasFieldCorrection"), a CommandLine Interface with command: N4BiasFieldCorrection --bspline-fitting [ 200 ] -d 3 --input-image /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_04_task_mid_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/merge/template.nii.gz --mask-image /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_04_task_mid_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/enhance_and_skullstrip_bold_wf/check_hdr/tpl-MNI152NLin2009cAsym_res-02_desc-brain_mask_trans_dil_hdr.nii.gz --output template_corrected.nii.gz 190731-15:38:55,913 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_rest_echo_1_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_matching_wf.enhance_and_skullstrip_bold_wf.fixhdr_unifize". 190731-15:38:56,438 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_rest_echo_1_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_dilate". 190731-15:38:57,959 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_rest_echo_1_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_matching_wf.enhance_and_skullstrip_bold_wf.skullstrip_second_pass" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/enhance_and_skullstrip_bold_wf/skullstrip_second_pass". 190731-15:38:57,962 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_rest_echo_1_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_mask" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_rest_echo_1_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_mask". 190731-15:38:57,963 nipype.workflow INFO: [Node] Running "skullstrip_second_pass" ("nipype.interfaces.afni.preprocess.Automask"), a CommandLine Interface with command: 3dAutomask -apply_prefix uni_xform_masked.nii.gz -dilate 1 -prefix uni_xform_mask.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/enhance_and_skullstrip_bold_wf/skullstrip_second_pass/uni_xform.nii.gz 190731-15:38:57,965 nipype.workflow INFO: [Node] Running "skullstrip_first_mask" ("nipype.interfaces.fsl.maths.ApplyMask"), a CommandLine Interface with command: fslmaths /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_rest_echo_1_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_pass/ref_bold_corrected_brain.nii.gz -mas /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_rest_echo_1_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_dilate/ref_bold_corrected_brain_mask_dil.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_rest_echo_1_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_mask/ref_bold_corrected_brain_masked.nii.gz 190731-15:38:58,128 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_rest_echo_1_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_mask". 190731-15:38:58,223 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_rest_echo_1_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_matching_wf.enhance_and_skullstrip_bold_wf.skullstrip_second_pass". 190731-15:38:58,678 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_04_task_mid_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_opposite_wf.enhance_and_skullstrip_bold_wf.n4_correct". 190731-15:38:59,982 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_rest_echo_1_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_matching_wf.enhance_and_skullstrip_bold_wf.fixhdr_skullstrip2" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/enhance_and_skullstrip_bold_wf/fixhdr_skullstrip2". 190731-15:38:59,984 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_rest_echo_1_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.unifize" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_rest_echo_1_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/unifize". 190731-15:38:59,985 nipype.workflow INFO: [Node] Running "fixhdr_skullstrip2" ("niworkflows.interfaces.utils.CopyXForm") 190731-15:38:59,986 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_04_task_mid_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_opposite_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_pass" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_04_task_mid_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_pass". 190731-15:38:59,987 nipype.workflow INFO: [Node] Running "unifize" ("nipype.interfaces.afni.utils.Unifize"), a CommandLine Interface with command: 3dUnifize -clfrac 0.2 -rbt 18.3 65.0 90.0 -prefix uni.nii.gz -T2 -input /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_rest_echo_1_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/unifize/ref_bold_corrected_brain_masked.nii.gz 190731-15:38:59,990 nipype.workflow INFO: [Node] Running "skullstrip_first_pass" ("nipype.interfaces.fsl.preprocess.BET"), a CommandLine Interface with command: bet /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_04_task_mid_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/enhance_and_skullstrip_bold_wf/n4_correct/template_corrected.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_04_task_mid_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_pass/template_corrected_brain.nii.gz -f 0.20 -m 190731-15:39:00,13 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_rest_echo_1_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_matching_wf.enhance_and_skullstrip_bold_wf.fixhdr_skullstrip2". 