subject is sub-F134 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). 191010-20:17:42,958 nipype.workflow IMPORTANT: Running fMRIPREP version 1.5.0: * BIDS dataset path: /scratch/punim0025/wave1_BIDS. * Participant list: ['F134']. * Run identifier: 20191010-201735_c952a813-8ad2-4e72-a4d2-d1fa98b3ac93. 191010-20:17:45,109 nipype.workflow IMPORTANT: Creating bold processing workflow for "/scratch/punim0025/wave1_BIDS/sub-F134/func/sub-F134_task-rest_bold.nii" (0.04 GB / 154 TRs). Memory resampled/largemem=0.18/0.25 GB. 191010-20:17:45,147 nipype.workflow IMPORTANT: No single-band-reference found for sub-F134_task-rest_bold.nii 191010-20:17:45,935 nipype.workflow IMPORTANT: Slice-timing correction will be included. 191010-20:17:45,956 nipype.workflow WARNING: SDC: no fieldmaps found or they were ignored (/scratch/punim0025/wave1_BIDS/sub-F134/func/sub-F134_task-rest_bold.nii). 191010-20:17:55,820 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 191010-20:18:06,869 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_F134_wf.func_preproc_task_rest_wf.func_derivatives_wf.raw_sources" in "/scratch/punim0025/work/fmriprep_wf/single_subject_F134_wf/func_preproc_task_rest_wf/func_derivatives_wf/raw_sources". 191010-20:18:06,967 nipype.workflow INFO: [Node] Running "raw_sources" ("nipype.interfaces.utility.wrappers.Function") 191010-20:18:07,19 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_F134_wf.func_preproc_task_rest_wf.func_derivatives_wf.raw_sources". 191010-20:18:15,780 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_F134_wf.func_preproc_task_rest_wf.bold_reference_wf.validate" in "/scratch/punim0025/work/fmriprep_wf/single_subject_F134_wf/func_preproc_task_rest_wf/bold_reference_wf/validate". 191010-20:18:15,863 nipype.workflow INFO: [Node] Running "validate" ("niworkflows.interfaces.images.ValidateImage") 191010-20:18:16,384 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_F134_wf.func_preproc_task_rest_wf.bold_reference_wf.validate". 191010-20:18:18,441 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_F134_wf.bidssrc" in "/scratch/punim0025/work/fmriprep_wf/single_subject_F134_wf/bidssrc". 191010-20:18:18,449 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_F134_wf.anat_preproc_wf.brain_extraction_wf.res_tmpl" in "/scratch/punim0025/work/fmriprep_wf/single_subject_F134_wf/anat_preproc_wf/brain_extraction_wf/res_tmpl". 191010-20:18:18,497 nipype.workflow INFO: [Node] Running "bidssrc" ("niworkflows.interfaces.bids.BIDSDataGrabber") 191010-20:18:18,499 nipype.interface WARNING: No "t2w" images found for sub- 191010-20:18:18,499 nipype.interface WARNING: No "flair" images found for sub- 191010-20:18:18,499 nipype.interface WARNING: No "fmap" images found for sub- 191010-20:18:18,499 nipype.interface WARNING: No "sbref" images found for sub- 191010-20:18:18,499 nipype.interface WARNING: No "roi" images found for sub- 191010-20:18:18,523 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 191010-20:18:18,542 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_F134_wf.bidssrc". 191010-20:18:18,767 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_F134_wf.anat_preproc_wf.brain_extraction_wf.lap_tmpl" in "/scratch/punim0025/work/fmriprep_wf/single_subject_F134_wf/anat_preproc_wf/brain_extraction_wf/lap_tmpl". 191010-20:18:18,773 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 191010-20:18:22,672 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_F134_wf.anat_preproc_wf.brain_extraction_wf.res_tmpl". 191010-20:18:32,482 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_F134_wf.func_preproc_task_rest_wf.bold_reference_wf.gen_ref" in "/scratch/punim0025/work/fmriprep_wf/single_subject_F134_wf/func_preproc_task_rest_wf/bold_reference_wf/gen_ref". 191010-20:18:32,554 nipype.workflow INFO: [Node] Running "gen_ref" ("niworkflows.interfaces.registration.EstimateReferenceImage") 191010-20:18:34,86 nipype.interface INFO: stderr 2019-10-10T20:18:34.086699:++ 3dvolreg: AFNI version=Debian-16.2.07~dfsg.1-5~nd16.04+1 (Jun 12 2017) [64-bit] 191010-20:18:34,87 nipype.interface INFO: stderr 2019-10-10T20:18:34.086699:++ Authored by: RW Cox 191010-20:18:34,249 nipype.interface INFO: stderr 2019-10-10T20:18:34.249573:*+ WARNING: If you are performing spatial transformations on an oblique dset, 191010-20:18:34,249 nipype.interface INFO: stderr 2019-10-10T20:18:34.249573: such as /scratch/punim0025/work/fmriprep_wf/single_subject_F134_wf/func_preproc_task_rest_wf/bold_reference_wf/gen_ref/slice.nii.gz, 191010-20:18:34,249 nipype.interface INFO: stderr 2019-10-10T20:18:34.249573: or viewing/combining it with volumes of differing obliquity, 191010-20:18:34,249 nipype.interface INFO: stderr 2019-10-10T20:18:34.249573: you should consider running: 191010-20:18:34,249 nipype.interface INFO: stderr 2019-10-10T20:18:34.249573: 3dWarp -deoblique 191010-20:18:34,249 nipype.interface INFO: stderr 2019-10-10T20:18:34.249573: on this and other oblique datasets in the same session. 191010-20:18:34,249 nipype.interface INFO: stderr 2019-10-10T20:18:34.249573: See 3dWarp -help for details. 191010-20:18:34,249 nipype.interface INFO: stderr 2019-10-10T20:18:34.249573:++ Oblique dataset:/scratch/punim0025/work/fmriprep_wf/single_subject_F134_wf/func_preproc_task_rest_wf/bold_reference_wf/gen_ref/slice.nii.gz is 8.110676 degrees from plumb. 191010-20:18:34,252 nipype.interface INFO: stderr 2019-10-10T20:18:34.252221:++ Coarse del was 10, replaced with 4 191010-20:18:35,626 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_F134_wf.anat_preproc_wf.anat_template_wf.t1_template_dimensions" in "/scratch/punim0025/work/fmriprep_wf/single_subject_F134_wf/anat_preproc_wf/anat_template_wf/t1_template_dimensions". 191010-20:18:35,641 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_F134_wf.anat_preproc_wf.brain_extraction_wf.lap_tmpl". 191010-20:18:35,651 nipype.workflow INFO: [Node] Running "t1_template_dimensions" ("niworkflows.interfaces.images.TemplateDimensions") 191010-20:18:35,765 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_F134_wf.anat_preproc_wf.anat_template_wf.t1_template_dimensions". 191010-20:18:36,64 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_F134_wf.bids_info" in "/scratch/punim0025/work/fmriprep_wf/single_subject_F134_wf/bids_info". 