subject is sub-F058 WARNING: seccomp requested but not enabled, seccomp library is missing or too old 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: 601 Files, 9.32GB rest T1w 150 - Subjects bold 1 - Session  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). 191004-13:43:53,506 nipype.workflow IMPORTANT: Running fMRIPREP version 1.5.0: * BIDS dataset path: /scratch/punim0025/wave1_BIDS. * Participant list: ['F058']. * Run identifier: 20191004-134346_d4d707d9-abb2-47f8-978a-65448fb6c869. 191004-13:43:55,439 nipype.workflow IMPORTANT: Creating bold processing workflow for "/scratch/punim0025/wave1_BIDS/sub-F058/func/sub-F058_task-rest_bold.nii" (0.04 GB / 154 TRs). Memory resampled/largemem=0.18/0.25 GB. 191004-13:43:55,471 nipype.workflow IMPORTANT: No single-band-reference found for sub-F058_task-rest_bold.nii 191004-13:43:56,180 nipype.workflow IMPORTANT: Slice-timing correction will be included. 191004-13:43:56,199 nipype.workflow WARNING: SDC: no fieldmaps found or they were ignored (/scratch/punim0025/wave1_BIDS/sub-F058/func/sub-F058_task-rest_bold.nii). 191004-13:44:04,786 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* 1.5.0 (@fmriprep1; @fmriprep2; RRID:SCR_016216), which is based on *Nipype* 1.2.2 (@nipype1; @nipype2; RRID:SCR_002502). Anatomical data preprocessing : The T1-weighted (T1w) image was corrected for intensity non-uniformity (INU) with `N4BiasFieldCorrection` [@n4], distributed with ANTs 2.2.0 [@ants, RRID:SCR_004757], and used as T1w-reference throughout the workflow. 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]. Volume-based spatial normalization to one standard space (MNIPediatricAsym) 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 template was selected for spatial normalization: *MNI's unbiased standard MRI template for pediatric data from the 4.5 to 18.5y age range* [@mnipediatricasym, RRID:SCR_008796; TemplateFlow ID: MNIPediatricAsym]. Functional data preprocessing : For each of the 1 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*. The BOLD reference was then co-registered to the T1w reference using `flirt` [FSL 5.0.9, @flirt] with the boundary-based registration [@bbr] cost-function. 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 (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 standard space, generating a *preprocessed BOLD run in ['MNIPediatricAsym'] space*. First, a reference volume and its skull-stripped version were generated using a custom methodology of *fMRIPrep*. 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"). ### Copyright Waiver The above boilerplate text was automatically generated by fMRIPrep with the express intention that users should copy and paste this text into their manuscripts *unchanged*. It is released under the [CC0](https://creativecommons.org/publicdomain/zero/1.0/) license. ### References 191004-13:44:16,270 nipype.workflow WARNING: Error while checking node hash, forcing re-run. Although this error may not prevent the workflow from running, it could indicate a major problem. Please report a new issue at https://github.com/nipy/nipype/issues adding the following information: Node: fmriprep_wf.single_subject_F058_wf.func_preproc_task_rest_wf.bold_hmc_wf.normalize_motion Interface: niworkflows.interfaces.utils.NormalizeMotionParams Traceback: Traceback (most recent call last): File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/plugins/base.py", line 337, in _local_hash_check cached, updated = self.procs[jobid].is_cached() File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py", line 297, in is_cached hashed_inputs, hashvalue = self._get_hashval() File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py", line 494, in _get_hashval self._get_inputs() File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py", line 525, in _get_inputs (%s) does not contain any outputs.""" % (key, self.name, results_file)) RuntimeError: Error populating the input "in_file" of node "normalize_motion": the results file of the source node (/scratch/punim0025/work/fmriprep_wf/single_subject_F058_wf/func_preproc_task_rest_wf/bold_hmc_wf/mcflirt/result_mcflirt.pklz) does not contain any outputs. 191004-13:44:16,271 nipype.workflow WARNING: Error while checking node hash, forcing re-run. Although this error may not prevent the workflow from running, it could indicate a major problem. Please report a new issue at https://github.com/nipy/nipype/issues adding the following information: Node: fmriprep_wf.single_subject_F058_wf.func_preproc_task_rest_wf.bold_hmc_wf.fsl2itk Interface: niworkflows.interfaces.itk.MCFLIRT2ITK Traceback: Traceback (most recent call last): File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/plugins/base.py", line 337, in _local_hash_check cached, updated = self.procs[jobid].is_cached() File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py", line 297, in is_cached hashed_inputs, hashvalue = self._get_hashval() File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py", line 494, in _get_hashval self._get_inputs() File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py", line 525, in _get_inputs (%s) does not contain any outputs.""" % (key, self.name, results_file)) RuntimeError: Error populating the input "in_files" of node "fsl2itk": the results file of the source node (/scratch/punim0025/work/fmriprep_wf/single_subject_F058_wf/func_preproc_task_rest_wf/bold_hmc_wf/mcflirt/result_mcflirt.pklz) does not contain any outputs. 191004-13:44:19,659 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_F058_wf.anat_preproc_wf.brain_extraction_wf.lap_tmpl" in "/scratch/punim0025/work/fmriprep_wf/single_subject_F058_wf/anat_preproc_wf/brain_extraction_wf/lap_tmpl". 191004-13:44:19,659 nipype.workflow INFO: [Node] Outdated cache found for "fmriprep_wf.single_subject_F058_wf.anat_preproc_wf.brain_extraction_wf.lap_tmpl". 191004-13:44:19,887 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/epozzi/.cache/templateflow/tpl-OASIS30ANTs/tpl-OASIS30ANTs_res-01_T1w.nii.gz 1.5 1 191004-13:44:20,22 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_F058_wf.anat_preproc_wf.brain_extraction_wf.res_tmpl" in "/scratch/punim0025/work/fmriprep_wf/single_subject_F058_wf/anat_preproc_wf/brain_extraction_wf/res_tmpl". 191004-13:44:20,32 nipype.workflow INFO: [Node] Outdated cache found for "fmriprep_wf.single_subject_F058_wf.anat_preproc_wf.brain_extraction_wf.res_tmpl". 191004-13:44:20,249 nipype.workflow INFO: [Node] Running "res_tmpl" ("niworkflows.interfaces.ants.ResampleImageBySpacing"), a CommandLine Interface with command: ResampleImageBySpacing 3 /home/epozzi/.cache/templateflow/tpl-OASIS30ANTs/tpl-OASIS30ANTs_res-01_T1w.nii.gz tpl-OASIS30ANTs_res-01_T1w_resampled.nii.gz 4 4 4 1 191004-13:44:25,986 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_F058_wf.anat_preproc_wf.brain_extraction_wf.res_tmpl". 191004-13:44:26,285 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_F058_wf.func_preproc_task_rest_wf.bold_hmc_wf.fsl2itk" in "/scratch/punim0025/work/fmriprep_wf/single_subject_F058_wf/func_preproc_task_rest_wf/bold_hmc_wf/fsl2itk". 191004-13:44:26,305 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_F058_wf.func_preproc_task_rest_wf.bold_hmc_wf.normalize_motion" in "/scratch/punim0025/work/fmriprep_wf/single_subject_F058_wf/func_preproc_task_rest_wf/bold_hmc_wf/normalize_motion". 191004-13:44:28,112 nipype.workflow ERROR: Node normalize_motion failed to run on host spartan-bm063.hpc.unimelb.edu.au. 191004-13:44:28,180 nipype.workflow ERROR: Saving crash info to /scratch/punim0025/output_wave1/fmriprep/sub-F058/log/20191004-134346_d4d707d9-abb2-47f8-978a-65448fb6c869/crash-20191004-134428-epozzi-normalize_motion-e36c4028-e1e5-4de7-ac6b-fed92a283366.txt Traceback (most recent call last): File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/plugins/multiproc.py", line 69, in run_node result['result'] = node.run(updatehash=updatehash) File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py", line 411, in run cached, updated = self.is_cached() File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py", line 297, in is_cached hashed_inputs, hashvalue = self._get_hashval() File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py", line 494, in _get_hashval self._get_inputs() File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py", line 525, in _get_inputs (%s) does not contain any outputs.""" % (key, self.name, results_file)) RuntimeError: Error populating the input "in_file" of node "normalize_motion": the results file of the source node (/scratch/punim0025/work/fmriprep_wf/single_subject_F058_wf/func_preproc_task_rest_wf/bold_hmc_wf/mcflirt/result_mcflirt.pklz) does not contain any outputs. 191004-13:44:28,199 nipype.workflow ERROR: Node fsl2itk failed to run on host spartan-bm063.hpc.unimelb.edu.au. 191004-13:44:28,205 nipype.workflow ERROR: Saving crash info to /scratch/punim0025/output_wave1/fmriprep/sub-F058/log/20191004-134346_d4d707d9-abb2-47f8-978a-65448fb6c869/crash-20191004-134428-epozzi-fsl2itk-ebfcef3f-a3e8-46cc-ae8a-00044b015383.txt Traceback (most recent call last): File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/plugins/multiproc.py", line 69, in run_node result['result'] = node.run(updatehash=updatehash) File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py", line 411, in run cached, updated = self.is_cached() File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py", line 297, in is_cached hashed_inputs, hashvalue = self._get_hashval() File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py", line 494, in _get_hashval self._get_inputs() File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py", line 525, in _get_inputs (%s) does not contain any outputs.""" % (key, self.name, results_file)) RuntimeError: Error populating the input "in_files" of node "fsl2itk": the results file of the source node (/scratch/punim0025/work/fmriprep_wf/single_subject_F058_wf/func_preproc_task_rest_wf/bold_hmc_wf/mcflirt/result_mcflirt.pklz) does not contain any outputs. 191004-13:44:32,100 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_F058_wf.anat_preproc_wf.brain_extraction_wf.init_aff" in "/scratch/punim0025/work/fmriprep_wf/single_subject_F058_wf/anat_preproc_wf/brain_extraction_wf/init_aff". 191004-13:44:32,101 nipype.workflow INFO: [Node] Outdated cache found for "fmriprep_wf.single_subject_F058_wf.anat_preproc_wf.brain_extraction_wf.init_aff". 191004-13:44:32,113 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/epozzi/.cache/templateflow/tpl-OASIS30ANTs/tpl-OASIS30ANTs_res-01_desc-BrainCerebellumExtraction_mask.nii.gz -m Mattes[/scratch/punim0025/work/fmriprep_wf/single_subject_F058_wf/anat_preproc_wf/brain_extraction_wf/res_tmpl/tpl-OASIS30ANTs_res-01_T1w_resampled.nii.gz,/scratch/punim0025/work/fmriprep_wf/single_subject_F058_wf/anat_preproc_wf/brain_extraction_wf/res_target/sub-F058_T1w_maths_corrected_resampled.nii,32,Regular,0.250000] -o initialization.mat -p 0 -s [15.000000,0.100000] -t Affine[0.100000] -v 1 191004-13:44:33,397 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_F058_wf.anat_preproc_wf.brain_extraction_wf.lap_tmpl". 