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Issues when running primarily fmriprep/mriqc/xcpengine (primarily on argon)
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CREST fmriprep: "grabbids has been renamed to layout in version 0.6.5, and will be removed in version 0.8" #9

Open ariveradompenciel opened 4 years ago

ariveradompenciel commented 4 years ago

Script/Job File

#!/bin/bash

#$ -pe smp 16
#$ -q UI
#$ -m bea
#$ -M adriana-rivera-dompenciel@uiowa.edu
#$ -o /Shared/vosslabhpc/Projects/CREST/code/fmriprep/out/
#$ -e /Shared/vosslabhpc/Projects/CREST/code/fmriprep/err/
OMP_NUM_THREADS=10
singularity run -H ${HOME}/singularity_home -B /Shared/vosslabhpc:/mnt \
/Shared/vosslabhpc/UniversalSoftware/SingularityContainers/fmriprep-1.2.1.simg \
/mnt/Projects/CREST/ /mnt/Projects/CREST/derivatives \
participant --participant_label BETTER120018 \
-w /nfsscratch/Users/ariveradompenciel/work/CRESTfmriprep \
--write-graph --mem_mb 35000 --omp-nthreads 10 --nthreads 16 --use-aroma \
--output-space template \
--template MNI152NLin2009cAsym \
--fs-license-file /mnt/UniversalSoftware/freesurfer_license.txt

Email Message

Job 5710530 (sub-BETTER120018.job) Complete
User             = ariveradompenciel
Queue            = UI@argon-lc-d7-21.hpc
Host             = argon-lc-d7-21.hpc
Start Time       = 03/15/2020 11:48:41
End Time         = 03/15/2020 11:50:28
User Time        = 00:00:19
System Time      = 00:00:03
Wallclock Time   = 00:01:47
CPU              = 00:00:47
Max vmem         = 710.324M
Exit Status      = 1

Output File

200306-13:14:04,940 nipype.workflow IMPORTANT:

    Running fMRIPREP version 1.2.1:
      * BIDS dataset path: /mnt/Projects/CREST.
      * Participant list: ['BETTER120018'].
      * Run identifier: 20200306-131404_1fa9934c-113a-4a1e-9fe3-8954283f0aa1.

200306-13:14:04,940 nipype.workflow WARNING:
     Option --debug is deprecated and has no effect
200306-13:14:11,246 nipype.workflow IMPORTANT:
     Creating bold processing workflow for "/mnt/Projects/CREST/sub-BETTER120018/func/sub-BETTER120018_task-rest_run-1_bold.nii.gz" (0.03 GB / 240 TRs). Memory resampled/largemem=0.11/0.18 GB.
200306-13:14:11,278 nipype.workflow IMPORTANT:
     No single-band-reference found for sub-BETTER120018_task-rest_run-1_bold.nii.gz
200306-13:14:11,735 nipype.workflow WARNING:
     SDC: no fieldmaps found or they were ignored (/mnt/Projects/CREST/sub-BETTER120018/func/sub-BETTER120018_task-rest_run-1_bold.nii.gz).
200306-13:14:14,732 nipype.workflow IMPORTANT:
     Creating bold processing workflow for "/mnt/Projects/CREST/sub-BETTER120018/func/sub-BETTER120018_task-rest_run-2_bold.nii.gz" (0.03 GB / 240 TRs). Memory resampled/largemem=0.11/0.18 GB.
200306-13:14:14,763 nipype.workflow IMPORTANT:
     No single-band-reference found for sub-BETTER120018_task-rest_run-2_bold.nii.gz
200306-13:14:15,298 nipype.workflow WARNING:
     SDC: no fieldmaps found or they were ignored (/mnt/Projects/CREST/sub-BETTER120018/func/sub-BETTER120018_task-rest_run-2_bold.nii.gz).
200306-13:14:20,499 nipype.workflow IMPORTANT:
     Works derived from this fMRIPrep execution should include the following boilerplate:

Results included in this manuscript come from preprocessing
performed using *fMRIPprep* 1.2.1
(@fmriprep1; @fmriprep2; RRID:SCR_016216),
which is based on *Nipype* 1.1.4
(@nipype1; @nipype2; RRID:SCR_002502).