191010-20:18:36,151 nipype.workflow INFO: [Node] Running "bids_info" ("niworkflows.interfaces.bids.BIDSInfo") 191010-20:18:38,438 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_F134_wf.anat_preproc_wf.brain_extraction_wf.mrg_tmpl" in "/scratch/punim0025/work/fmriprep_wf/single_subject_F134_wf/anat_preproc_wf/brain_extraction_wf/mrg_tmpl". 191010-20:18:39,209 nipype.workflow INFO: [Node] Running "mrg_tmpl" ("nipype.interfaces.utility.base.Merge") 191010-20:18:40,688 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_F134_wf.anat_preproc_wf.brain_extraction_wf.mrg_tmpl". 191010-20:18:44,804 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_F134_wf.anat_preproc_wf.anat_derivatives_wf.raw_sources" in "/scratch/punim0025/work/fmriprep_wf/single_subject_F134_wf/anat_preproc_wf/anat_derivatives_wf/raw_sources". 191010-20:18:44,862 nipype.workflow INFO: [Node] Running "raw_sources" ("nipype.interfaces.utility.wrappers.Function") 191010-20:18:44,903 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_F134_wf.anat_preproc_wf.anat_derivatives_wf.raw_sources". 191010-20:18:45,967 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_F134_wf.anat_preproc_wf.anat_derivatives_wf.t1_name" in "/scratch/punim0025/work/fmriprep_wf/single_subject_F134_wf/anat_preproc_wf/anat_derivatives_wf/t1_name". 191010-20:18:46,26 nipype.workflow INFO: [Node] Running "t1_name" ("nipype.interfaces.utility.wrappers.Function") 191010-20:18:46,96 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_F134_wf.anat_preproc_wf.anat_derivatives_wf.t1_name". 191010-20:18:49,14 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_F134_wf.bids_info". 191010-20:18:52,875 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_F134_wf.anat_preproc_wf.anat_template_wf.t1_conform" in "/scratch/punim0025/work/fmriprep_wf/single_subject_F134_wf/anat_preproc_wf/anat_template_wf/t1_conform". 191010-20:18:52,882 nipype.workflow INFO: [Node] Setting-up "_t1_conform0" in "/scratch/punim0025/work/fmriprep_wf/single_subject_F134_wf/anat_preproc_wf/anat_template_wf/t1_conform/mapflow/_t1_conform0". 191010-20:18:52,886 nipype.workflow INFO: [Node] Running "_t1_conform0" ("niworkflows.interfaces.images.Conform") 191010-20:18:52,915 nipype.workflow INFO: [Node] Finished "_t1_conform0". 191010-20:18:52,918 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_F134_wf.anat_preproc_wf.anat_template_wf.t1_conform". 191010-20:18:54,698 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_F134_wf.anat_preproc_wf.anat_template_wf.get1st" in "/scratch/punim0025/work/fmriprep_wf/single_subject_F134_wf/anat_preproc_wf/anat_template_wf/get1st". 191010-20:18:54,702 nipype.workflow INFO: [Node] Running "get1st" ("nipype.interfaces.utility.base.Select") 191010-20:18:54,709 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_F134_wf.anat_preproc_wf.anat_template_wf.get1st". 191010-20:18:56,451 nipype.interface INFO: stderr 2019-10-10T20:18:56.451133:++ Max displacement in automask = 2.01 (mm) at sub-brick 16 191010-20:18:56,451 nipype.interface INFO: stderr 2019-10-10T20:18:56.451133:++ Max delta displ in automask = 0.89 (mm) at sub-brick 17 191010-20:18:57,356 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_F134_wf.func_preproc_task_rest_wf.bold_reference_wf.gen_ref". 191010-20:18:57,375 nipype.workflow ERROR: Node truncate_images failed to run on host spartan-snowy005.hpc.unimelb.edu.au. 191010-20:18:57,384 nipype.workflow ERROR: Saving crash info to /scratch/punim0025/output_wave1/fmriprep/sub-F134/log/20191010-201735_c952a813-8ad2-4e72-a4d2-d1fa98b3ac93/crash-20191010-201857-epozzi-truncate_images-da132b03-5463-475b-89bb-c8f2d91a4637.txt Traceback (most recent call last): File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/plugins/multiproc.py", line 269, in _send_procs_to_workers num_subnodes = self.procs[jobid].num_subnodes() File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py", line 1204, in num_subnodes self._get_inputs() File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py", line 1219, in _get_inputs super(MapNode, self)._get_inputs() File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py", line 521, in _get_inputs outputs = _load_resultfile(results_file)[0].outputs File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/engine/utils.py", line 300, in load_resultfile result = loadpkl(results_file) File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/utils/filemanip.py", line 687, in loadpkl pkl_file = pklopen(infile.name, 'rb') File "/usr/local/miniconda/lib/python3.7/gzip.py", line 53, in open binary_file = GzipFile(filename, gz_mode, compresslevel) File "/usr/local/miniconda/lib/python3.7/gzip.py", line 163, in __init__ fileobj = self.myfileobj = builtins.open(filename, mode or 'rb') FileNotFoundError: [Errno 2] No such file or directory: 'result_anat_validate.pklz' 191010-20:19:01,56 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_F134_wf.func_preproc_task_rest_wf.bold_hmc_wf.mcflirt" in "/scratch/punim0025/work/fmriprep_wf/single_subject_F134_wf/func_preproc_task_rest_wf/bold_hmc_wf/mcflirt". 191010-20:19:01,62 nipype.workflow INFO: [Node] Running "mcflirt" ("nipype.interfaces.fsl.preprocess.MCFLIRT"), a CommandLine Interface with command: mcflirt -in /scratch/punim0025/wave1_BIDS/sub-F134/func/sub-F134_task-rest_bold.nii -out /scratch/punim0025/work/fmriprep_wf/single_subject_F134_wf/func_preproc_task_rest_wf/bold_hmc_wf/mcflirt/sub-F134_task-rest_bold_mcf.nii.gz -reffile /scratch/punim0025/work/fmriprep_wf/single_subject_F134_wf/func_preproc_task_rest_wf/bold_reference_wf/gen_ref/ref_bold.nii.gz -mats -plots 191010-20:19:04,379 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_F134_wf.func_preproc_task_rest_wf.bold_stc_wf.slice_timing_correction" in "/scratch/punim0025/work/fmriprep_wf/single_subject_F134_wf/func_preproc_task_rest_wf/bold_stc_wf/slice_timing_correction". 