190731-15:39:01,310 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_mid_run_1_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.init_aff". 190731-15:39:01,327 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_rest_echo_1_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.unifize". 190731-15:39:01,880 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_mid_run_1_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.norm" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_1_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/norm". 190731-15:39:01,882 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_rest_echo_1_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_matching_wf.enhance_and_skullstrip_bold_wf.combine_masks" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/enhance_and_skullstrip_bold_wf/combine_masks". 190731-15:39:01,884 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_rest_echo_1_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.fixhdr_unifize" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_rest_echo_1_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/fixhdr_unifize". 190731-15:39:01,886 nipype.workflow INFO: [Node] Running "norm" ("niworkflows.interfaces.fixes.FixHeaderRegistration"), a CommandLine Interface with command: antsRegistration --collapse-output-transforms 1 --dimensionality 3 --float 1 --initial-moving-transform [ /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_1_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/init_aff/initialization.mat, 0 ] --initialize-transforms-per-stage 0 --interpolation Linear --output transform --transform Affine[ 0.1 ] --metric Mattes[ /home/sahad3/.cache/templateflow/tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_res-02_desc-fMRIPrep_boldref.nii.gz, /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_mid_run_1_wf/bold_bold_trans_wf/bold_reference_wf/gen_ref/ref_bold.nii.gz, 1, 64, Random, 0.2 ] --convergence [ 200, 1e-09, 10 ] --smoothing-sigmas 2.0mm --shrink-factors 2 --use-estimate-learning-rate-once 1 --use-histogram-matching 1 --winsorize-image-intensities [ 0.05, 0.98 ] --write-composite-transform 0 190731-15:39:01,886 nipype.workflow INFO: [Node] Running "combine_masks" ("nipype.interfaces.fsl.maths.BinaryMaths"), a CommandLine Interface with command: fslmaths /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_pass/template_corrected_brain_mask.nii.gz -mul /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/enhance_and_skullstrip_bold_wf/fixhdr_skullstrip2/uni_xform_mask_xform.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/enhance_and_skullstrip_bold_wf/combine_masks/template_corrected_brain_mask_maths.nii.gz 190731-15:39:01,887 nipype.workflow INFO: [Node] Running "fixhdr_unifize" ("niworkflows.interfaces.utils.CopyXForm") 190731-15:39:01,931 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_rest_echo_1_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.fixhdr_unifize". 190731-15:39:02,21 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_rest_echo_1_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_matching_wf.enhance_and_skullstrip_bold_wf.combine_masks". 190731-15:39:02,209 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_04_task_mid_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_opposite_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_pass". 190731-15:39:03,965 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_rest_echo_1_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_matching_wf.enhance_and_skullstrip_bold_wf.apply_mask" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/enhance_and_skullstrip_bold_wf/apply_mask". 190731-15:39:03,966 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_03_task_rest_echo_1_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.skullstrip_second_pass" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_rest_echo_1_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_second_pass". 190731-15:39:03,967 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_23649_wf.func_preproc_ses_04_task_mid_wf.sdc_wf.pepolar_unwarp_wf.prepare_epi_opposite_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_dilate" in "/lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_04_task_mid_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_opposite_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_dilate". 190731-15:39:03,968 nipype.workflow INFO: [Node] Running "apply_mask" ("nipype.interfaces.fsl.maths.ApplyMask"), a CommandLine Interface with command: fslmaths /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/enhance_and_skullstrip_bold_wf/fixhdr_unifize/uni_xform.nii.gz -mas /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/enhance_and_skullstrip_bold_wf/combine_masks/template_corrected_brain_mask_maths.nii.gz /lscratch/32709976/wrk/fmriprep_wf/single_subject_23649_wf/func_preproc_ses_03_task_rest_echo_1_wf/sdc_wf/pepolar_unwarp_wf/prepare_epi_matching_wf/enhance_and_skullstrip_bold_wf/apply_mask/uni_xform_masked.nii.gz 190731-15:39:03,969 nipype.workflow INFO: [Node] Running "skullstrip_second_pass" ("nipype.interfaces.afni.preprocess.Automask"), a CommandLine Interface with command: 3dAutomask -apply_prefix uni_xform_masked.nii.gz -dilate 1 -prefix uni_xform_mask.nii.gz