Anatomical data preprocessing

: The T1-weighted (T1w) image was corrected for intensity non-uniformity (INU)
using `N4BiasFieldCorrection` [@n4, ANTs 2.2.0],
and used as T1w-reference throughout the workflow.
The T1w-reference was then skull-stripped using `antsBrainExtraction.sh`
(ANTs 2.2.0), using OASIS as target template.
Brain surfaces were reconstructed using `recon-all` [FreeSurfer 6.0.1,
RRID:SCR_001847, @fs_reconall], and the brain mask estimated
previously was refined with a custom variation of the method to reconcile
ANTs-derived and FreeSurfer-derived segmentations of the cortical
gray-matter of Mindboggle [RRID:SCR_002438, @mindboggle].
Spatial normalization to the ICBM 152 Nonlinear Asymmetrical
template version 2009c [@mni, RRID:SCR_008796] was performed
through nonlinear registration with `antsRegistration`
[ANTs 2.2.0, RRID:SCR_004757, @ants], using
brain-extracted versions of both T1w volume and 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].

Functional data preprocessing

: For each of the 2 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
`bbregister` (FreeSurfer) which implements boundary-based registration [@bbr].
Co-registration was configured with nine degrees of freedom to account
for distortions remaining in the BOLD reference.
Head-motion parameters with respect to the BOLD reference
(transformation matrices, and six corresponding rotation and translation
parameters) are estimated before any spatiotemporal filtering using
`mcflirt` [FSL 5.0.9, @mcflirt].
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*.
First, a reference volume and its skull-stripped version were generated
using a custom methodology of *fMRIPrep*.
Automatic removal of motion artifacts using independent component analysis
[ICA-AROMA, @aroma] was performed on the *preprocessed BOLD on MNI space*
time-series after removal of non-steady state volumes and spatial smoothing
with an isotropic, Gaussian kernel of 6mm FWHM (full-width half-maximum).
Corresponding "non-aggresively" denoised runs were produced after such
smoothing.
Additionally, the "aggressive" noise-regressors were collected and placed
in the corresponding confounds file.
The BOLD time-series were resampled to MNI152NLin2009cAsym standard space,
generating a *preprocessed BOLD run in MNI152NLin2009cAsym 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).
Six 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, six 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).
The head-motion estimates calculated in the correction step were also
placed within the corresponding confounds file.
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 template 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* 0.4.2 [@nilearn, RRID:SCR_001362],
mostly within the functional processing workflow.
For more details of the pipeline, see [the section corresponding
to workflows in *fMRIPrep*'s documentation](https://fmriprep.readthedocs.io/en/latest/workflows.html "FMRIPrep's documentation").