191010-20:19:04,500 nipype.workflow INFO: [Node] Running "slice_timing_correction" ("nipype.interfaces.afni.preprocess.TShift"), a CommandLine Interface with command: 3dTshift -ignore 0 -prefix sub-F134_task-rest_bold_tshift.nii.gz -tpattern @slice_timing.1D -TR 2.4s /scratch/punim0025/work/fmriprep_wf/single_subject_F134_wf/func_preproc_task_rest_wf/bold_stc_wf/slice_timing_correction/sub-F134_task-rest_bold.nii 191010-20:19:09,731 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_F134_wf.func_preproc_task_rest_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.init_aff" in "/scratch/punim0025/work/fmriprep_wf/single_subject_F134_wf/func_preproc_task_rest_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/init_aff". 191010-20:19:09,827 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-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_res-02_desc-brain_mask.nii.gz -m Mattes[/home/epozzi/.cache/templateflow/tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_res-02_desc-fMRIPrep_boldref.nii.gz,/scratch/punim0025/work/fmriprep_wf/single_subject_F134_wf/func_preproc_task_rest_wf/bold_reference_wf/gen_ref/ref_bold.nii.gz,32,Regular,0.200000] -o initialization.mat -p 0 -s [20.000000,0.120000] -t Affine[0.100000] -v 1 191010-20:19:16,415 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_F134_wf.func_preproc_task_rest_wf.bold_stc_wf.slice_timing_correction". 191010-20:19:27,299 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_F134_wf.func_preproc_task_rest_wf.bold_stc_wf.copy_xform" in "/scratch/punim0025/work/fmriprep_wf/single_subject_F134_wf/func_preproc_task_rest_wf/bold_stc_wf/copy_xform". 191010-20:19:27,424 nipype.workflow INFO: [Node] Running "copy_xform" ("niworkflows.interfaces.utils.CopyXForm") 191010-20:19:29,635 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_F134_wf.func_preproc_task_rest_wf.bold_stc_wf.copy_xform". 191010-20:19:33,837 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_F134_wf.func_preproc_task_rest_wf.bold_split" in "/scratch/punim0025/work/fmriprep_wf/single_subject_F134_wf/func_preproc_task_rest_wf/bold_split". 191010-20:19:33,857 nipype.workflow INFO: [Node] Running "bold_split" ("nipype.interfaces.fsl.utils.Split"), a CommandLine Interface with command: fslsplit /scratch/punim0025/work/fmriprep_wf/single_subject_F134_wf/func_preproc_task_rest_wf/bold_stc_wf/copy_xform/sub-F134_task-rest_bold_tshift_xform.nii.gz -t 191010-20:19:37,827 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_F134_wf.func_preproc_task_rest_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.init_aff". 191010-20:19:41,801 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_F134_wf.func_preproc_task_rest_wf.bold_hmc_wf.mcflirt". 191010-20:19:44,651 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_F134_wf.func_preproc_task_rest_wf.bold_split". 191010-20:19:49,828 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_F134_wf.func_preproc_task_rest_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.norm" in "/scratch/punim0025/work/fmriprep_wf/single_subject_F134_wf/func_preproc_task_rest_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/norm". 191010-20:19:49,908 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_F134_wf/func_preproc_task_rest_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/init_aff/initialization.mat, 0 ] --initialize-transforms-per-stage 0 --interpolation Linear --output transform --transform Affine[ 0.1 ] --metric Mattes[ /home/epozzi/.cache/templateflow/tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_res-02_desc-fMRIPrep_boldref.nii.gz, /scratch/punim0025/work/fmriprep_wf/single_subject_F134_wf/func_preproc_task_rest_wf/bold_reference_wf/gen_ref/ref_bold.nii.gz, 1, 64, Random, 0.2 ] --convergence [ 200, 1e-09, 10 ] --smoothing-sigmas 2.0mm --shrink-factors 2 --use-estimate-learning-rate-once 1 --use-histogram-matching 1 --winsorize-image-intensities [ 0.05, 0.98 ] --write-composite-transform 0 191010-20:19:52,49 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_F134_wf.func_preproc_task_rest_wf.bold_hmc_wf.normalize_motion" in "/scratch/punim0025/work/fmriprep_wf/single_subject_F134_wf/func_preproc_task_rest_wf/bold_hmc_wf/normalize_motion". 191010-20:19:52,58 nipype.workflow INFO: [Node] Running "normalize_motion" ("niworkflows.interfaces.utils.NormalizeMotionParams") 191010-20:19:52,68 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_F134_wf.func_preproc_task_rest_wf.bold_hmc_wf.normalize_motion". 191010-20:19:53,636 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_F134_wf.func_preproc_task_rest_wf.bold_hmc_wf.fsl2itk" in "/scratch/punim0025/work/fmriprep_wf/single_subject_F134_wf/func_preproc_task_rest_wf/bold_hmc_wf/fsl2itk". 191010-20:19:53,679 nipype.workflow INFO: [Node] Running "fsl2itk" ("niworkflows.interfaces.itk.MCFLIRT2ITK") 191010-20:19:56,347 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_F134_wf.func_preproc_task_rest_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.norm". 191010-20:19:56,568 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_F134_wf.func_preproc_task_rest_wf.bold_confounds_wf.fdisp" in "/scratch/punim0025/work/fmriprep_wf/single_subject_F134_wf/func_preproc_task_rest_wf/bold_confounds_wf/fdisp". 191010-20:19:56,616 nipype.workflow INFO: [Node] Running "fdisp" ("nipype.algorithms.confounds.FramewiseDisplacement") 191010-20:19:56,715 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_F134_wf.func_preproc_task_rest_wf.bold_confounds_wf.fdisp". 191010-20:20:06,371 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_F134_wf.func_preproc_task_rest_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.map_brainmask" in "/scratch/punim0025/work/fmriprep_wf/single_subject_F134_wf/func_preproc_task_rest_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/map_brainmask". 191010-20:20:06,440 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-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_res-02_desc-brain_mask.nii.gz --interpolation MultiLabel --output tpl-MNI152NLin2009cAsym_res-02_desc-brain_mask_trans.nii.gz --reference-image /scratch/punim0025/work/fmriprep_wf/single_subject_F134_wf/func_preproc_task_rest_wf/bold_reference_wf/gen_ref/ref_bold.nii.gz --transform [ /scratch/punim0025/work/fmriprep_wf/single_subject_F134_wf/func_preproc_task_rest_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/norm/transform0GenericAffine.mat, 1 ] 191010-20:20:10,988 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_F134_wf.func_preproc_task_rest_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.map_brainmask". 