191004-13:44:35,634 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_F058_wf.anat_preproc_wf.brain_extraction_wf.mrg_tmpl" in "/scratch/punim0025/work/fmriprep_wf/single_subject_F058_wf/anat_preproc_wf/brain_extraction_wf/mrg_tmpl". 191004-13:44:35,634 nipype.workflow INFO: [Node] Outdated cache found for "fmriprep_wf.single_subject_F058_wf.anat_preproc_wf.brain_extraction_wf.mrg_tmpl". 191004-13:44:35,661 nipype.workflow INFO: [Node] Running "mrg_tmpl" ("nipype.interfaces.utility.base.Merge") 191004-13:44:35,669 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_F058_wf.anat_preproc_wf.brain_extraction_wf.mrg_tmpl". 191004-13:44:37,840 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_F058_wf.anat_preproc_wf.brain_extraction_wf.init_aff". 191004-13:44:43,935 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_F058_wf.anat_preproc_wf.brain_extraction_wf.norm" in "/scratch/punim0025/work/fmriprep_wf/single_subject_F058_wf/anat_preproc_wf/brain_extraction_wf/norm". 191004-13:44:43,935 nipype.workflow INFO: [Node] Outdated cache found for "fmriprep_wf.single_subject_F058_wf.anat_preproc_wf.brain_extraction_wf.norm". 191004-13:44:43,952 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 [ /scratch/punim0025/work/fmriprep_wf/single_subject_F058_wf/anat_preproc_wf/brain_extraction_wf/init_aff/initialization.mat, 0 ] --initialize-transforms-per-stage 0 --interpolation LanczosWindowedSinc --output [ anat_to_template, anat_to_template_Warped.nii.gz ] --transform Rigid[ 0.1 ] --metric MI[ /home/epozzi/.cache/templateflow/tpl-OASIS30ANTs/tpl-OASIS30ANTs_res-01_T1w.nii.gz, /scratch/punim0025/work/fmriprep_wf/single_subject_F058_wf/anat_preproc_wf/brain_extraction_wf/inu_n4/mapflow/_inu_n40/sub-F058_T1w_maths_corrected.nii, 1, 32, Regular, 0.25 ] --convergence [ 1000x500x250x100, 1e-08, 10 ] --smoothing-sigmas 4.0x2.0x1.0x0.0vox --shrink-factors 8x4x2x1 --use-histogram-matching 1 --masks [ /home/epozzi/.cache/templateflow/tpl-OASIS30ANTs/tpl-OASIS30ANTs_res-01_desc-BrainCerebellumExtraction_mask.nii.gz, NULL ] --transform Affine[ 0.1 ] --metric MI[ /home/epozzi/.cache/templateflow/tpl-OASIS30ANTs/tpl-OASIS30ANTs_res-01_T1w.nii.gz, /scratch/punim0025/work/fmriprep_wf/single_subject_F058_wf/anat_preproc_wf/brain_extraction_wf/inu_n4/mapflow/_inu_n40/sub-F058_T1w_maths_corrected.nii, 1, 32, Regular, 0.25 ] --convergence [ 1000x500x250x100, 1e-08, 10 ] --smoothing-sigmas 4.0x2.0x1.0x0.0vox --shrink-factors 8x4x2x1 --use-histogram-matching 1 --masks [ /home/epozzi/.cache/templateflow/tpl-OASIS30ANTs/tpl-OASIS30ANTs_res-01_desc-BrainCerebellumExtraction_mask.nii.gz, NULL ] --transform SyN[ 0.1, 3.0, 0.0 ] --metric CC[ /home/epozzi/.cache/templateflow/tpl-OASIS30ANTs/tpl-OASIS30ANTs_res-01_T1w.nii.gz, /scratch/punim0025/work/fmriprep_wf/single_subject_F058_wf/anat_preproc_wf/brain_extraction_wf/inu_n4/mapflow/_inu_n40/sub-F058_T1w_maths_corrected.nii, 0.5, 4, None, 1 ] --metric CC[ /scratch/punim0025/work/fmriprep_wf/single_subject_F058_wf/anat_preproc_wf/brain_extraction_wf/lap_tmpl/tpl-OASIS30ANTs_res-01_T1w_maths.nii.gz, /scratch/punim0025/work/fmriprep_wf/single_subject_F058_wf/anat_preproc_wf/brain_extraction_wf/lap_target/sub-F058_T1w_maths_corrected_maths.nii, 0.5, 4, None, 1 ] --convergence [ 50x10x0, 1e-09, 15 ] --smoothing-sigmas 2.0x1.0x0.0vox --shrink-factors 4x2x1 --use-histogram-matching 1 --masks [ /home/epozzi/.cache/templateflow/tpl-OASIS30ANTs/tpl-OASIS30ANTs_res-01_desc-BrainCerebellumExtraction_mask.nii.gz, NULL ] -v --winsorize-image-intensities [ 0.025, 0.975 ] --write-composite-transform 0 191004-14:29:39,463 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_F058_wf.anat_preproc_wf.brain_extraction_wf.norm". 191004-14:29:45,786 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_F058_wf.anat_preproc_wf.brain_extraction_wf.map_brainmask" in "/scratch/punim0025/work/fmriprep_wf/single_subject_F058_wf/anat_preproc_wf/brain_extraction_wf/map_brainmask". 191004-14:29:45,786 nipype.workflow INFO: [Node] Outdated cache found for "fmriprep_wf.single_subject_F058_wf.anat_preproc_wf.brain_extraction_wf.map_brainmask". 191004-14:29:45,798 nipype.workflow INFO: [Node] Running "map_brainmask" ("niworkflows.interfaces.fixes.FixHeaderApplyTransforms"), a CommandLine Interface with command: antsApplyTransforms --default-value 0 --float 1 --input /home/epozzi/.cache/templateflow/tpl-OASIS30ANTs/tpl-OASIS30ANTs_res-01_label-brain_probseg.nii.gz --interpolation Gaussian --output tpl-OASIS30ANTs_res-01_label-brain_probseg_trans.nii.gz --reference-image /scratch/punim0025/wave1_BIDS/sub-F058/anat/sub-F058_T1w.nii --transform [ /scratch/punim0025/work/fmriprep_wf/single_subject_F058_wf/anat_preproc_wf/brain_extraction_wf/norm/anat_to_template0GenericAffine.mat, 1 ] --transform [ /scratch/punim0025/work/fmriprep_wf/single_subject_F058_wf/anat_preproc_wf/brain_extraction_wf/norm/anat_to_template1InverseWarp.nii.gz, 0 ] 191004-14:30:17,861 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_F058_wf.anat_preproc_wf.brain_extraction_wf.map_brainmask". 191004-14:30:23,780 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_F058_wf.anat_preproc_wf.brain_extraction_wf.thr_brainmask" in "/scratch/punim0025/work/fmriprep_wf/single_subject_F058_wf/anat_preproc_wf/brain_extraction_wf/thr_brainmask". 191004-14:30:23,780 nipype.workflow INFO: [Node] Outdated cache found for "fmriprep_wf.single_subject_F058_wf.anat_preproc_wf.brain_extraction_wf.thr_brainmask". 191004-14:30:23,791 nipype.workflow INFO: [Node] Running "thr_brainmask" ("niworkflows.interfaces.ants.ThresholdImage"), a CommandLine Interface with command: ThresholdImage 3 /scratch/punim0025/work/fmriprep_wf/single_subject_F058_wf/anat_preproc_wf/brain_extraction_wf/map_brainmask/tpl-OASIS30ANTs_res-01_label-brain_probseg_trans.nii.gz tpl-OASIS30ANTs_res-01_label-brain_probseg_trans_resampled.nii.gz 0.500000 1.000000 1.000000 0.000000 191004-14:30:24,514 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_F058_wf.anat_preproc_wf.brain_extraction_wf.thr_brainmask". 191004-14:30:31,968 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_F058_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.03_pad_mask" in "/scratch/punim0025/work/fmriprep_wf/single_subject_F058_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/03_pad_mask". 191004-14:30:31,968 nipype.workflow INFO: [Node] Outdated cache found for "fmriprep_wf.single_subject_F058_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.03_pad_mask". 191004-14:30:31,983 nipype.workflow INFO: [Node] Running "03_pad_mask" ("niworkflows.interfaces.ants.ImageMath"), a CommandLine Interface with command: ImageMath 3 tpl-OASIS30ANTs_res-01_label-brain_probseg_trans_resampled_maths.nii.gz PadImage /scratch/punim0025/work/fmriprep_wf/single_subject_F058_wf/anat_preproc_wf/brain_extraction_wf/thr_brainmask/tpl-OASIS30ANTs_res-01_label-brain_probseg_trans_resampled.nii.gz 10 191004-14:30:32,172 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_F058_wf.anat_preproc_wf.brain_extraction_wf.dil_brainmask" in "/scratch/punim0025/work/fmriprep_wf/single_subject_F058_wf/anat_preproc_wf/brain_extraction_wf/dil_brainmask". 191004-14:30:32,172 nipype.workflow INFO: [Node] Outdated cache found for "fmriprep_wf.single_subject_F058_wf.anat_preproc_wf.brain_extraction_wf.dil_brainmask". 191004-14:30:32,189 nipype.workflow INFO: [Node] Running "dil_brainmask" ("niworkflows.interfaces.ants.ImageMath"), a CommandLine Interface with command: ImageMath 3 tpl-OASIS30ANTs_res-01_label-brain_probseg_trans_resampled_maths.nii.gz MD /scratch/punim0025/work/fmriprep_wf/single_subject_F058_wf/anat_preproc_wf/brain_extraction_wf/thr_brainmask/tpl-OASIS30ANTs_res-01_label-brain_probseg_trans_resampled.nii.gz 2 191004-14:30:32,897 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_F058_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.03_pad_mask". 191004-14:30:33,468 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_F058_wf.anat_preproc_wf.brain_extraction_wf.dil_brainmask". 191004-14:30:39,787 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_F058_wf.anat_preproc_wf.brain_extraction_wf.get_brainmask" in "/scratch/punim0025/work/fmriprep_wf/single_subject_F058_wf/anat_preproc_wf/brain_extraction_wf/get_brainmask". 191004-14:30:39,788 nipype.workflow INFO: [Node] Outdated cache found for "fmriprep_wf.single_subject_F058_wf.anat_preproc_wf.brain_extraction_wf.get_brainmask". 191004-14:30:39,799 nipype.workflow INFO: [Node] Running "get_brainmask" ("niworkflows.interfaces.ants.ImageMath"), a CommandLine Interface with command: ImageMath 3 tpl-OASIS30ANTs_res-01_label-brain_probseg_trans_resampled_maths_maths.nii.gz GetLargestComponent /scratch/punim0025/work/fmriprep_wf/single_subject_F058_wf/anat_preproc_wf/brain_extraction_wf/dil_brainmask/tpl-OASIS30ANTs_res-01_label-brain_probseg_trans_resampled_maths.nii.gz 191004-14:30:40,871 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_F058_wf.anat_preproc_wf.brain_extraction_wf.get_brainmask". 191004-14:30:43,312 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_F058_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.01_atropos" in "/scratch/punim0025/work/fmriprep_wf/single_subject_F058_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/01_atropos". 191004-14:30:43,313 nipype.workflow INFO: [Node] Outdated cache found for "fmriprep_wf.single_subject_F058_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.01_atropos". 191004-14:30:43,324 nipype.workflow INFO: [Node] Running "01_atropos" ("nipype.interfaces.ants.segmentation.Atropos"), a CommandLine Interface with command: Atropos --image-dimensionality 3 --initialization KMeans[3] --intensity-image /scratch/punim0025/work/fmriprep_wf/single_subject_F058_wf/anat_preproc_wf/brain_extraction_wf/inu_n4/mapflow/_inu_n40/sub-F058_T1w_maths_corrected.nii --likelihood-model Gaussian --mask-image /scratch/punim0025/work/fmriprep_wf/single_subject_F058_wf/anat_preproc_wf/brain_extraction_wf/get_brainmask/tpl-OASIS30ANTs_res-01_label-brain_probseg_trans_resampled_maths_maths.nii.gz --mrf [0.1,1x1x1] --convergence [3,0] --output [sub-F058_T1w_maths_corrected_labeled.nii] --use-random-seed 1 191004-14:31:39,451 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_F058_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.01_atropos". 