### References

200306-13:14:53,667 nipype.workflow INFO:
     [Node] Setting-up "fmriprep_wf.single_subject_BETTER120018_wf.func_preproc_task_rest_run_1_wf.bold_reference_wf.validate" in "/nfsscratch/Users/ariveradompenciel/work/CRESTfmriprep/fmriprep_wf/single_subject_BETTER120018_wf/func_preproc_task_rest_run_1_wf/bold_reference_wf/validate".
200306-13:14:53,675 nipype.workflow INFO:
     [Node] Setting-up "fmriprep_wf.single_subject_BETTER120018_wf.func_preproc_task_rest_run_2_wf.bold_reference_wf.validate" in "/nfsscratch/Users/ariveradompenciel/work/CRESTfmriprep/fmriprep_wf/single_subject_BETTER120018_wf/func_preproc_task_rest_run_2_wf/bold_reference_wf/validate".
200306-13:14:53,687 nipype.workflow INFO:
     [Node] Running "validate" ("fmriprep.interfaces.images.ValidateImage")
200306-13:14:53,692 nipype.workflow INFO:
     [Node] Running "validate" ("fmriprep.interfaces.images.ValidateImage")
200306-13:14:53,727 nipype.workflow INFO:
     [Node] Finished "fmriprep_wf.single_subject_BETTER120018_wf.func_preproc_task_rest_run_1_wf.bold_reference_wf.validate".
200306-13:14:53,741 nipype.workflow INFO:
     [Node] Finished "fmriprep_wf.single_subject_BETTER120018_wf.func_preproc_task_rest_run_2_wf.bold_reference_wf.validate".
200306-13:14:53,806 nipype.workflow INFO:
     [Node] Setting-up "fmriprep_wf.single_subject_BETTER120018_wf.bidssrc" in "/nfsscratch/Users/ariveradompenciel/work/CRESTfmriprep/fmriprep_wf/single_subject_BETTER120018_wf/bidssrc".
200306-13:14:53,821 nipype.workflow INFO:
     [Node] Running "bidssrc" ("fmriprep.interfaces.bids.BIDSDataGrabber")
200306-13:14:53,822 nipype.interface WARNING:
     No 't2w' images found for sub-<undefined>
200306-13:14:53,822 nipype.interface WARNING:
     No 'flair' images found for sub-<undefined>
200306-13:14:53,822 nipype.interface WARNING:
     No 'sbref' images found for sub-<undefined>
200306-13:14:53,822 nipype.interface WARNING:
     No 'roi' images found for sub-<undefined>
200306-13:14:53,840 nipype.workflow INFO:
     [Node] Finished "fmriprep_wf.single_subject_BETTER120018_wf.bidssrc".
200306-13:14:56,763 nipype.workflow INFO:
     [Node] Setting-up "fmriprep_wf.single_subject_BETTER120018_wf.func_preproc_task_rest_run_1_wf.bold_split" in "/nfsscratch/Users/ariveradompenciel/work/CRESTfmriprep/fmriprep_wf/single_subject_BETTER120018_wf/func_preproc_task_rest_run_1_wf/bold_split".
200306-13:14:56,780 nipype.workflow INFO:
     [Node] Running "bold_split" ("nipype.interfaces.fsl.utils.Split"), a CommandLine Interface with command:
fslsplit /mnt/Projects/CREST/sub-BETTER120018/func/sub-BETTER120018_task-rest_run-1_bold.nii.gz -t
200306-13:14:56,894 nipype.workflow INFO:
     [Node] Setting-up "fmriprep_wf.single_subject_BETTER120018_wf.func_preproc_task_rest_run_2_wf.bold_split" in "/nfsscratch/Users/ariveradompenciel/work/CRESTfmriprep/fmriprep_wf/single_subject_BETTER120018_wf/func_preproc_task_rest_run_2_wf/bold_split".
200306-13:14:56,948 nipype.workflow INFO:
     [Node] Running "bold_split" ("nipype.interfaces.fsl.utils.Split"), a CommandLine Interface with command:
fslsplit /mnt/Projects/CREST/sub-BETTER120018/func/sub-BETTER120018_task-rest_run-2_bold.nii.gz -t
200306-13:14:57,642 nipype.workflow INFO:
     [Node] Setting-up "fmriprep_wf.single_subject_BETTER120018_wf.func_preproc_task_rest_run_1_wf.bold_reference_wf.gen_ref" in "/nfsscratch/Users/ariveradompenciel/work/CRESTfmriprep/fmriprep_wf/single_subject_BETTER120018_wf/func_preproc_task_rest_run_1_wf/bold_reference_wf/gen_ref".