191010-20:20:13,331 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_F134_wf.func_preproc_task_rest_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.pre_mask_dilate" in "/scratch/punim0025/work/fmriprep_wf/single_subject_F134_wf/func_preproc_task_rest_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/pre_mask_dilate". 191010-20:20:13,377 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_F134_wf/func_preproc_task_rest_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/map_brainmask/tpl-MNI152NLin2009cAsym_res-02_desc-brain_mask_trans.nii.gz -kernel sphere 3.0000 -dilF /scratch/punim0025/work/fmriprep_wf/single_subject_F134_wf/func_preproc_task_rest_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/pre_mask_dilate/tpl-MNI152NLin2009cAsym_res-02_desc-brain_mask_trans_dil.nii.gz 191010-20:20:13,719 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_F134_wf.func_preproc_task_rest_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.pre_mask_dilate". 191010-20:20:14,579 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_F134_wf.func_preproc_task_rest_wf.bold_hmc_wf.fsl2itk". 191010-20:20:24,230 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_F134_wf.func_preproc_task_rest_wf.bold_bold_trans_wf.bold_transform" in "/scratch/punim0025/work/fmriprep_wf/single_subject_F134_wf/func_preproc_task_rest_wf/bold_bold_trans_wf/bold_transform". 191010-20:20:24,247 nipype.workflow INFO: [Node] Running "bold_transform" ("niworkflows.interfaces.itk.MultiApplyTransforms") 191010-20:20:24,343 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_F134_wf.func_preproc_task_rest_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.n4_correct" in "/scratch/punim0025/work/fmriprep_wf/single_subject_F134_wf/func_preproc_task_rest_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/n4_correct". 191010-20:20:24,411 nipype.workflow INFO: [Node] Running "n4_correct" ("niworkflows.interfaces.fixes.FixN4BiasFieldCorrection"), a CommandLine Interface with command: N4BiasFieldCorrection --bspline-fitting [ 200 ] -d 3 --input-image /scratch/punim0025/work/fmriprep_wf/single_subject_F134_wf/func_preproc_task_rest_wf/bold_reference_wf/gen_ref/ref_bold.nii.gz --mask-image /scratch/punim0025/work/fmriprep_wf/single_subject_F134_wf/func_preproc_task_rest_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/check_hdr/tpl-MNI152NLin2009cAsym_res-02_desc-brain_mask_trans_dil_hdr.nii.gz --output ref_bold_corrected.nii.gz -r 191010-20:20:35,352 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_F134_wf.func_preproc_task_rest_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.n4_correct". 191010-20:20:40,706 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_F134_wf.func_preproc_task_rest_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_pass" in "/scratch/punim0025/work/fmriprep_wf/single_subject_F134_wf/func_preproc_task_rest_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_pass". 191010-20:20:40,801 nipype.workflow INFO: [Node] Running "skullstrip_first_pass" ("nipype.interfaces.fsl.preprocess.BET"), a CommandLine Interface with command: bet /scratch/punim0025/work/fmriprep_wf/single_subject_F134_wf/func_preproc_task_rest_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/n4_correct/ref_bold_corrected.nii.gz /scratch/punim0025/work/fmriprep_wf/single_subject_F134_wf/func_preproc_task_rest_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_pass/ref_bold_corrected_brain.nii.gz -f 0.20 -m 191010-20:20:46,626 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_F134_wf.func_preproc_task_rest_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_pass". 191010-20:20:52,530 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_F134_wf.func_preproc_task_rest_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_dilate" in "/scratch/punim0025/work/fmriprep_wf/single_subject_F134_wf/func_preproc_task_rest_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_dilate". 191010-20:20:52,625 nipype.workflow INFO: [Node] Running "skullstrip_first_dilate" ("nipype.interfaces.fsl.maths.DilateImage"), a CommandLine Interface with command: fslmaths -dt char /scratch/punim0025/work/fmriprep_wf/single_subject_F134_wf/func_preproc_task_rest_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_pass/ref_bold_corrected_brain_mask.nii.gz -kernel sphere 6.0000 -dilF /scratch/punim0025/work/fmriprep_wf/single_subject_F134_wf/func_preproc_task_rest_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_dilate/ref_bold_corrected_brain_mask_dil.nii.gz 191010-20:20:54,330 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_F134_wf.func_preproc_task_rest_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_dilate". 191010-20:21:02,306 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_F134_wf.func_preproc_task_rest_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_mask" in "/scratch/punim0025/work/fmriprep_wf/single_subject_F134_wf/func_preproc_task_rest_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_mask". 191010-20:21:02,399 nipype.workflow INFO: [Node] Running "skullstrip_first_mask" ("nipype.interfaces.fsl.maths.ApplyMask"), a CommandLine Interface with command: fslmaths /scratch/punim0025/work/fmriprep_wf/single_subject_F134_wf/func_preproc_task_rest_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_pass/ref_bold_corrected_brain.nii.gz -mas /scratch/punim0025/work/fmriprep_wf/single_subject_F134_wf/func_preproc_task_rest_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_dilate/ref_bold_corrected_brain_mask_dil.nii.gz /scratch/punim0025/work/fmriprep_wf/single_subject_F134_wf/func_preproc_task_rest_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_mask/ref_bold_corrected_brain_masked.nii.gz 191010-20:21:02,836 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_F134_wf.func_preproc_task_rest_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_mask". 191010-20:21:10,290 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_F134_wf.func_preproc_task_rest_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.unifize" in "/scratch/punim0025/work/fmriprep_wf/single_subject_F134_wf/func_preproc_task_rest_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/unifize". 