191004-14:31:45,827 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_F058_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.02_pad_segm" in "/scratch/punim0025/work/fmriprep_wf/single_subject_F058_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/02_pad_segm". 191004-14:31:45,828 nipype.workflow INFO: [Node] Outdated cache found for "fmriprep_wf.single_subject_F058_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.02_pad_segm". 191004-14:31:45,840 nipype.workflow INFO: [Node] Running "02_pad_segm" ("niworkflows.interfaces.ants.ImageMath"), a CommandLine Interface with command: ImageMath 3 sub-F058_T1w_maths_corrected_labeled_maths.nii PadImage /scratch/punim0025/work/fmriprep_wf/single_subject_F058_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/01_atropos/sub-F058_T1w_maths_corrected_labeled.nii 10 191004-14:31:46,211 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_F058_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.02_pad_segm". 191004-14:31:49,313 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_F058_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.04_sel_labels" in "/scratch/punim0025/work/fmriprep_wf/single_subject_F058_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/04_sel_labels". 191004-14:31:49,313 nipype.workflow INFO: [Node] Outdated cache found for "fmriprep_wf.single_subject_F058_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.04_sel_labels". 191004-14:31:49,323 nipype.workflow INFO: [Node] Running "04_sel_labels" ("nipype.interfaces.utility.wrappers.Function") 191004-14:31:49,524 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_F058_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.04_sel_labels". 191004-14:32:02,333 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_F058_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.27_depad_csf" in "/scratch/punim0025/work/fmriprep_wf/single_subject_F058_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/27_depad_csf". 191004-14:32:02,334 nipype.workflow INFO: [Node] Outdated cache found for "fmriprep_wf.single_subject_F058_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.27_depad_csf". 191004-14:32:02,346 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_F058_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.10_me_csf" in "/scratch/punim0025/work/fmriprep_wf/single_subject_F058_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/10_me_csf". 191004-14:32:02,347 nipype.workflow INFO: [Node] Outdated cache found for "fmriprep_wf.single_subject_F058_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.10_me_csf". 191004-14:32:02,432 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_F058_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.06_get_gm" in "/scratch/punim0025/work/fmriprep_wf/single_subject_F058_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/06_get_gm". 191004-14:32:02,432 nipype.workflow INFO: [Node] Outdated cache found for "fmriprep_wf.single_subject_F058_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.06_get_gm". 191004-14:32:02,433 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_F058_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.05_get_wm" in "/scratch/punim0025/work/fmriprep_wf/single_subject_F058_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/05_get_wm". 191004-14:32:02,433 nipype.workflow INFO: [Node] Outdated cache found for "fmriprep_wf.single_subject_F058_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.05_get_wm". 191004-14:32:02,448 nipype.workflow INFO: [Node] Running "10_me_csf" ("niworkflows.interfaces.ants.ImageMath"), a CommandLine Interface with command: ImageMath 3 sub-F058_T1w_maths_corrected_labeled_maths_class-01_maths.nii ME /scratch/punim0025/work/fmriprep_wf/single_subject_F058_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/04_sel_labels/sub-F058_T1w_maths_corrected_labeled_maths_class-01.nii 10 191004-14:32:02,449 nipype.workflow INFO: [Node] Running "27_depad_csf" ("niworkflows.interfaces.ants.ImageMath"), a CommandLine Interface with command: ImageMath 3 sub-F058_T1w_maths_corrected_labeled_maths_class-01_maths.nii PadImage /scratch/punim0025/work/fmriprep_wf/single_subject_F058_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/04_sel_labels/sub-F058_T1w_maths_corrected_labeled_maths_class-01.nii -10 191004-14:32:02,457 nipype.workflow INFO: [Node] Running "05_get_wm" ("niworkflows.interfaces.ants.ImageMath"), a CommandLine Interface with command: ImageMath 3 sub-F058_T1w_maths_corrected_labeled_maths_class-03_maths.nii GetLargestComponent /scratch/punim0025/work/fmriprep_wf/single_subject_F058_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/04_sel_labels/sub-F058_T1w_maths_corrected_labeled_maths_class-03.nii 191004-14:32:02,462 nipype.workflow INFO: [Node] Running "06_get_gm" ("niworkflows.interfaces.ants.ImageMath"), a CommandLine Interface with command: ImageMath 3 sub-F058_T1w_maths_corrected_labeled_maths_class-02_maths.nii GetLargestComponent /scratch/punim0025/work/fmriprep_wf/single_subject_F058_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/04_sel_labels/sub-F058_T1w_maths_corrected_labeled_maths_class-02.nii 191004-14:32:03,317 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_F058_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.27_depad_csf". 191004-14:32:04,214 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_F058_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.05_get_wm". 191004-14:32:04,344 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_F058_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.06_get_gm". 191004-14:32:06,768 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_F058_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.10_me_csf". 191004-14:32:07,652 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_F058_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.09_relabel_wm" in "/scratch/punim0025/work/fmriprep_wf/single_subject_F058_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/09_relabel_wm". 191004-14:32:07,653 nipype.workflow INFO: [Node] Outdated cache found for "fmriprep_wf.single_subject_F058_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.09_relabel_wm". 191004-14:32:07,666 nipype.workflow INFO: [Node] Running "09_relabel_wm" ("nipype.interfaces.ants.utils.MultiplyImages"), a CommandLine Interface with command: MultiplyImages 3 /scratch/punim0025/work/fmriprep_wf/single_subject_F058_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/05_get_wm/sub-F058_T1w_maths_corrected_labeled_maths_class-03_maths.nii 3.0 09_relabel_wm.nii.gz 191004-14:32:08,469 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_F058_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.09_relabel_wm". 191004-14:32:12,109 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_F058_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.07_fill_gm" in "/scratch/punim0025/work/fmriprep_wf/single_subject_F058_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/07_fill_gm". 191004-14:32:12,109 nipype.workflow INFO: [Node] Outdated cache found for "fmriprep_wf.single_subject_F058_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.07_fill_gm". 191004-14:32:12,180 nipype.workflow INFO: [Node] Running "07_fill_gm" ("niworkflows.interfaces.ants.ImageMath"), a CommandLine Interface with command: ImageMath 3 sub-F058_T1w_maths_corrected_labeled_maths_class-02_maths_maths.nii FillHoles /scratch/punim0025/work/fmriprep_wf/single_subject_F058_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/06_get_gm/sub-F058_T1w_maths_corrected_labeled_maths_class-02_maths.nii 2 191004-14:32:15,964 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_F058_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.26_depad_wm" in "/scratch/punim0025/work/fmriprep_wf/single_subject_F058_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/26_depad_wm". 191004-14:32:15,975 nipype.workflow INFO: [Node] Outdated cache found for "fmriprep_wf.single_subject_F058_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.26_depad_wm". 191004-14:32:16,431 nipype.workflow INFO: [Node] Running "26_depad_wm" ("niworkflows.interfaces.ants.ImageMath"), a CommandLine Interface with command: ImageMath 3 09_relabel_wm_maths.nii.gz PadImage /scratch/punim0025/work/fmriprep_wf/single_subject_F058_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/09_relabel_wm/09_relabel_wm.nii.gz -10 191004-14:32:17,285 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_F058_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.26_depad_wm". 191004-14:32:18,934 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_F058_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.07_fill_gm". 191004-14:32:21,381 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_F058_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.08_mult_gm" in "/scratch/punim0025/work/fmriprep_wf/single_subject_F058_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/08_mult_gm". 191004-14:32:21,382 nipype.workflow INFO: [Node] Outdated cache found for "fmriprep_wf.single_subject_F058_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.08_mult_gm". 191004-14:32:21,392 nipype.workflow INFO: [Node] Running "08_mult_gm" ("nipype.interfaces.ants.utils.MultiplyImages"), a CommandLine Interface with command: MultiplyImages 3 /scratch/punim0025/work/fmriprep_wf/single_subject_F058_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/06_get_gm/sub-F058_T1w_maths_corrected_labeled_maths_class-02_maths.nii /scratch/punim0025/work/fmriprep_wf/single_subject_F058_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/07_fill_gm/sub-F058_T1w_maths_corrected_labeled_maths_class-02_maths_maths.nii 08_mult_gm.nii.gz 191004-14:32:22,123 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_F058_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.08_mult_gm". 191004-14:32:29,857 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_F058_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.11_add_gm" in "/scratch/punim0025/work/fmriprep_wf/single_subject_F058_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/11_add_gm". 191004-14:32:29,857 nipype.workflow INFO: [Node] Outdated cache found for "fmriprep_wf.single_subject_F058_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.11_add_gm". 191004-14:32:29,866 nipype.workflow INFO: [Node] Running "11_add_gm" ("niworkflows.interfaces.ants.ImageMath"), a CommandLine Interface with command: ImageMath 3 08_mult_gm_maths.nii.gz addtozero /scratch/punim0025/work/fmriprep_wf/single_subject_F058_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/08_mult_gm/08_mult_gm.nii.gz /scratch/punim0025/work/fmriprep_wf/single_subject_F058_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/10_me_csf/sub-F058_T1w_maths_corrected_labeled_maths_class-01_maths.nii 191004-14:32:33,152 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_F058_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.11_add_gm". 191004-14:32:35,389 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_F058_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.12_relabel_gm" in "/scratch/punim0025/work/fmriprep_wf/single_subject_F058_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/12_relabel_gm". 191004-14:32:35,390 nipype.workflow INFO: [Node] Outdated cache found for "fmriprep_wf.single_subject_F058_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.12_relabel_gm". 191004-14:32:35,404 nipype.workflow INFO: [Node] Running "12_relabel_gm" ("nipype.interfaces.ants.utils.MultiplyImages"), a CommandLine Interface with command: MultiplyImages 3 /scratch/punim0025/work/fmriprep_wf/single_subject_F058_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/11_add_gm/08_mult_gm_maths.nii.gz 2.0 12_relabel_gm.nii.gz 191004-14:32:36,186 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_F058_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.12_relabel_gm". 191004-14:32:44,46 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_F058_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.25_depad_gm" in "/scratch/punim0025/work/fmriprep_wf/single_subject_F058_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/25_depad_gm". 191004-14:32:44,47 nipype.workflow INFO: [Node] Outdated cache found for "fmriprep_wf.single_subject_F058_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.25_depad_gm". 191004-14:32:44,57 nipype.workflow INFO: [Node] Running "25_depad_gm" ("niworkflows.interfaces.ants.ImageMath"), a CommandLine Interface with command: ImageMath 3 12_relabel_gm_maths.nii.gz PadImage /scratch/punim0025/work/fmriprep_wf/single_subject_F058_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/12_relabel_gm/12_relabel_gm.nii.gz -10 191004-14:32:44,310 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_F058_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.13_add_gm_wm" in "/scratch/punim0025/work/fmriprep_wf/single_subject_F058_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/13_add_gm_wm". 191004-14:32:44,311 nipype.workflow INFO: [Node] Outdated cache found for "fmriprep_wf.single_subject_F058_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.13_add_gm_wm". 191004-14:32:44,321 nipype.workflow INFO: [Node] Running "13_add_gm_wm" ("niworkflows.interfaces.ants.ImageMath"), a CommandLine Interface with command: ImageMath 3 09_relabel_wm_maths.nii.gz addtozero /scratch/punim0025/work/fmriprep_wf/single_subject_F058_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/09_relabel_wm/09_relabel_wm.nii.gz /scratch/punim0025/work/fmriprep_wf/single_subject_F058_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/12_relabel_gm/12_relabel_gm.nii.gz 191004-14:32:45,7 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_F058_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.25_depad_gm". 191004-14:32:47,366 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_F058_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.merge_tpms" in "/scratch/punim0025/work/fmriprep_wf/single_subject_F058_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/merge_tpms". 191004-14:32:47,366 nipype.workflow INFO: [Node] Outdated cache found for "fmriprep_wf.single_subject_F058_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.merge_tpms". 191004-14:32:47,383 nipype.workflow INFO: [Node] Running "merge_tpms" ("nipype.interfaces.utility.base.Merge") 191004-14:32:47,387 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_F058_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.merge_tpms". 191004-14:32:47,774 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_F058_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.13_add_gm_wm". 191004-14:32:49,374 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_F058_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.14_sel_labels2" in "/scratch/punim0025/work/fmriprep_wf/single_subject_F058_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/14_sel_labels2". 191004-14:32:49,374 nipype.workflow INFO: [Node] Outdated cache found for "fmriprep_wf.single_subject_F058_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.14_sel_labels2". 191004-14:32:49,384 nipype.workflow INFO: [Node] Running "14_sel_labels2" ("nipype.interfaces.utility.wrappers.Function") 191004-14:32:49,758 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_F058_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.14_sel_labels2". 191004-14:32:54,54 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_F058_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.24_depad_segm" in "/scratch/punim0025/work/fmriprep_wf/single_subject_F058_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/24_depad_segm". 191004-14:32:54,55 nipype.workflow INFO: [Node] Outdated cache found for "fmriprep_wf.single_subject_F058_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.24_depad_segm". 191004-14:32:54,66 nipype.workflow INFO: [Node] Running "24_depad_segm" ("niworkflows.interfaces.ants.ImageMath"), a CommandLine Interface with command: ImageMath 3 09_relabel_wm_maths_maths.nii.gz PadImage /scratch/punim0025/work/fmriprep_wf/single_subject_F058_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/13_add_gm_wm/09_relabel_wm_maths.nii.gz -10 191004-14:32:55,77 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_F058_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.24_depad_segm". 191004-14:32:56,166 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_F058_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.15_add_7" in "/scratch/punim0025/work/fmriprep_wf/single_subject_F058_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/15_add_7". 191004-14:32:56,167 nipype.workflow INFO: [Node] Outdated cache found for "fmriprep_wf.single_subject_F058_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.15_add_7". 191004-14:32:56,179 nipype.workflow INFO: [Node] Running "15_add_7" ("niworkflows.interfaces.ants.ImageMath"), a CommandLine Interface with command: ImageMath 3 09_relabel_wm_maths_class-03_maths.nii.gz addtozero /scratch/punim0025/work/fmriprep_wf/single_subject_F058_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/14_sel_labels2/09_relabel_wm_maths_class-03.nii.gz /scratch/punim0025/work/fmriprep_wf/single_subject_F058_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/14_sel_labels2/09_relabel_wm_maths_class-02.nii.gz 191004-14:32:59,318 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_F058_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.15_add_7". 191004-14:33:05,888 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_F058_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.16_me_7" in "/scratch/punim0025/work/fmriprep_wf/single_subject_F058_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/16_me_7". 191004-14:33:05,888 nipype.workflow INFO: [Node] Outdated cache found for "fmriprep_wf.single_subject_F058_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.16_me_7". 191004-14:33:05,899 nipype.workflow INFO: [Node] Running "16_me_7" ("niworkflows.interfaces.ants.ImageMath"), a CommandLine Interface with command: ImageMath 3 09_relabel_wm_maths_class-03_maths_maths.nii.gz ME /scratch/punim0025/work/fmriprep_wf/single_subject_F058_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/15_add_7/09_relabel_wm_maths_class-03_maths.nii.gz 2 191004-14:33:08,534 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_F058_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.16_me_7". 191004-14:33:10,188 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_F058_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.17_comp_7" in "/scratch/punim0025/work/fmriprep_wf/single_subject_F058_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/17_comp_7". 191004-14:33:10,188 nipype.workflow INFO: [Node] Outdated cache found for "fmriprep_wf.single_subject_F058_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.17_comp_7". 191004-14:33:10,201 nipype.workflow INFO: [Node] Running "17_comp_7" ("niworkflows.interfaces.ants.ImageMath"), a CommandLine Interface with command: ImageMath 3 09_relabel_wm_maths_class-03_maths_maths_maths.nii.gz GetLargestComponent /scratch/punim0025/work/fmriprep_wf/single_subject_F058_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/16_me_7/09_relabel_wm_maths_class-03_maths_maths.nii.gz 191004-14:33:11,481 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_F058_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.17_comp_7". 191004-14:33:12,196 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_F058_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.18_md_7" in "/scratch/punim0025/work/fmriprep_wf/single_subject_F058_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/18_md_7". 191004-14:33:12,197 nipype.workflow INFO: [Node] Outdated cache found for "fmriprep_wf.single_subject_F058_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.18_md_7". 191004-14:33:12,215 nipype.workflow INFO: [Node] Running "18_md_7" ("niworkflows.interfaces.ants.ImageMath"), a CommandLine Interface with command: ImageMath 3 09_relabel_wm_maths_class-03_maths_maths_maths_maths.nii.gz MD /scratch/punim0025/work/fmriprep_wf/single_subject_F058_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/17_comp_7/09_relabel_wm_maths_class-03_maths_maths_maths.nii.gz 4 191004-14:33:13,890 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_F058_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.18_md_7". 191004-14:33:14,196 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_F058_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.19_fill_7" in "/scratch/punim0025/work/fmriprep_wf/single_subject_F058_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/19_fill_7". 191004-14:33:14,196 nipype.workflow INFO: [Node] Outdated cache found for "fmriprep_wf.single_subject_F058_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.19_fill_7". 191004-14:33:14,209 nipype.workflow INFO: [Node] Running "19_fill_7" ("niworkflows.interfaces.ants.ImageMath"), a CommandLine Interface with command: ImageMath 3 09_relabel_wm_maths_class-03_maths_maths_maths_maths_maths.nii.gz FillHoles /scratch/punim0025/work/fmriprep_wf/single_subject_F058_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/18_md_7/09_relabel_wm_maths_class-03_maths_maths_maths_maths.nii.gz 2 191004-14:33:20,962 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_F058_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.19_fill_7". 191004-14:33:22,195 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_F058_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.20_add_7_2" in "/scratch/punim0025/work/fmriprep_wf/single_subject_F058_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/20_add_7_2". 