191010-20:21:10,370 nipype.workflow INFO: [Node] Running "unifize" ("nipype.interfaces.afni.utils.Unifize"), a CommandLine Interface with command: 3dUnifize -clfrac 0.2 -rbt 18.3 65.0 90.0 -prefix uni.nii.gz -T2 -input /scratch/punim0025/work/fmriprep_wf/single_subject_F134_wf/func_preproc_task_rest_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/unifize/ref_bold_corrected_brain_masked.nii.gz 191010-20:21:16,146 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_F134_wf.func_preproc_task_rest_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.unifize". 191010-20:21:44,910 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_F134_wf.func_preproc_task_rest_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.fixhdr_unifize" in "/scratch/punim0025/work/fmriprep_wf/single_subject_F134_wf/func_preproc_task_rest_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/fixhdr_unifize". 191010-20:21:45,615 nipype.workflow INFO: [Node] Running "fixhdr_unifize" ("niworkflows.interfaces.utils.CopyXForm") 191010-20:21:45,833 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_F134_wf.func_preproc_task_rest_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.fixhdr_unifize". 191010-20:21:52,497 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_F134_wf.func_preproc_task_rest_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.skullstrip_second_pass" in "/scratch/punim0025/work/fmriprep_wf/single_subject_F134_wf/func_preproc_task_rest_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_second_pass". 191010-20:21:52,565 nipype.workflow INFO: [Node] Running "skullstrip_second_pass" ("nipype.interfaces.afni.preprocess.Automask"), a CommandLine Interface with command: 3dAutomask -apply_prefix uni_xform_masked.nii.gz -dilate 1 -prefix uni_xform_mask.nii.gz /scratch/punim0025/work/fmriprep_wf/single_subject_F134_wf/func_preproc_task_rest_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_second_pass/uni_xform.nii.gz 191010-20:21:53,920 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_F134_wf.func_preproc_task_rest_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.skullstrip_second_pass". 191010-20:22:16,573 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_F134_wf.func_preproc_task_rest_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.fixhdr_skullstrip2" in "/scratch/punim0025/work/fmriprep_wf/single_subject_F134_wf/func_preproc_task_rest_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/fixhdr_skullstrip2". 191010-20:22:16,628 nipype.workflow INFO: [Node] Running "fixhdr_skullstrip2" ("niworkflows.interfaces.utils.CopyXForm") 191010-20:22:16,744 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_F134_wf.func_preproc_task_rest_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.fixhdr_skullstrip2". 191010-20:22:19,131 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_F134_wf.func_preproc_task_rest_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.combine_masks" in "/scratch/punim0025/work/fmriprep_wf/single_subject_F134_wf/func_preproc_task_rest_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/combine_masks". 191010-20:22:19,201 nipype.workflow INFO: [Node] Running "combine_masks" ("nipype.interfaces.fsl.maths.BinaryMaths"), a CommandLine Interface with command: fslmaths /scratch/punim0025/work/fmriprep_wf/single_subject_F134_wf/func_preproc_task_rest_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_pass/ref_bold_corrected_brain_mask.nii.gz -mul /scratch/punim0025/work/fmriprep_wf/single_subject_F134_wf/func_preproc_task_rest_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/fixhdr_skullstrip2/uni_xform_mask_xform.nii.gz /scratch/punim0025/work/fmriprep_wf/single_subject_F134_wf/func_preproc_task_rest_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/combine_masks/ref_bold_corrected_brain_mask_maths.nii.gz 191010-20:22:20,839 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_F134_wf.func_preproc_task_rest_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.combine_masks". 191010-20:22:21,919 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_F134_wf.func_preproc_task_rest_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.apply_mask" in "/scratch/punim0025/work/fmriprep_wf/single_subject_F134_wf/func_preproc_task_rest_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/apply_mask". 191010-20:22:22,4 nipype.workflow INFO: [Node] Running "apply_mask" ("nipype.interfaces.fsl.maths.ApplyMask"), a CommandLine Interface with command: fslmaths /scratch/punim0025/work/fmriprep_wf/single_subject_F134_wf/func_preproc_task_rest_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/fixhdr_unifize/uni_xform.nii.gz -mas /scratch/punim0025/work/fmriprep_wf/single_subject_F134_wf/func_preproc_task_rest_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/combine_masks/ref_bold_corrected_brain_mask_maths.nii.gz /scratch/punim0025/work/fmriprep_wf/single_subject_F134_wf/func_preproc_task_rest_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/apply_mask/uni_xform_masked.nii.gz 191010-20:22:22,553 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_F134_wf.func_preproc_task_rest_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.apply_mask". 191010-20:22:22,969 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_F134_wf.func_preproc_task_rest_wf.bold_bold_trans_wf.bold_transform". 191010-20:22:24,363 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_F134_wf.func_preproc_task_rest_wf.bold_bold_trans_wf.merge" in "/scratch/punim0025/work/fmriprep_wf/single_subject_F134_wf/func_preproc_task_rest_wf/bold_bold_trans_wf/merge". 191010-20:22:24,378 nipype.workflow INFO: [Node] Running "merge" ("fmriprep.interfaces.nilearn.Merge") 191010-20:22:33,539 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_F134_wf.func_preproc_task_rest_wf.bold_bold_trans_wf.merge". 191010-20:22:33,835 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_F134_wf.func_preproc_task_rest_wf.bold_bold_trans_wf.bold_reference_wf.validate" in "/scratch/punim0025/work/fmriprep_wf/single_subject_F134_wf/func_preproc_task_rest_wf/bold_bold_trans_wf/bold_reference_wf/validate". 