191004-14:33:22,195 nipype.workflow INFO: [Node] Outdated cache found for "fmriprep_wf.single_subject_F058_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.20_add_7_2". 191004-14:33:22,207 nipype.workflow INFO: [Node] Running "20_add_7_2" ("niworkflows.interfaces.ants.ImageMath"), a CommandLine Interface with command: ImageMath 3 09_relabel_wm_maths_class-03_maths_maths_maths_maths_maths_maths.nii.gz addtozero /scratch/punim0025/work/fmriprep_wf/single_subject_F058_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/19_fill_7/09_relabel_wm_maths_class-03_maths_maths_maths_maths_maths.nii.gz /scratch/punim0025/work/fmriprep_wf/single_subject_F058_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/03_pad_mask/tpl-OASIS30ANTs_res-01_label-brain_probseg_trans_resampled_maths.nii.gz 191004-14:33:25,430 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_F058_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.20_add_7_2". 191004-14:33:30,703 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_F058_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.21_md_7_2" in "/scratch/punim0025/work/fmriprep_wf/single_subject_F058_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/21_md_7_2". 191004-14:33:30,704 nipype.workflow INFO: [Node] Outdated cache found for "fmriprep_wf.single_subject_F058_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.21_md_7_2". 191004-14:33:30,713 nipype.workflow INFO: [Node] Running "21_md_7_2" ("niworkflows.interfaces.ants.ImageMath"), a CommandLine Interface with command: ImageMath 3 09_relabel_wm_maths_class-03_maths_maths_maths_maths_maths_maths_maths.nii.gz MD /scratch/punim0025/work/fmriprep_wf/single_subject_F058_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/20_add_7_2/09_relabel_wm_maths_class-03_maths_maths_maths_maths_maths_maths.nii.gz 5 191004-14:33:32,354 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_F058_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.21_md_7_2". 191004-14:33:34,200 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_F058_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.22_me_7_2" in "/scratch/punim0025/work/fmriprep_wf/single_subject_F058_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/22_me_7_2". 191004-14:33:34,200 nipype.workflow INFO: [Node] Outdated cache found for "fmriprep_wf.single_subject_F058_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.22_me_7_2". 191004-14:33:34,210 nipype.workflow INFO: [Node] Running "22_me_7_2" ("niworkflows.interfaces.ants.ImageMath"), a CommandLine Interface with command: ImageMath 3 09_relabel_wm_maths_class-03_maths_maths_maths_maths_maths_maths_maths_maths.nii.gz ME /scratch/punim0025/work/fmriprep_wf/single_subject_F058_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/21_md_7_2/09_relabel_wm_maths_class-03_maths_maths_maths_maths_maths_maths_maths.nii.gz 5 191004-14:33:36,768 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_F058_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.22_me_7_2". 191004-14:33:38,211 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_F058_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.23_depad_mask" in "/scratch/punim0025/work/fmriprep_wf/single_subject_F058_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/23_depad_mask". 191004-14:33:38,211 nipype.workflow INFO: [Node] Outdated cache found for "fmriprep_wf.single_subject_F058_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.23_depad_mask". 191004-14:33:38,221 nipype.workflow INFO: [Node] Running "23_depad_mask" ("niworkflows.interfaces.ants.ImageMath"), a CommandLine Interface with command: ImageMath 3 09_relabel_wm_maths_class-03_maths_maths_maths_maths_maths_maths_maths_maths_maths.nii.gz PadImage /scratch/punim0025/work/fmriprep_wf/single_subject_F058_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/22_me_7_2/09_relabel_wm_maths_class-03_maths_maths_maths_maths_maths_maths_maths_maths.nii.gz -10 191004-14:33:38,912 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_F058_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.23_depad_mask". 191004-14:33:40,203 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_F058_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.msk_conform" in "/scratch/punim0025/work/fmriprep_wf/single_subject_F058_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/msk_conform". 191004-14:33:40,203 nipype.workflow INFO: [Node] Outdated cache found for "fmriprep_wf.single_subject_F058_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.msk_conform". 191004-14:33:40,212 nipype.workflow INFO: [Node] Running "msk_conform" ("nipype.interfaces.utility.wrappers.Function") 191004-14:33:40,378 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_F058_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.msk_conform". 191004-14:33:46,214 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_F058_wf.anat_preproc_wf.brain_extraction_wf.inu_n4_final" in "/scratch/punim0025/work/fmriprep_wf/single_subject_F058_wf/anat_preproc_wf/brain_extraction_wf/inu_n4_final". 191004-14:33:46,215 nipype.workflow INFO: [Node] Outdated cache found for "fmriprep_wf.single_subject_F058_wf.anat_preproc_wf.brain_extraction_wf.inu_n4_final". 191004-14:33:46,227 nipype.workflow INFO: [Node] Setting-up "_inu_n4_final0" in "/scratch/punim0025/work/fmriprep_wf/single_subject_F058_wf/anat_preproc_wf/brain_extraction_wf/inu_n4_final/mapflow/_inu_n4_final0". 191004-14:33:46,228 nipype.workflow INFO: [Node] Outdated cache found for "_inu_n4_final0". 191004-14:33:46,244 nipype.workflow INFO: [Node] Running "_inu_n4_final0" ("nipype.interfaces.ants.segmentation.N4BiasFieldCorrection"), a CommandLine Interface with command: N4BiasFieldCorrection --bspline-fitting [ 200 ] -d 3 --input-image /scratch/punim0025/wave1_BIDS/sub-F058/anat/sub-F058_T1w.nii --convergence [ 50x50x50x50x50, 1e-07 ] --output [ sub-F058_T1w_corrected.nii, sub-F058_T1w_bias.nii ] -r --shrink-factor 4 --weight-image /scratch/punim0025/work/fmriprep_wf/single_subject_F058_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/copy_xform/09_relabel_wm_maths_xform.nii.gz 191004-14:34:29,355 nipype.workflow INFO: [Node] Finished "_inu_n4_final0". 191004-14:34:29,360 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_F058_wf.anat_preproc_wf.brain_extraction_wf.inu_n4_final". 191004-14:34:30,262 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_F058_wf.anat_preproc_wf.brain_extraction_wf.apply_mask" in "/scratch/punim0025/work/fmriprep_wf/single_subject_F058_wf/anat_preproc_wf/brain_extraction_wf/apply_mask". 191004-14:34:30,263 nipype.workflow INFO: [Node] Outdated cache found for "fmriprep_wf.single_subject_F058_wf.anat_preproc_wf.brain_extraction_wf.apply_mask". 191004-14:34:30,279 nipype.workflow INFO: [Node] Setting-up "_apply_mask0" in "/scratch/punim0025/work/fmriprep_wf/single_subject_F058_wf/anat_preproc_wf/brain_extraction_wf/apply_mask/mapflow/_apply_mask0". 191004-14:34:30,280 nipype.workflow INFO: [Node] Outdated cache found for "_apply_mask0". 191004-14:34:30,290 nipype.workflow INFO: [Node] Running "_apply_mask0" ("nipype.interfaces.fsl.maths.ApplyMask"), a CommandLine Interface with command: fslmaths /scratch/punim0025/work/fmriprep_wf/single_subject_F058_wf/anat_preproc_wf/brain_extraction_wf/inu_n4_final/mapflow/_inu_n4_final0/sub-F058_T1w_corrected.nii -mas /scratch/punim0025/work/fmriprep_wf/single_subject_F058_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/copy_xform/09_relabel_wm_mask_xform.nii.gz /scratch/punim0025/work/fmriprep_wf/single_subject_F058_wf/anat_preproc_wf/brain_extraction_wf/apply_mask/mapflow/_apply_mask0/sub-F058_T1w_corrected_masked.nii.gz 191004-14:34:31,274 nipype.workflow INFO: [Node] Finished "_apply_mask0". 191004-14:34:31,279 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_F058_wf.anat_preproc_wf.brain_extraction_wf.apply_mask". 191004-14:34:36,836 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_F058_wf.anat_preproc_wf.anat_norm_wf.trunc_mov" in "/scratch/punim0025/work/fmriprep_wf/single_subject_F058_wf/anat_preproc_wf/anat_norm_wf/_template_MNIPediatricAsym/trunc_mov". 191004-14:34:36,837 nipype.workflow INFO: [Node] Outdated cache found for "fmriprep_wf.single_subject_F058_wf.anat_preproc_wf.anat_norm_wf.trunc_mov". 191004-14:34:36,849 nipype.workflow INFO: [Node] Running "trunc_mov" ("niworkflows.interfaces.ants.ImageMath"), a CommandLine Interface with command: ImageMath 3 sub-F058_T1w_corrected_xform_maths.nii TruncateImageIntensity /scratch/punim0025/work/fmriprep_wf/single_subject_F058_wf/anat_preproc_wf/brain_extraction_wf/copy_xform/sub-F058_T1w_corrected_xform.nii 0.01 0.999 256 191004-14:34:37,930 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_F058_wf.anat_preproc_wf.anat_norm_wf.trunc_mov". 191004-14:34:42,870 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_F058_wf.func_preproc_task_rest_wf.bold_t1_trans_wf.gen_ref" in "/scratch/punim0025/work/fmriprep_wf/single_subject_F058_wf/func_preproc_task_rest_wf/bold_t1_trans_wf/gen_ref". 191004-14:34:42,870 nipype.workflow INFO: [Node] Outdated cache found for "fmriprep_wf.single_subject_F058_wf.func_preproc_task_rest_wf.bold_t1_trans_wf.gen_ref". 191004-14:34:42,957 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_F058_wf.anat_preproc_wf.t1_seg" in "/scratch/punim0025/work/fmriprep_wf/single_subject_F058_wf/anat_preproc_wf/t1_seg". 191004-14:34:42,957 nipype.workflow INFO: [Node] Outdated cache found for "fmriprep_wf.single_subject_F058_wf.anat_preproc_wf.t1_seg". 191004-14:34:43,32 nipype.workflow INFO: [Node] Running "gen_ref" ("niworkflows.interfaces.utils.GenerateSamplingReference") 191004-14:34:43,196 nipype.workflow INFO: [Node] Running "t1_seg" ("nipype.interfaces.fsl.preprocess.FAST"), a CommandLine Interface with command: fast -N -p -g -S 1 /scratch/punim0025/work/fmriprep_wf/single_subject_F058_wf/anat_preproc_wf/t1_seg/sub-F058_T1w_corrected_masked_xform.nii.gz 191004-14:34:43,965 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_F058_wf.func_preproc_task_rest_wf.bold_t1_trans_wf.gen_ref". 191004-14:34:51,214 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_F058_wf.func_preproc_task_rest_wf.bold_reg_wf.fsl_bbr_wf.flt_bbr_init" in "/scratch/punim0025/work/fmriprep_wf/single_subject_F058_wf/func_preproc_task_rest_wf/bold_reg_wf/fsl_bbr_wf/flt_bbr_init". 191004-14:34:51,215 nipype.workflow INFO: [Node] Outdated cache found for "fmriprep_wf.single_subject_F058_wf.func_preproc_task_rest_wf.bold_reg_wf.fsl_bbr_wf.flt_bbr_init". 