191010-20:22:33,841 nipype.workflow INFO: [Node] Running "validate" ("niworkflows.interfaces.images.ValidateImage") 191010-20:22:33,880 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_F134_wf.func_preproc_task_rest_wf.bold_bold_trans_wf.bold_reference_wf.validate". 191010-20:22:35,831 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_F134_wf.func_preproc_task_rest_wf.bold_bold_trans_wf.bold_reference_wf.gen_ref" in "/scratch/punim0025/work/fmriprep_wf/single_subject_F134_wf/func_preproc_task_rest_wf/bold_bold_trans_wf/bold_reference_wf/gen_ref". 191010-20:22:35,836 nipype.workflow INFO: [Node] Running "gen_ref" ("niworkflows.interfaces.registration.EstimateReferenceImage") 191010-20:22:36,626 nipype.interface INFO: stderr 2019-10-10T20:22:36.626515:++ 3dvolreg: AFNI version=Debian-16.2.07~dfsg.1-5~nd16.04+1 (Jun 12 2017) [64-bit] 191010-20:22:36,626 nipype.interface INFO: stderr 2019-10-10T20:22:36.626515:++ Authored by: RW Cox 191010-20:22:36,627 nipype.interface INFO: stderr 2019-10-10T20:22:36.626985:** AFNI converts NIFTI_datatype=4 (INT16) in file /scratch/punim0025/work/fmriprep_wf/single_subject_F134_wf/func_preproc_task_rest_wf/bold_bold_trans_wf/bold_reference_wf/gen_ref/slice.nii.gz to FLOAT32 191010-20:22:36,627 nipype.interface INFO: stderr 2019-10-10T20:22:36.626985: Warnings of this type will be muted for this session. 191010-20:22:36,627 nipype.interface INFO: stderr 2019-10-10T20:22:36.626985: Set AFNI_NIFTI_TYPE_WARN to YES to see them all, NO to see none. 191010-20:22:36,627 nipype.interface INFO: stderr 2019-10-10T20:22:36.627304:*+ WARNING: If you are performing spatial transformations on an oblique dset, 191010-20:22:36,627 nipype.interface INFO: stderr 2019-10-10T20:22:36.627304: such as /scratch/punim0025/work/fmriprep_wf/single_subject_F134_wf/func_preproc_task_rest_wf/bold_bold_trans_wf/bold_reference_wf/gen_ref/slice.nii.gz, 191010-20:22:36,627 nipype.interface INFO: stderr 2019-10-10T20:22:36.627304: or viewing/combining it with volumes of differing obliquity, 191010-20:22:36,627 nipype.interface INFO: stderr 2019-10-10T20:22:36.627304: you should consider running: 191010-20:22:36,627 nipype.interface INFO: stderr 2019-10-10T20:22:36.627304: 3dWarp -deoblique 191010-20:22:36,627 nipype.interface INFO: stderr 2019-10-10T20:22:36.627304: on this and other oblique datasets in the same session. 191010-20:22:36,627 nipype.interface INFO: stderr 2019-10-10T20:22:36.627304: See 3dWarp -help for details. 191010-20:22:36,627 nipype.interface INFO: stderr 2019-10-10T20:22:36.627304:++ Oblique dataset:/scratch/punim0025/work/fmriprep_wf/single_subject_F134_wf/func_preproc_task_rest_wf/bold_bold_trans_wf/bold_reference_wf/gen_ref/slice.nii.gz is 8.110676 degrees from plumb. 191010-20:22:36,627 nipype.interface INFO: stderr 2019-10-10T20:22:36.627697:++ Coarse del was 10, replaced with 4 191010-20:22:56,44 nipype.interface INFO: stderr 2019-10-10T20:22:56.044258:++ Max displacement in automask = 0.28 (mm) at sub-brick 17 191010-20:22:56,44 nipype.interface INFO: stderr 2019-10-10T20:22:56.044258:++ Max delta displ in automask = 0.32 (mm) at sub-brick 17 191010-20:22:57,78 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_F134_wf.func_preproc_task_rest_wf.bold_bold_trans_wf.bold_reference_wf.gen_ref". 191010-20:23:02,818 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_F134_wf.func_preproc_task_rest_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.init_aff" in "/scratch/punim0025/work/fmriprep_wf/single_subject_F134_wf/func_preproc_task_rest_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/init_aff". 191010-20:23:02,824 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-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_res-02_desc-brain_mask.nii.gz -m Mattes[/home/epozzi/.cache/templateflow/tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_res-02_desc-fMRIPrep_boldref.nii.gz,/scratch/punim0025/work/fmriprep_wf/single_subject_F134_wf/func_preproc_task_rest_wf/bold_bold_trans_wf/bold_reference_wf/gen_ref/ref_bold.nii.gz,32,Regular,0.200000] -o initialization.mat -p 0 -s [20.000000,0.120000] -t Affine[0.100000] -v 1 191010-20:23:12,230 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_F134_wf.func_preproc_task_rest_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.init_aff". 191010-20:23:19,55 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_F134_wf.func_preproc_task_rest_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.norm" in "/scratch/punim0025/work/fmriprep_wf/single_subject_F134_wf/func_preproc_task_rest_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/norm". 191010-20:23:19,63 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_F134_wf/func_preproc_task_rest_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/init_aff/initialization.mat, 0 ] --initialize-transforms-per-stage 0 --interpolation Linear --output transform --transform Affine[ 0.1 ] --metric Mattes[ /home/epozzi/.cache/templateflow/tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_res-02_desc-fMRIPrep_boldref.nii.gz, /scratch/punim0025/work/fmriprep_wf/single_subject_F134_wf/func_preproc_task_rest_wf/bold_bold_trans_wf/bold_reference_wf/gen_ref/ref_bold.nii.gz, 1, 64, Random, 0.2 ] --convergence [ 200, 1e-09, 10 ] --smoothing-sigmas 2.0mm --shrink-factors 2 --use-estimate-learning-rate-once 1 --use-histogram-matching 1 --winsorize-image-intensities [ 0.05, 0.98 ] --write-composite-transform 0 191010-20:23:21,431 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_F134_wf.func_preproc_task_rest_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.norm". 191010-20:23:27,23 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_F134_wf.func_preproc_task_rest_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.map_brainmask" in "/scratch/punim0025/work/fmriprep_wf/single_subject_F134_wf/func_preproc_task_rest_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/map_brainmask". 191010-20:23:27,31 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-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_res-02_desc-brain_mask.nii.gz --interpolation MultiLabel --output tpl-MNI152NLin2009cAsym_res-02_desc-brain_mask_trans.nii.gz --reference-image /scratch/punim0025/work/fmriprep_wf/single_subject_F134_wf/func_preproc_task_rest_wf/bold_bold_trans_wf/bold_reference_wf/gen_ref/ref_bold.nii.gz --transform [ /scratch/punim0025/work/fmriprep_wf/single_subject_F134_wf/func_preproc_task_rest_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/norm/transform0GenericAffine.mat, 1 ] 191010-20:23:29,162 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_F134_wf.func_preproc_task_rest_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.map_brainmask". 