191004-14:34:51,347 nipype.workflow INFO: [Node] Running "flt_bbr_init" ("niworkflows.interfaces.registration.FLIRTRPT"), a CommandLine Interface with command: flirt -in /scratch/punim0025/work/fmriprep_wf/single_subject_F058_wf/func_preproc_task_rest_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/apply_mask/uni_xform_masked.nii.gz -ref /scratch/punim0025/work/fmriprep_wf/single_subject_F058_wf/anat_preproc_wf/brain_extraction_wf/copy_xform/sub-F058_T1w_corrected_masked_xform.nii.gz -out uni_xform_masked_flirt.nii.gz -omat uni_xform_masked_flirt.mat -dof 6 -usesqform 191004-14:34:51,409 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_F058_wf.anat_preproc_wf.anat_norm_wf.registration" in "/scratch/punim0025/work/fmriprep_wf/single_subject_F058_wf/anat_preproc_wf/anat_norm_wf/_template_MNIPediatricAsym/registration". 191004-14:34:51,409 nipype.workflow INFO: [Node] Outdated cache found for "fmriprep_wf.single_subject_F058_wf.anat_preproc_wf.anat_norm_wf.registration". 191004-14:34:51,601 nipype.workflow INFO: [Node] Running "registration" ("niworkflows.interfaces.mni.RobustMNINormalization") 191004-14:36:51,315 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_F058_wf.func_preproc_task_rest_wf.bold_reg_wf.fsl_bbr_wf.flt_bbr_init". 191004-14:40:03,734 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_F058_wf.anat_preproc_wf.t1_seg". 191004-14:40:16,328 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_F058_wf.anat_preproc_wf.anat_derivatives_wf.lut_t1_seg" in "/scratch/punim0025/work/fmriprep_wf/single_subject_F058_wf/anat_preproc_wf/anat_derivatives_wf/lut_t1_seg". 191004-14:40:16,329 nipype.workflow INFO: [Node] Outdated cache found for "fmriprep_wf.single_subject_F058_wf.anat_preproc_wf.anat_derivatives_wf.lut_t1_seg". 191004-14:40:16,355 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_F058_wf.func_preproc_task_rest_wf.bold_confounds_wf.wm_roi" in "/scratch/punim0025/work/fmriprep_wf/single_subject_F058_wf/func_preproc_task_rest_wf/bold_confounds_wf/wm_roi". 191004-14:40:16,355 nipype.workflow INFO: [Node] Outdated cache found for "fmriprep_wf.single_subject_F058_wf.func_preproc_task_rest_wf.bold_confounds_wf.wm_roi". 191004-14:40:16,359 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_F058_wf.func_preproc_task_rest_wf.bold_confounds_wf.csf_roi" in "/scratch/punim0025/work/fmriprep_wf/single_subject_F058_wf/func_preproc_task_rest_wf/bold_confounds_wf/csf_roi". 191004-14:40:16,359 nipype.workflow INFO: [Node] Outdated cache found for "fmriprep_wf.single_subject_F058_wf.func_preproc_task_rest_wf.bold_confounds_wf.csf_roi". 191004-14:40:16,362 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_F058_wf.func_preproc_task_rest_wf.bold_confounds_wf.tpms_add_csf_wm" in "/scratch/punim0025/work/fmriprep_wf/single_subject_F058_wf/func_preproc_task_rest_wf/bold_confounds_wf/tpms_add_csf_wm". 191004-14:40:16,362 nipype.workflow INFO: [Node] Outdated cache found for "fmriprep_wf.single_subject_F058_wf.func_preproc_task_rest_wf.bold_confounds_wf.tpms_add_csf_wm". 191004-14:40:16,369 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_F058_wf.func_preproc_task_rest_wf.bold_reg_wf.fsl_bbr_wf.wm_mask" in "/scratch/punim0025/work/fmriprep_wf/single_subject_F058_wf/func_preproc_task_rest_wf/bold_reg_wf/fsl_bbr_wf/wm_mask". 191004-14:40:16,369 nipype.workflow INFO: [Node] Outdated cache found for "fmriprep_wf.single_subject_F058_wf.func_preproc_task_rest_wf.bold_reg_wf.fsl_bbr_wf.wm_mask". 191004-14:40:16,407 nipype.workflow INFO: [Node] Running "lut_t1_seg" ("nipype.interfaces.utility.wrappers.Function") 191004-14:40:16,410 nipype.workflow INFO: [Node] Running "wm_roi" ("niworkflows.interfaces.utils.TPM2ROI") 191004-14:40:16,424 nipype.workflow INFO: [Node] Running "wm_mask" ("nipype.interfaces.utility.wrappers.Function") 191004-14:40:16,439 nipype.workflow INFO: [Node] Running "tpms_add_csf_wm" ("niworkflows.interfaces.utils.AddTPMs") 191004-14:40:16,463 nipype.workflow INFO: [Node] Running "csf_roi" ("niworkflows.interfaces.utils.TPM2ROI") 191004-14:40:16,978 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_F058_wf.anat_preproc_wf.seg_rpt" in "/scratch/punim0025/work/fmriprep_wf/single_subject_F058_wf/anat_preproc_wf/seg_rpt". 191004-14:40:16,979 nipype.workflow INFO: [Node] Outdated cache found for "fmriprep_wf.single_subject_F058_wf.anat_preproc_wf.seg_rpt". 191004-14:40:17,180 nipype.workflow INFO: [Node] Running "seg_rpt" ("niworkflows.interfaces.masks.ROIsPlot") 191004-14:40:18,264 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_F058_wf.anat_preproc_wf.anat_derivatives_wf.lut_t1_seg". 191004-14:40:18,511 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_F058_wf.func_preproc_task_rest_wf.bold_reg_wf.fsl_bbr_wf.wm_mask". 191004-14:40:19,211 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_F058_wf.func_preproc_task_rest_wf.bold_confounds_wf.csf_roi". 191004-14:40:20,981 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_F058_wf.func_preproc_task_rest_wf.bold_confounds_wf.tpms_add_csf_wm". 191004-14:40:26,984 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_F058_wf.func_preproc_task_rest_wf.bold_confounds_wf.acc_roi" in "/scratch/punim0025/work/fmriprep_wf/single_subject_F058_wf/func_preproc_task_rest_wf/bold_confounds_wf/acc_roi". 191004-14:40:26,985 nipype.workflow INFO: [Node] Outdated cache found for "fmriprep_wf.single_subject_F058_wf.func_preproc_task_rest_wf.bold_confounds_wf.acc_roi". 191004-14:40:27,175 nipype.workflow INFO: [Node] Running "acc_roi" ("niworkflows.interfaces.utils.TPM2ROI") 191004-14:40:32,620 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_F058_wf.func_preproc_task_rest_wf.bold_confounds_wf.wm_roi". 191004-14:40:42,379 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_F058_wf.func_preproc_task_rest_wf.bold_confounds_wf.acc_roi". 191004-14:40:45,42 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_F058_wf.func_preproc_task_rest_wf.bold_reg_wf.fsl_bbr_wf.flt_bbr" in "/scratch/punim0025/work/fmriprep_wf/single_subject_F058_wf/func_preproc_task_rest_wf/bold_reg_wf/fsl_bbr_wf/flt_bbr". 191004-14:40:45,43 nipype.workflow INFO: [Node] Outdated cache found for "fmriprep_wf.single_subject_F058_wf.func_preproc_task_rest_wf.bold_reg_wf.fsl_bbr_wf.flt_bbr". 191004-14:40:45,269 nipype.workflow INFO: [Node] Running "flt_bbr" ("niworkflows.interfaces.registration.FLIRTRPT"), a CommandLine Interface with command: flirt -in /scratch/punim0025/work/fmriprep_wf/single_subject_F058_wf/func_preproc_task_rest_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/apply_mask/uni_xform_masked.nii.gz -ref /scratch/punim0025/work/fmriprep_wf/single_subject_F058_wf/anat_preproc_wf/brain_extraction_wf/copy_xform/sub-F058_T1w_corrected_masked_xform.nii.gz -out uni_xform_masked_flirt.nii.gz -omat uni_xform_masked_flirt.mat -searchcost bbr -dof 6 -init /scratch/punim0025/work/fmriprep_wf/single_subject_F058_wf/func_preproc_task_rest_wf/bold_reg_wf/fsl_bbr_wf/flt_bbr_init/uni_xform_masked_flirt.mat -schedule /usr/share/fsl/5.0/etc/flirtsch/bbr.sch -wmseg /scratch/punim0025/work/fmriprep_wf/single_subject_F058_wf/anat_preproc_wf/t1_seg/sub-F058_T1w_corrected_masked_xform_seg_wm.nii.gz 191004-14:42:36,201 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_F058_wf.anat_preproc_wf.seg_rpt". 191004-14:50:16,781 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_F058_wf.func_preproc_task_rest_wf.bold_reg_wf.fsl_bbr_wf.flt_bbr". 191004-14:50:25,819 nipype.workflow INFO: [Node] Setting-up "_fsl_to_lta0" in "/scratch/punim0025/work/fmriprep_wf/single_subject_F058_wf/func_preproc_task_rest_wf/bold_reg_wf/fsl_bbr_wf/fsl_to_lta/mapflow/_fsl_to_lta0". 191004-14:50:25,819 nipype.workflow INFO: [Node] Outdated cache found for "_fsl_to_lta0". 191004-14:50:26,81 nipype.workflow INFO: [Node] Running "_fsl_to_lta0" ("niworkflows.interfaces.freesurfer.PatchedLTAConvert"), a CommandLine Interface with command: lta_convert --infsl /scratch/punim0025/work/fmriprep_wf/single_subject_F058_wf/func_preproc_task_rest_wf/bold_reg_wf/fsl_bbr_wf/flt_bbr/uni_xform_masked_flirt.mat --outlta /scratch/punim0025/work/fmriprep_wf/single_subject_F058_wf/func_preproc_task_rest_wf/bold_reg_wf/fsl_bbr_wf/fsl_to_lta/mapflow/_fsl_to_lta0/out.lta --src /scratch/punim0025/work/fmriprep_wf/single_subject_F058_wf/func_preproc_task_rest_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/apply_mask/uni_xform_masked.nii.gz --trg /scratch/punim0025/work/fmriprep_wf/single_subject_F058_wf/anat_preproc_wf/brain_extraction_wf/copy_xform/sub-F058_T1w_corrected_masked_xform.nii.gz 191004-14:50:26,807 nipype.workflow INFO: [Node] Finished "_fsl_to_lta0". 191004-14:50:40,281 nipype.workflow INFO: [Node] Setting-up "_fsl_to_lta1" in "/scratch/punim0025/work/fmriprep_wf/single_subject_F058_wf/func_preproc_task_rest_wf/bold_reg_wf/fsl_bbr_wf/fsl_to_lta/mapflow/_fsl_to_lta1". 191004-14:50:40,293 nipype.workflow INFO: [Node] Outdated cache found for "_fsl_to_lta1". 191004-14:50:40,516 nipype.workflow INFO: [Node] Running "_fsl_to_lta1" ("niworkflows.interfaces.freesurfer.PatchedLTAConvert"), a CommandLine Interface with command: lta_convert --infsl /scratch/punim0025/work/fmriprep_wf/single_subject_F058_wf/func_preproc_task_rest_wf/bold_reg_wf/fsl_bbr_wf/flt_bbr_init/uni_xform_masked_flirt.mat --outlta /scratch/punim0025/work/fmriprep_wf/single_subject_F058_wf/func_preproc_task_rest_wf/bold_reg_wf/fsl_bbr_wf/fsl_to_lta/mapflow/_fsl_to_lta1/out.lta --src /scratch/punim0025/work/fmriprep_wf/single_subject_F058_wf/func_preproc_task_rest_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/apply_mask/uni_xform_masked.nii.gz --trg /scratch/punim0025/work/fmriprep_wf/single_subject_F058_wf/anat_preproc_wf/brain_extraction_wf/copy_xform/sub-F058_T1w_corrected_masked_xform.nii.gz 191004-14:50:40,857 nipype.workflow INFO: [Node] Finished "_fsl_to_lta1". 191004-14:50:43,109 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_F058_wf.func_preproc_task_rest_wf.bold_reg_wf.fsl_bbr_wf.fsl_to_lta" in "/scratch/punim0025/work/fmriprep_wf/single_subject_F058_wf/func_preproc_task_rest_wf/bold_reg_wf/fsl_bbr_wf/fsl_to_lta". 191004-14:50:43,110 nipype.workflow INFO: [Node] Outdated cache found for "fmriprep_wf.single_subject_F058_wf.func_preproc_task_rest_wf.bold_reg_wf.fsl_bbr_wf.fsl_to_lta". 191004-14:50:43,255 nipype.workflow INFO: [Node] Setting-up "_fsl_to_lta0" in "/scratch/punim0025/work/fmriprep_wf/single_subject_F058_wf/func_preproc_task_rest_wf/bold_reg_wf/fsl_bbr_wf/fsl_to_lta/mapflow/_fsl_to_lta0". 191004-14:50:43,267 nipype.workflow INFO: [Node] Cached "_fsl_to_lta0" - collecting precomputed outputs 191004-14:50:43,267 nipype.workflow INFO: [Node] "_fsl_to_lta0" found cached. 191004-14:50:43,268 nipype.workflow INFO: [Node] Setting-up "_fsl_to_lta1" in "/scratch/punim0025/work/fmriprep_wf/single_subject_F058_wf/func_preproc_task_rest_wf/bold_reg_wf/fsl_bbr_wf/fsl_to_lta/mapflow/_fsl_to_lta1". 191004-14:50:43,281 nipype.workflow INFO: [Node] Cached "_fsl_to_lta1" - collecting precomputed outputs 191004-14:50:43,281 nipype.workflow INFO: [Node] "_fsl_to_lta1" found cached. 191004-14:50:43,354 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_F058_wf.func_preproc_task_rest_wf.bold_reg_wf.fsl_bbr_wf.fsl_to_lta". 