191010-20:23:29,877 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_F134_wf.func_preproc_task_rest_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.pre_mask_dilate" in "/scratch/punim0025/work/fmriprep_wf/single_subject_F134_wf/func_preproc_task_rest_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/pre_mask_dilate". 191010-20:23:29,881 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_F134_wf/func_preproc_task_rest_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/map_brainmask/tpl-MNI152NLin2009cAsym_res-02_desc-brain_mask_trans.nii.gz -kernel sphere 3.0000 -dilF /scratch/punim0025/work/fmriprep_wf/single_subject_F134_wf/func_preproc_task_rest_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/pre_mask_dilate/tpl-MNI152NLin2009cAsym_res-02_desc-brain_mask_trans_dil.nii.gz 191010-20:23:30,62 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_F134_wf.func_preproc_task_rest_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.pre_mask_dilate". 191010-20:23:33,855 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_F134_wf.func_preproc_task_rest_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.n4_correct" in "/scratch/punim0025/work/fmriprep_wf/single_subject_F134_wf/func_preproc_task_rest_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/n4_correct". 191010-20:23:33,893 nipype.workflow INFO: [Node] Running "n4_correct" ("niworkflows.interfaces.fixes.FixN4BiasFieldCorrection"), a CommandLine Interface with command: N4BiasFieldCorrection --bspline-fitting [ 200 ] -d 3 --input-image /scratch/punim0025/work/fmriprep_wf/single_subject_F134_wf/func_preproc_task_rest_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/n4_correct/ref_bold_scaled.nii.gz --mask-image /scratch/punim0025/work/fmriprep_wf/single_subject_F134_wf/func_preproc_task_rest_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/check_hdr/tpl-MNI152NLin2009cAsym_res-02_desc-brain_mask_trans_dil_hdr.nii.gz --output ref_bold_corrected.nii.gz -r 191010-20:23:36,640 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_F134_wf.func_preproc_task_rest_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.n4_correct". 191010-20:23:38,150 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_F134_wf.func_preproc_task_rest_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_pass" in "/scratch/punim0025/work/fmriprep_wf/single_subject_F134_wf/func_preproc_task_rest_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_pass". 191010-20:23:38,184 nipype.workflow INFO: [Node] Running "skullstrip_first_pass" ("nipype.interfaces.fsl.preprocess.BET"), a CommandLine Interface with command: bet /scratch/punim0025/work/fmriprep_wf/single_subject_F134_wf/func_preproc_task_rest_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/n4_correct/ref_bold_corrected.nii.gz /scratch/punim0025/work/fmriprep_wf/single_subject_F134_wf/func_preproc_task_rest_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_pass/ref_bold_corrected_brain.nii.gz -f 0.20 -m 191010-20:23:39,879 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_F134_wf.func_preproc_task_rest_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_pass". 191010-20:23:41,884 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_F134_wf.func_preproc_task_rest_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_dilate" in "/scratch/punim0025/work/fmriprep_wf/single_subject_F134_wf/func_preproc_task_rest_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_dilate". 191010-20:23:41,891 nipype.workflow INFO: [Node] Running "skullstrip_first_dilate" ("nipype.interfaces.fsl.maths.DilateImage"), a CommandLine Interface with command: fslmaths -dt char /scratch/punim0025/work/fmriprep_wf/single_subject_F134_wf/func_preproc_task_rest_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_pass/ref_bold_corrected_brain_mask.nii.gz -kernel sphere 6.0000 -dilF /scratch/punim0025/work/fmriprep_wf/single_subject_F134_wf/func_preproc_task_rest_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_dilate/ref_bold_corrected_brain_mask_dil.nii.gz 191010-20:23:42,304 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_F134_wf.func_preproc_task_rest_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_dilate". 191010-20:23:44,142 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_F134_wf.func_preproc_task_rest_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_mask" in "/scratch/punim0025/work/fmriprep_wf/single_subject_F134_wf/func_preproc_task_rest_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_mask". 191010-20:23:44,148 nipype.workflow INFO: [Node] Running "skullstrip_first_mask" ("nipype.interfaces.fsl.maths.ApplyMask"), a CommandLine Interface with command: fslmaths /scratch/punim0025/work/fmriprep_wf/single_subject_F134_wf/func_preproc_task_rest_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_pass/ref_bold_corrected_brain.nii.gz -mas /scratch/punim0025/work/fmriprep_wf/single_subject_F134_wf/func_preproc_task_rest_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_dilate/ref_bold_corrected_brain_mask_dil.nii.gz /scratch/punim0025/work/fmriprep_wf/single_subject_F134_wf/func_preproc_task_rest_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_mask/ref_bold_corrected_brain_masked.nii.gz 191010-20:23:44,217 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_F134_wf.func_preproc_task_rest_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_mask". 191010-20:23:45,892 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_F134_wf.func_preproc_task_rest_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.unifize" in "/scratch/punim0025/work/fmriprep_wf/single_subject_F134_wf/func_preproc_task_rest_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/unifize". 