191004-14:50:44,542 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_F058_wf.func_preproc_task_rest_wf.bold_reg_wf.fsl_bbr_wf.compare_transforms" in "/scratch/punim0025/work/fmriprep_wf/single_subject_F058_wf/func_preproc_task_rest_wf/bold_reg_wf/fsl_bbr_wf/compare_transforms". 191004-14:50:44,542 nipype.workflow INFO: [Node] Outdated cache found for "fmriprep_wf.single_subject_F058_wf.func_preproc_task_rest_wf.bold_reg_wf.fsl_bbr_wf.compare_transforms". 191004-14:50:44,564 nipype.workflow INFO: [Node] Running "compare_transforms" ("nipype.interfaces.utility.wrappers.Function") 191004-14:50:58,126 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_F058_wf.func_preproc_task_rest_wf.bold_reg_wf.fsl_bbr_wf.compare_transforms". 191004-14:51:00,927 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_F058_wf.func_preproc_task_rest_wf.bold_reg_wf.fsl_bbr_wf.fsl2itk_fwd" in "/scratch/punim0025/work/fmriprep_wf/single_subject_F058_wf/func_preproc_task_rest_wf/bold_reg_wf/fsl_bbr_wf/fsl2itk_fwd". 191004-14:51:00,928 nipype.workflow INFO: [Node] Outdated cache found for "fmriprep_wf.single_subject_F058_wf.func_preproc_task_rest_wf.bold_reg_wf.fsl_bbr_wf.fsl2itk_fwd". 191004-14:51:01,120 nipype.workflow INFO: [Node] Running "fsl2itk_fwd" ("nipype.interfaces.c3.C3dAffineTool"), a CommandLine Interface with command: c3d_affine_tool -ref /scratch/punim0025/work/fmriprep_wf/single_subject_F058_wf/anat_preproc_wf/brain_extraction_wf/copy_xform/sub-F058_T1w_corrected_masked_xform.nii.gz -src /scratch/punim0025/work/fmriprep_wf/single_subject_F058_wf/func_preproc_task_rest_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/apply_mask/uni_xform_masked.nii.gz /scratch/punim0025/work/fmriprep_wf/single_subject_F058_wf/func_preproc_task_rest_wf/bold_reg_wf/fsl_bbr_wf/flt_bbr/uni_xform_masked_flirt.mat -fsl2ras -oitk /scratch/punim0025/work/fmriprep_wf/single_subject_F058_wf/func_preproc_task_rest_wf/bold_reg_wf/fsl_bbr_wf/fsl2itk_fwd/affine.txt 191004-14:51:01,189 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_F058_wf.func_preproc_task_rest_wf.bold_reg_wf.fsl_bbr_wf.invt_bbr" in "/scratch/punim0025/work/fmriprep_wf/single_subject_F058_wf/func_preproc_task_rest_wf/bold_reg_wf/fsl_bbr_wf/invt_bbr". 191004-14:51:01,202 nipype.workflow INFO: [Node] Outdated cache found for "fmriprep_wf.single_subject_F058_wf.func_preproc_task_rest_wf.bold_reg_wf.fsl_bbr_wf.invt_bbr". 191004-14:51:01,388 nipype.workflow INFO: [Node] Running "invt_bbr" ("nipype.interfaces.fsl.utils.ConvertXFM"), a CommandLine Interface with command: convert_xfm -omat /scratch/punim0025/work/fmriprep_wf/single_subject_F058_wf/func_preproc_task_rest_wf/bold_reg_wf/fsl_bbr_wf/invt_bbr/uni_xform_masked_flirt_inv.mat -inverse /scratch/punim0025/work/fmriprep_wf/single_subject_F058_wf/func_preproc_task_rest_wf/bold_reg_wf/fsl_bbr_wf/flt_bbr/uni_xform_masked_flirt.mat 191004-14:51:01,604 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_F058_wf.func_preproc_task_rest_wf.bold_reg_wf.fsl_bbr_wf.invt_bbr". 191004-14:51:02,702 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_F058_wf.func_preproc_task_rest_wf.bold_reg_wf.fsl_bbr_wf.fsl2itk_inv" in "/scratch/punim0025/work/fmriprep_wf/single_subject_F058_wf/func_preproc_task_rest_wf/bold_reg_wf/fsl_bbr_wf/fsl2itk_inv". 191004-14:51:02,702 nipype.workflow INFO: [Node] Outdated cache found for "fmriprep_wf.single_subject_F058_wf.func_preproc_task_rest_wf.bold_reg_wf.fsl_bbr_wf.fsl2itk_inv". 191004-14:51:02,909 nipype.workflow INFO: [Node] Running "fsl2itk_inv" ("nipype.interfaces.c3.C3dAffineTool"), a CommandLine Interface with command: c3d_affine_tool -ref /scratch/punim0025/work/fmriprep_wf/single_subject_F058_wf/func_preproc_task_rest_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/apply_mask/uni_xform_masked.nii.gz -src /scratch/punim0025/work/fmriprep_wf/single_subject_F058_wf/anat_preproc_wf/brain_extraction_wf/copy_xform/sub-F058_T1w_corrected_masked_xform.nii.gz /scratch/punim0025/work/fmriprep_wf/single_subject_F058_wf/func_preproc_task_rest_wf/bold_reg_wf/fsl_bbr_wf/invt_bbr/uni_xform_masked_flirt_inv.mat -fsl2ras -oitk /scratch/punim0025/work/fmriprep_wf/single_subject_F058_wf/func_preproc_task_rest_wf/bold_reg_wf/fsl_bbr_wf/fsl2itk_inv/affine.txt 191004-14:51:04,219 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_F058_wf.func_preproc_task_rest_wf.bold_reg_wf.fsl_bbr_wf.fsl2itk_fwd". 191004-14:51:04,336 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_F058_wf.func_preproc_task_rest_wf.bold_reg_wf.fsl_bbr_wf.fsl2itk_inv". 191004-14:51:04,423 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_F058_wf.func_preproc_task_rest_wf.bold_t1_trans_wf.mask_t1w_tfm" in "/scratch/punim0025/work/fmriprep_wf/single_subject_F058_wf/func_preproc_task_rest_wf/bold_t1_trans_wf/mask_t1w_tfm". 191004-14:51:04,424 nipype.workflow INFO: [Node] Outdated cache found for "fmriprep_wf.single_subject_F058_wf.func_preproc_task_rest_wf.bold_t1_trans_wf.mask_t1w_tfm". 191004-14:51:04,607 nipype.workflow INFO: [Node] Running "mask_t1w_tfm" ("niworkflows.interfaces.fixes.FixHeaderApplyTransforms"), a CommandLine Interface with command: antsApplyTransforms --default-value 0 --float 1 --input /scratch/punim0025/work/fmriprep_wf/single_subject_F058_wf/func_preproc_task_rest_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/combine_masks/ref_bold_corrected_brain_mask_maths.nii.gz --interpolation MultiLabel --output ref_bold_corrected_brain_mask_maths_trans.nii.gz --reference-image /scratch/punim0025/work/fmriprep_wf/single_subject_F058_wf/func_preproc_task_rest_wf/bold_t1_trans_wf/gen_ref/sub-F058_T1w_corrected_masked_xform_reference.nii.gz --transform /scratch/punim0025/work/fmriprep_wf/single_subject_F058_wf/func_preproc_task_rest_wf/bold_reg_wf/fsl_bbr_wf/fsl2itk_fwd/affine.txt 191004-14:51:09,127 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_F058_wf.func_preproc_task_rest_wf.bold_t1_trans_wf.mask_t1w_tfm". 191004-14:51:10,629 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_F058_wf.func_preproc_task_rest_wf.bold_t1_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.pre_mask_dilate" in "/scratch/punim0025/work/fmriprep_wf/single_subject_F058_wf/func_preproc_task_rest_wf/bold_t1_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/pre_mask_dilate". 191004-14:51:10,629 nipype.workflow INFO: [Node] Outdated cache found for "fmriprep_wf.single_subject_F058_wf.func_preproc_task_rest_wf.bold_t1_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.pre_mask_dilate". 191004-14:51:10,835 nipype.workflow INFO: [Node] Running "pre_mask_dilate" ("nipype.interfaces.fsl.maths.DilateImage"), a CommandLine Interface with command: fslmaths -dt char /scratch/punim0025/work/fmriprep_wf/single_subject_F058_wf/func_preproc_task_rest_wf/bold_t1_trans_wf/mask_t1w_tfm/ref_bold_corrected_brain_mask_maths_trans.nii.gz -kernel sphere 3.0000 -dilF /scratch/punim0025/work/fmriprep_wf/single_subject_F058_wf/func_preproc_task_rest_wf/bold_t1_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/pre_mask_dilate/ref_bold_corrected_brain_mask_maths_trans_dil.nii.gz 191004-14:51:11,342 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_F058_wf.func_preproc_task_rest_wf.bold_t1_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.pre_mask_dilate". 191004-16:41:46,494 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_F058_wf.anat_preproc_wf.anat_norm_wf.registration". 191004-16:41:47,731 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_F058_wf.anat_preproc_wf.anat_norm_wf.tpl_mask" in "/scratch/punim0025/work/fmriprep_wf/single_subject_F058_wf/anat_preproc_wf/anat_norm_wf/_template_MNIPediatricAsym/tpl_mask". 191004-16:41:47,731 nipype.workflow INFO: [Node] Outdated cache found for "fmriprep_wf.single_subject_F058_wf.anat_preproc_wf.anat_norm_wf.tpl_mask". 191004-16:41:47,738 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_F058_wf.anat_preproc_wf.anat_norm_wf.tpl_moving" in "/scratch/punim0025/work/fmriprep_wf/single_subject_F058_wf/anat_preproc_wf/anat_norm_wf/_template_MNIPediatricAsym/tpl_moving". 191004-16:41:47,738 nipype.workflow INFO: [Node] Outdated cache found for "fmriprep_wf.single_subject_F058_wf.anat_preproc_wf.anat_norm_wf.tpl_moving". 191004-16:41:47,751 nipype.workflow INFO: [Node] Running "tpl_mask" ("niworkflows.interfaces.fixes.FixHeaderApplyTransforms"), a CommandLine Interface with command: antsApplyTransforms --default-value 0 --dimensionality 3 --float 1 --input /scratch/punim0025/work/fmriprep_wf/single_subject_F058_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/copy_xform/09_relabel_wm_mask_xform.nii.gz --interpolation MultiLabel --output 09_relabel_wm_mask_xform_trans.nii.gz --reference-image /scratch/punim0025/templateflow/tpl-MNIPediatricAsym/cohort-3/tpl-MNIPediatricAsym_cohort-3_res-1_T1w.nii.gz --transform /scratch/punim0025/work/fmriprep_wf/single_subject_F058_wf/anat_preproc_wf/anat_norm_wf/_template_MNIPediatricAsym/registration/ants_t1_to_mniComposite.h5 191004-16:41:47,758 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_F058_wf.anat_preproc_wf.anat_norm_wf.tpl_seg" in "/scratch/punim0025/work/fmriprep_wf/single_subject_F058_wf/anat_preproc_wf/anat_norm_wf/_template_MNIPediatricAsym/tpl_seg". 191004-16:41:47,758 nipype.workflow INFO: [Node] Outdated cache found for "fmriprep_wf.single_subject_F058_wf.anat_preproc_wf.anat_norm_wf.tpl_seg". 191004-16:41:47,765 nipype.workflow INFO: [Node] Running "tpl_moving" ("niworkflows.interfaces.fixes.FixHeaderApplyTransforms"), a CommandLine Interface with command: antsApplyTransforms --default-value 0 --dimensionality 3 --float 1 --input /scratch/punim0025/work/fmriprep_wf/single_subject_F058_wf/anat_preproc_wf/brain_extraction_wf/copy_xform/sub-F058_T1w_corrected_xform.nii --interpolation LanczosWindowedSinc --output sub-F058_T1w_corrected_xform_trans.nii --reference-image /scratch/punim0025/templateflow/tpl-MNIPediatricAsym/cohort-3/tpl-MNIPediatricAsym_cohort-3_res-1_T1w.nii.gz --transform /scratch/punim0025/work/fmriprep_wf/single_subject_F058_wf/anat_preproc_wf/anat_norm_wf/_template_MNIPediatricAsym/registration/ants_t1_to_mniComposite.h5 191004-16:41:47,806 nipype.workflow INFO: [Node] Running "tpl_seg" ("niworkflows.interfaces.fixes.FixHeaderApplyTransforms"), a CommandLine Interface with command: antsApplyTransforms --default-value 0 --dimensionality 3 --float 1 --input /scratch/punim0025/work/fmriprep_wf/single_subject_F058_wf/anat_preproc_wf/t1_seg/sub-F058_T1w_corrected_masked_xform_seg.nii.gz --interpolation MultiLabel --output sub-F058_T1w_corrected_masked_xform_seg_trans.nii.gz --reference-image /scratch/punim0025/templateflow/tpl-MNIPediatricAsym/cohort-3/tpl-MNIPediatricAsym_cohort-3_res-1_T1w.nii.gz --transform /scratch/punim0025/work/fmriprep_wf/single_subject_F058_wf/anat_preproc_wf/anat_norm_wf/_template_MNIPediatricAsym/registration/ants_t1_to_mniComposite.h5 191004-16:41:49,582 nipype.workflow INFO: [Node] Setting-up "_tpl_tpms0" in "/scratch/punim0025/work/fmriprep_wf/single_subject_F058_wf/anat_preproc_wf/anat_norm_wf/_template_MNIPediatricAsym/tpl_tpms/mapflow/_tpl_tpms0". 191004-16:41:49,582 nipype.workflow INFO: [Node] Outdated cache found for "_tpl_tpms0". 191004-16:41:49,603 nipype.workflow INFO: [Node] Setting-up "_tpl_tpms1" in "/scratch/punim0025/work/fmriprep_wf/single_subject_F058_wf/anat_preproc_wf/anat_norm_wf/_template_MNIPediatricAsym/tpl_tpms/mapflow/_tpl_tpms1". 191004-16:41:49,603 nipype.workflow INFO: [Node] Outdated cache found for "_tpl_tpms1". 191004-16:41:49,614 nipype.workflow INFO: [Node] Setting-up "_tpl_tpms2" in "/scratch/punim0025/work/fmriprep_wf/single_subject_F058_wf/anat_preproc_wf/anat_norm_wf/_template_MNIPediatricAsym/tpl_tpms/mapflow/_tpl_tpms2". 191004-16:41:49,614 nipype.workflow INFO: [Node] Outdated cache found for "_tpl_tpms2". 191004-16:41:49,756 nipype.workflow INFO: [Node] Running "_tpl_tpms0" ("niworkflows.interfaces.fixes.FixHeaderApplyTransforms"), a CommandLine Interface with command: antsApplyTransforms --default-value 0 --dimensionality 3 --float 1 --input /scratch/punim0025/work/fmriprep_wf/single_subject_F058_wf/anat_preproc_wf/t1_seg/sub-F058_T1w_corrected_masked_xform_prob_0.nii.gz --interpolation Gaussian --output sub-F058_T1w_corrected_masked_xform_prob_0_trans.nii.gz --reference-image /scratch/punim0025/templateflow/tpl-MNIPediatricAsym/cohort-3/tpl-MNIPediatricAsym_cohort-3_res-1_T1w.nii.gz --transform /scratch/punim0025/work/fmriprep_wf/single_subject_F058_wf/anat_preproc_wf/anat_norm_wf/_template_MNIPediatricAsym/registration/ants_t1_to_mniComposite.h5 191004-16:41:49,792 nipype.workflow INFO: [Node] Running "_tpl_tpms1" ("niworkflows.interfaces.fixes.FixHeaderApplyTransforms"), a CommandLine Interface with command: antsApplyTransforms --default-value 0 --dimensionality 3 --float 1 --input /scratch/punim0025/work/fmriprep_wf/single_subject_F058_wf/anat_preproc_wf/t1_seg/sub-F058_T1w_corrected_masked_xform_prob_1.nii.gz --interpolation Gaussian --output sub-F058_T1w_corrected_masked_xform_prob_1_trans.nii.gz --reference-image /scratch/punim0025/templateflow/tpl-MNIPediatricAsym/cohort-3/tpl-MNIPediatricAsym_cohort-3_res-1_T1w.nii.gz --transform /scratch/punim0025/work/fmriprep_wf/single_subject_F058_wf/anat_preproc_wf/anat_norm_wf/_template_MNIPediatricAsym/registration/ants_t1_to_mniComposite.h5 191004-16:41:49,826 nipype.workflow INFO: [Node] Running "_tpl_tpms2" ("niworkflows.interfaces.fixes.FixHeaderApplyTransforms"), a CommandLine Interface with command: antsApplyTransforms --default-value 0 --dimensionality 3 --float 1 --input /scratch/punim0025/work/fmriprep_wf/single_subject_F058_wf/anat_preproc_wf/t1_seg/sub-F058_T1w_corrected_masked_xform_prob_2.nii.gz --interpolation Gaussian --output sub-F058_T1w_corrected_masked_xform_prob_2_trans.nii.gz --reference-image /scratch/punim0025/templateflow/tpl-MNIPediatricAsym/cohort-3/tpl-MNIPediatricAsym_cohort-3_res-1_T1w.nii.gz --transform /scratch/punim0025/work/fmriprep_wf/single_subject_F058_wf/anat_preproc_wf/anat_norm_wf/_template_MNIPediatricAsym/registration/ants_t1_to_mniComposite.h5 191004-16:43:15,474 nipype.workflow INFO: [Node] Finished "_tpl_tpms0". 191004-16:43:19,887 nipype.workflow INFO: [Node] Finished "_tpl_tpms2". 191004-16:43:21,162 nipype.workflow INFO: [Node] Finished "_tpl_tpms1". 191004-16:43:21,799 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_F058_wf.anat_preproc_wf.anat_norm_wf.tpl_tpms" in "/scratch/punim0025/work/fmriprep_wf/single_subject_F058_wf/anat_preproc_wf/anat_norm_wf/_template_MNIPediatricAsym/tpl_tpms". 191004-16:43:21,800 nipype.workflow INFO: [Node] Outdated cache found for "fmriprep_wf.single_subject_F058_wf.anat_preproc_wf.anat_norm_wf.tpl_tpms". 191004-16:43:21,921 nipype.workflow INFO: [Node] Setting-up "_tpl_tpms0" in "/scratch/punim0025/work/fmriprep_wf/single_subject_F058_wf/anat_preproc_wf/anat_norm_wf/_template_MNIPediatricAsym/tpl_tpms/mapflow/_tpl_tpms0". 191004-16:43:21,945 nipype.workflow INFO: [Node] Cached "_tpl_tpms0" - collecting precomputed outputs 191004-16:43:21,945 nipype.workflow INFO: [Node] "_tpl_tpms0" found cached. 191004-16:43:21,946 nipype.workflow INFO: [Node] Setting-up "_tpl_tpms1" in "/scratch/punim0025/work/fmriprep_wf/single_subject_F058_wf/anat_preproc_wf/anat_norm_wf/_template_MNIPediatricAsym/tpl_tpms/mapflow/_tpl_tpms1". 191004-16:43:21,971 nipype.workflow INFO: [Node] Cached "_tpl_tpms1" - collecting precomputed outputs 191004-16:43:21,971 nipype.workflow INFO: [Node] "_tpl_tpms1" found cached. 191004-16:43:21,972 nipype.workflow INFO: [Node] Setting-up "_tpl_tpms2" in "/scratch/punim0025/work/fmriprep_wf/single_subject_F058_wf/anat_preproc_wf/anat_norm_wf/_template_MNIPediatricAsym/tpl_tpms/mapflow/_tpl_tpms2". 191004-16:43:21,997 nipype.workflow INFO: [Node] Cached "_tpl_tpms2" - collecting precomputed outputs 191004-16:43:21,997 nipype.workflow INFO: [Node] "_tpl_tpms2" found cached. 191004-16:43:22,81 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_F058_wf.anat_preproc_wf.anat_norm_wf.tpl_tpms". 191004-16:43:44,989 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_F058_wf.anat_preproc_wf.anat_norm_wf.tpl_moving". 191004-16:44:55,838 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_F058_wf.anat_preproc_wf.anat_norm_wf.tpl_mask". 191004-16:44:57,963 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_F058_wf.anat_preproc_wf.anat_norm_wf.norm_msk" in "/scratch/punim0025/work/fmriprep_wf/single_subject_F058_wf/anat_preproc_wf/anat_norm_wf/_template_MNIPediatricAsym/norm_msk". 191004-16:44:57,963 nipype.workflow INFO: [Node] Outdated cache found for "fmriprep_wf.single_subject_F058_wf.anat_preproc_wf.anat_norm_wf.norm_msk". 191004-16:44:57,979 nipype.workflow INFO: [Node] Running "norm_msk" ("nipype.interfaces.utility.wrappers.Function") 191004-16:44:58,962 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_F058_wf.anat_preproc_wf.anat_norm_wf.norm_msk". 191004-16:44:59,370 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_F058_wf.anat_preproc_wf.anat_norm_wf.norm_rpt" in "/scratch/punim0025/work/fmriprep_wf/single_subject_F058_wf/anat_preproc_wf/anat_norm_wf/_template_MNIPediatricAsym/norm_rpt". 191004-16:44:59,371 nipype.workflow INFO: [Node] Outdated cache found for "fmriprep_wf.single_subject_F058_wf.anat_preproc_wf.anat_norm_wf.norm_rpt". 191004-16:44:59,383 nipype.workflow INFO: [Node] Running "norm_rpt" ("niworkflows.interfaces.registration.SimpleBeforeAfterRPT") 191004-16:45:06,643 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_F058_wf.anat_preproc_wf.anat_norm_wf.tpl_seg". 191004-16:45:07,388 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_F058_wf.anat_preproc_wf.anat_norm_wf.outputnode" in "/scratch/punim0025/work/fmriprep_wf/single_subject_F058_wf/anat_preproc_wf/anat_norm_wf/outputnode". 191004-16:45:07,388 nipype.workflow INFO: [Node] Outdated cache found for "fmriprep_wf.single_subject_F058_wf.anat_preproc_wf.anat_norm_wf.outputnode". 191004-16:45:07,391 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_F058_wf.anat_preproc_wf.anat_derivatives_wf.lut_tpl_seg" in "/scratch/punim0025/work/fmriprep_wf/single_subject_F058_wf/anat_preproc_wf/anat_derivatives_wf/_template_MNIPediatricAsym/lut_tpl_seg". 191004-16:45:07,391 nipype.workflow INFO: [Node] Outdated cache found for "fmriprep_wf.single_subject_F058_wf.anat_preproc_wf.anat_derivatives_wf.lut_tpl_seg". 191004-16:45:07,403 nipype.workflow INFO: [Node] Running "outputnode" ("nipype.interfaces.utility.base.IdentityInterface") 191004-16:45:07,408 nipype.workflow INFO: [Node] Running "lut_tpl_seg" ("nipype.interfaces.utility.wrappers.Function") 191004-16:45:07,435 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_F058_wf.anat_preproc_wf.anat_norm_wf.outputnode". 191004-16:45:07,499 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_F058_wf.anat_preproc_wf.anat_norm_wf.norm_rpt". 191004-16:45:07,660 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_F058_wf.anat_preproc_wf.anat_derivatives_wf.lut_tpl_seg". 191004-16:45:13,603 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_F058_wf.func_preproc_task_rest_wf.bold_std_trans_wf.gen_ref" in "/scratch/punim0025/work/fmriprep_wf/single_subject_F058_wf/func_preproc_task_rest_wf/bold_std_trans_wf/_key_MNIPediatricAsym/gen_ref". 191004-16:45:13,603 nipype.workflow INFO: [Node] Outdated cache found for "fmriprep_wf.single_subject_F058_wf.func_preproc_task_rest_wf.bold_std_trans_wf.gen_ref". 191004-16:45:13,617 nipype.workflow INFO: [Node] Running "gen_ref" ("niworkflows.interfaces.utils.GenerateSamplingReference") 191004-16:45:13,621 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_F058_wf.func_preproc_task_rest_wf.bold_std_trans_wf.gen_ref". 191004-16:45:17,503 nipype.workflow ERROR: could not run node: fmriprep_wf.single_subject_F058_wf.func_preproc_task_rest_wf.bold_hmc_wf.normalize_motion 191004-16:45:17,509 nipype.workflow ERROR: could not run node: fmriprep_wf.single_subject_F058_wf.func_preproc_task_rest_wf.bold_hmc_wf.fsl2itk fMRIPrep failed: Workflow did not execute cleanly. Check log for details pandoc-citeproc: reference mnipediatricasym not found Preprocessing did not finish successfully. Errors occurred while processing data from participants: F058 (2). Check the HTML reports for details. /usr/local/miniconda/lib/python3.7/site-packages/nilearn/image/resampling.py:510: UserWarning: Casting data from int32 to float32 warnings.warn("Casting data from %s to %s" % (data.dtype.name, aux)) /usr/local/miniconda/lib/python3.7/site-packages/nilearn/image/resampling.py:510: UserWarning: Casting data from int16 to float32 warnings.warn("Casting data from %s to %s" % (data.dtype.name, aux)) /usr/local/miniconda/lib/python3.7/site-packages/nilearn/image/resampling.py:510: UserWarning: Casting data from int32 to float32 warnings.warn("Casting data from %s to %s" % (data.dtype.name, aux)) /usr/local/miniconda/lib/python3.7/site-packages/nilearn/image/resampling.py:510: UserWarning: Casting data from int16 to float32 warnings.warn("Casting data from %s to %s" % (data.dtype.name, aux)) /usr/local/miniconda/lib/python3.7/site-packages/nilearn/image/resampling.py:510: UserWarning: Casting data from int32 to float32 warnings.warn("Casting data from %s to %s" % (data.dtype.name, aux)) /usr/local/miniconda/lib/python3.7/site-packages/nilearn/image/resampling.py:510: UserWarning: Casting data from int16 to float32 warnings.warn("Casting data from %s to %s" % (data.dtype.name, aux)) Sentry is attempting to send 0 pending error messages Waiting up to 2 seconds Press Ctrl-C to quit