191010-20:23:45,898 nipype.workflow INFO: [Node] Running "unifize" ("nipype.interfaces.afni.utils.Unifize"), a CommandLine Interface with command: 3dUnifize -clfrac 0.2 -rbt 18.3 65.0 90.0 -prefix uni.nii.gz -T2 -input /scratch/punim0025/work/fmriprep_wf/single_subject_F134_wf/func_preproc_task_rest_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/unifize/ref_bold_corrected_brain_masked.nii.gz 191010-20:23:47,240 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_F134_wf.func_preproc_task_rest_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.unifize". 191010-20:23:47,893 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_F134_wf.func_preproc_task_rest_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.fixhdr_unifize" in "/scratch/punim0025/work/fmriprep_wf/single_subject_F134_wf/func_preproc_task_rest_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/fixhdr_unifize". 191010-20:23:47,897 nipype.workflow INFO: [Node] Running "fixhdr_unifize" ("niworkflows.interfaces.utils.CopyXForm") 191010-20:23:47,954 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_F134_wf.func_preproc_task_rest_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.fixhdr_unifize". 191010-20:23:49,976 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_F134_wf.func_preproc_task_rest_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.skullstrip_second_pass" in "/scratch/punim0025/work/fmriprep_wf/single_subject_F134_wf/func_preproc_task_rest_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_second_pass". 191010-20:23:49,984 nipype.workflow INFO: [Node] Running "skullstrip_second_pass" ("nipype.interfaces.afni.preprocess.Automask"), a CommandLine Interface with command: 3dAutomask -apply_prefix uni_xform_masked.nii.gz -dilate 1 -prefix uni_xform_mask.nii.gz /scratch/punim0025/work/fmriprep_wf/single_subject_F134_wf/func_preproc_task_rest_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_second_pass/uni_xform.nii.gz 191010-20:23:50,107 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_F134_wf.func_preproc_task_rest_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.skullstrip_second_pass". 191010-20:23:56,844 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_F134_wf.func_preproc_task_rest_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.fixhdr_skullstrip2" in "/scratch/punim0025/work/fmriprep_wf/single_subject_F134_wf/func_preproc_task_rest_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/fixhdr_skullstrip2". 191010-20:23:56,850 nipype.workflow INFO: [Node] Running "fixhdr_skullstrip2" ("niworkflows.interfaces.utils.CopyXForm") 191010-20:23:56,894 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_F134_wf.func_preproc_task_rest_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.fixhdr_skullstrip2". 191010-20:23:57,891 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_F134_wf.func_preproc_task_rest_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.combine_masks" in "/scratch/punim0025/work/fmriprep_wf/single_subject_F134_wf/func_preproc_task_rest_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/combine_masks". 191010-20:23:57,896 nipype.workflow INFO: [Node] Running "combine_masks" ("nipype.interfaces.fsl.maths.BinaryMaths"), a CommandLine Interface with command: fslmaths /scratch/punim0025/work/fmriprep_wf/single_subject_F134_wf/func_preproc_task_rest_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_pass/ref_bold_corrected_brain_mask.nii.gz -mul /scratch/punim0025/work/fmriprep_wf/single_subject_F134_wf/func_preproc_task_rest_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/fixhdr_skullstrip2/uni_xform_mask_xform.nii.gz /scratch/punim0025/work/fmriprep_wf/single_subject_F134_wf/func_preproc_task_rest_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/combine_masks/ref_bold_corrected_brain_mask_maths.nii.gz 191010-20:23:58,11 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_F134_wf.func_preproc_task_rest_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.combine_masks". 191010-20:23:59,892 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_F134_wf.func_preproc_task_rest_wf.bold_confounds_wf.dvars" in "/scratch/punim0025/work/fmriprep_wf/single_subject_F134_wf/func_preproc_task_rest_wf/bold_confounds_wf/dvars". 191010-20:23:59,897 nipype.workflow INFO: [Node] Running "dvars" ("nipype.algorithms.confounds.ComputeDVARS") 191010-20:24:00,29 nipype.workflow INFO: [Node] Setting-up "fmriprep_wf.single_subject_F134_wf.func_preproc_task_rest_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.apply_mask" in "/scratch/punim0025/work/fmriprep_wf/single_subject_F134_wf/func_preproc_task_rest_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/apply_mask". 191010-20:24:00,33 nipype.workflow INFO: [Node] Running "apply_mask" ("nipype.interfaces.fsl.maths.ApplyMask"), a CommandLine Interface with command: fslmaths /scratch/punim0025/work/fmriprep_wf/single_subject_F134_wf/func_preproc_task_rest_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/fixhdr_unifize/uni_xform.nii.gz -mas /scratch/punim0025/work/fmriprep_wf/single_subject_F134_wf/func_preproc_task_rest_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/combine_masks/ref_bold_corrected_brain_mask_maths.nii.gz /scratch/punim0025/work/fmriprep_wf/single_subject_F134_wf/func_preproc_task_rest_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/apply_mask/uni_xform_masked.nii.gz 191010-20:24:00,994 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_F134_wf.func_preproc_task_rest_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.apply_mask". 191010-20:24:11,986 nipype.workflow INFO: [Node] Finished "fmriprep_wf.single_subject_F134_wf.func_preproc_task_rest_wf.bold_confounds_wf.dvars". /usr/local/miniconda/lib/python3.7/site-packages/scipy/fftpack/basic.py:160: FutureWarning: Using a non-tuple sequence for multidimensional indexing is deprecated; use `arr[tuple(seq)]` instead of `arr[seq]`. In the future this will be interpreted as an array index, `arr[np.array(seq)]`, which will result either in an error or a different result. z[index] = x pandoc-citeproc: reference mnipediatricasym not found Preprocessing did not finish successfully. Errors occurred while processing data from participants: F134 (1). Check the HTML reports for details. Sentry is attempting to send 1 pending error messages Waiting up to 2 seconds Press Ctrl-C to quit