200306-13:14:57,656 nipype.workflow INFO:
     [Node] Running "gen_ref" ("niworkflows.interfaces.registration.EstimateReferenceImage")
200306-13:14:57,821 nipype.workflow INFO:
     [Node] Setting-up "fmriprep_wf.single_subject_BETTER120018_wf.func_preproc_task_rest_run_2_wf.bold_reference_wf.gen_ref" in "/nfsscratch/Users/ariveradompenciel/work/CRESTfmriprep/fmriprep_wf/single_subject_BETTER120018_wf/func_preproc_task_rest_run_2_wf/bold_reference_wf/gen_ref".
200306-13:14:57,838 nipype.workflow INFO:
     [Node] Running "gen_ref" ("niworkflows.interfaces.registration.EstimateReferenceImage")
200306-13:14:57,998 nipype.workflow INFO:
     [Node] Finished "fmriprep_wf.single_subject_BETTER120018_wf.func_preproc_task_rest_run_1_wf.bold_reference_wf.gen_ref".
200306-13:14:58,80 nipype.workflow INFO:
     [Node] Setting-up "fmriprep_wf.single_subject_BETTER120018_wf.anat_preproc_wf.anat_template_wf.t1_template_dimensions" in "/nfsscratch/Users/ariveradompenciel/work/CRESTfmriprep/fmriprep_wf/single_subject_BETTER120018_wf/anat_preproc_wf/anat_template_wf/t1_template_dimensions".
200306-13:14:58,101 nipype.workflow INFO:
     [Node] Running "t1_template_dimensions" ("fmriprep.interfaces.images.TemplateDimensions")
200306-13:14:58,177 nipype.workflow INFO:
     [Node] Finished "fmriprep_wf.single_subject_BETTER120018_wf.func_preproc_task_rest_run_2_wf.bold_reference_wf.gen_ref".
200306-13:14:58,253 nipype.workflow INFO:
     [Node] Finished "fmriprep_wf.single_subject_BETTER120018_wf.anat_preproc_wf.anat_template_wf.t1_template_dimensions".
200306-13:15:01,109 nipype.workflow INFO:
     [Node] Setting-up "fmriprep_wf.single_subject_BETTER120018_wf.anat_preproc_wf.anat_derivatives_wf.t1_name" in "/nfsscratch/Users/ariveradompenciel/work/CRESTfmriprep/fmriprep_wf/single_subject_BETTER120018_wf/anat_preproc_wf/anat_derivatives_wf/t1_name".
200306-13:15:01,154 nipype.workflow INFO:
     [Node] Running "t1_name" ("nipype.interfaces.utility.wrappers.Function")
200306-13:15:01,174 nipype.workflow INFO:
     [Node] Finished "fmriprep_wf.single_subject_BETTER120018_wf.anat_preproc_wf.anat_derivatives_wf.t1_name".
200306-13:15:01,819 nipype.workflow INFO:
     [Node] Setting-up "fmriprep_wf.single_subject_BETTER120018_wf.func_preproc_task_rest_run_2_wf.bold_reference_wf.validate_ref" in "/nfsscratch/Users/ariveradompenciel/work/CRESTfmriprep/fmriprep_wf/single_subject_BETTER120018_wf/func_preproc_task_rest_run_2_wf/bold_reference_wf/validate_ref".
200306-13:15:01,832 nipype.workflow INFO:
     [Node] Setting-up "fmriprep_wf.single_subject_BETTER120018_wf.func_preproc_task_rest_run_1_wf.bold_reference_wf.validate_ref" in "/nfsscratch/Users/ariveradompenciel/work/CRESTfmriprep/fmriprep_wf/single_subject_BETTER120018_wf/func_preproc_task_rest_run_1_wf/bold_reference_wf/validate_ref".
200306-13:15:01,834 nipype.workflow INFO:
     [Node] Running "validate_ref" ("fmriprep.interfaces.images.ValidateImage")
200306-13:15:01,849 nipype.workflow INFO:
     [Node] Running "validate_ref" ("fmriprep.interfaces.images.ValidateImage")
200306-13:15:02,191 nipype.workflow INFO:
     [Node] Setting-up "fmriprep_wf.single_subject_BETTER120018_wf.anat_preproc_wf.anat_template_wf.t1_conform" in "/nfsscratch/Users/ariveradompenciel/work/CRESTfmriprep/fmriprep_wf/single_subject_BETTER120018_wf/anat_preproc_wf/anat_template_wf/t1_conform".
200306-13:15:02,209 nipype.workflow INFO:
     [Node] Setting-up "_t1_conform0" in "/nfsscratch/Users/ariveradompenciel/work/CRESTfmriprep/fmriprep_wf/single_subject_BETTER120018_wf/anat_preproc_wf/anat_template_wf/t1_conform/mapflow/_t1_conform0".
200306-13:15:02,228 nipype.workflow INFO:
     [Node] Running "_t1_conform0" ("fmriprep.interfaces.images.Conform")
200306-13:15:03,251 nipype.workflow INFO:
     [Node] Finished "fmriprep_wf.single_subject_BETTER120018_wf.func_preproc_task_rest_run_1_wf.bold_split".
200306-13:15:04,233 nipype.workflow INFO:
     [Node] Finished "fmriprep_wf.single_subject_BETTER120018_wf.func_preproc_task_rest_run_2_wf.bold_split".
200306-13:15:05,434 nipype.workflow INFO:
     [Node] Setting-up "fmriprep_wf.single_subject_BETTER120018_wf.func_preproc_task_rest_run_1_wf.bold_mni_trans_wf.gen_ref" in "/nfsscratch/Users/ariveradompenciel/work/CRESTfmriprep/fmriprep_wf/single_subject_BETTER120018_wf/func_preproc_task_rest_run_1_wf/bold_mni_trans_wf/gen_ref".
200306-13:15:05,450 nipype.workflow INFO:
     [Node] Running "gen_ref" ("niworkflows.interfaces.utils.GenerateSamplingReference")
200306-13:15:05,470 nipype.workflow INFO:
     [Node] Setting-up "fmriprep_wf.single_subject_BETTER120018_wf.func_preproc_task_rest_run_1_wf.ica_aroma_wf.bold_mni_trans_wf.gen_ref" in "/nfsscratch/Users/ariveradompenciel/work/CRESTfmriprep/fmriprep_wf/single_subject_BETTER120018_wf/func_preproc_task_rest_run_1_wf/ica_aroma_wf/bold_mni_trans_wf/gen_ref".
200306-13:15:05,534 nipype.workflow INFO:
     [Node] Running "gen_ref" ("niworkflows.interfaces.utils.GenerateSamplingReference")
200306-13:15:06,32 nipype.workflow INFO:
     [Node] Finished "fmriprep_wf.single_subject_BETTER120018_wf.func_preproc_task_rest_run_1_wf.bold_mni_trans_wf.gen_ref".
200306-13:15:06,37 nipype.workflow INFO:
     [Node] Finished "fmriprep_wf.single_subject_BETTER120018_wf.func_preproc_task_rest_run_1_wf.ica_aroma_wf.bold_mni_trans_wf.gen_ref".
200306-13:15:06,403 nipype.workflow INFO:
     [Node] Finished "fmriprep_wf.single_subject_BETTER120018_wf.func_preproc_task_rest_run_1_wf.bold_reference_wf.validate_ref".
200306-13:15:06,403 nipype.workflow INFO:
     [Node] Finished "fmriprep_wf.single_subject_BETTER120018_wf.func_preproc_task_rest_run_2_wf.bold_reference_wf.validate_ref".
200306-13:15:06,403 nipype.workflow INFO:
     [Node] Finished "_t1_conform0".
200306-13:15:06,415 nipype.workflow INFO:
     [Node] Finished "fmriprep_wf.single_subject_BETTER120018_wf.anat_preproc_wf.anat_template_wf.t1_conform".
200306-13:15:07,549 nipype.workflow INFO:
     [Node] Setting-up "fmriprep_wf.single_subject_BETTER120018_wf.func_preproc_task_rest_run_2_wf.bold_mni_trans_wf.gen_ref" in "/nfsscratch/Users/ariveradompenciel/work/CRESTfmriprep/fmriprep_wf/single_subject_BETTER120018_wf/func_preproc_task_rest_run_2_wf/bold_mni_trans_wf/gen_ref".
200306-13:15:07,565 nipype.workflow INFO:
     [Node] Setting-up "fmriprep_wf.single_subject_BETTER120018_wf.func_preproc_task_rest_run_2_wf.ica_aroma_wf.bold_mni_trans_wf.gen_ref" in "/nfsscratch/Users/ariveradompenciel/work/CRESTfmriprep/fmriprep_wf/single_subject_BETTER120018_wf/func_preproc_task_rest_run_2_wf/ica_aroma_wf/bold_mni_trans_wf/gen_ref".
200306-13:15:07,566 nipype.workflow INFO:
     [Node] Running "gen_ref" ("niworkflows.interfaces.utils.GenerateSamplingReference")
200306-13:15:07,582 nipype.workflow INFO:
     [Node] Running "gen_ref" ("niworkflows.interfaces.utils.GenerateSamplingReference")
200306-13:15:07,716 nipype.workflow INFO:
     [Node] Setting-up "fmriprep_wf.single_subject_BETTER120018_wf.func_preproc_task_rest_run_1_wf.bold_hmc_wf.mcflirt" in "/nfsscratch/Users/ariveradompenciel/work/CRESTfmriprep/fmriprep_wf/single_subject_BETTER120018_wf/func_preproc_task_rest_run_1_wf/bold_hmc_wf/mcflirt".
200306-13:15:07,725 nipype.workflow INFO:
     [Node] Setting-up "fmriprep_wf.single_subject_BETTER120018_wf.func_preproc_task_rest_run_2_wf.bold_hmc_wf.mcflirt" in "/nfsscratch/Users/ariveradompenciel/work/CRESTfmriprep/fmriprep_wf/single_subject_BETTER120018_wf/func_preproc_task_rest_run_2_wf/bold_hmc_wf/mcflirt".
200306-13:15:07,726 nipype.workflow INFO:
     [Node] Setting-up "fmriprep_wf.single_subject_BETTER120018_wf.func_preproc_task_rest_run_1_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.init_aff" in "/nfsscratch/Users/ariveradompenciel/work/CRESTfmriprep/fmriprep_wf/single_subject_BETTER120018_wf/func_preproc_task_rest_run_1_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/init_aff".
200306-13:15:07,734 nipype.workflow INFO:
     [Node] Running "mcflirt" ("nipype.interfaces.fsl.preprocess.MCFLIRT"), a CommandLine Interface with command:
mcflirt -in /mnt/Projects/CREST/sub-BETTER120018/func/sub-BETTER120018_task-rest_run-1_bold.nii.gz -out /nfsscratch/Users/ariveradompenciel/work/CRESTfmriprep/fmriprep_wf/single_subject_BETTER120018_wf/func_preproc_task_rest_run_1_wf/bold_hmc_wf/mcflirt/sub-BETTER120018_task-rest_run-1_bold_mcf.nii.gz -reffile /nfsscratch/Users/ariveradompenciel/work/CRESTfmriprep/fmriprep_wf/single_subject_BETTER120018_wf/func_preproc_task_rest_run_1_wf/bold_reference_wf/gen_ref/ref_image.nii.gz -mats -plots
200306-13:15:07,745 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 /niworkflows_data/tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_space-MNI_res-02_brainmask.nii.gz -m Mattes[/niworkflows_data/tpl-fMRIPrep/tpl-fMRIPrep_space-MNI_res-02_boldref.nii.gz,/nfsscratch/Users/ariveradompenciel/work/CRESTfmriprep/fmriprep_wf/single_subject_BETTER120018_wf/func_preproc_task_rest_run_1_wf/bold_reference_wf/gen_ref/ref_image.nii.gz,32,Regular,0.200000] -o initialization.mat -p 0 -s [20.000000,0.120000] -t Affine[0.100000] -v 1
200306-13:15:07,750 nipype.workflow INFO:
     [Node] Running "mcflirt" ("nipype.interfaces.fsl.preprocess.MCFLIRT"), a CommandLine Interface with command:
mcflirt -in /mnt/Projects/CREST/sub-BETTER120018/func/sub-BETTER120018_task-rest_run-2_bold.nii.gz -out /nfsscratch/Users/ariveradompenciel/work/CRESTfmriprep/fmriprep_wf/single_subject_BETTER120018_wf/func_preproc_task_rest_run_2_wf/bold_hmc_wf/mcflirt/sub-BETTER120018_task-rest_run-2_bold_mcf.nii.gz -reffile /nfsscratch/Users/ariveradompenciel/work/CRESTfmriprep/fmriprep_wf/single_subject_BETTER120018_wf/func_preproc_task_rest_run_2_wf/bold_reference_wf/gen_ref/ref_image.nii.gz -mats -plots
200306-13:15:07,974 nipype.workflow INFO:
     [Node] Setting-up "fmriprep_wf.single_subject_BETTER120018_wf.anat_preproc_wf.surface_recon_wf.recon_config" in "/nfsscratch/Users/ariveradompenciel/work/CRESTfmriprep/fmriprep_wf/single_subject_BETTER120018_wf/anat_preproc_wf/surface_recon_wf/recon_config".
200306-13:15:07,990 nipype.workflow INFO:
     [Node] Running "recon_config" ("fmriprep.interfaces.freesurfer.FSDetectInputs")
200306-13:15:08,70 nipype.workflow INFO:
     [Node] Finished "fmriprep_wf.single_subject_BETTER120018_wf.anat_preproc_wf.surface_recon_wf.recon_config".
200306-13:15:08,76 nipype.workflow INFO:
     [Node] Finished "fmriprep_wf.single_subject_BETTER120018_wf.func_preproc_task_rest_run_2_wf.ica_aroma_wf.bold_mni_trans_wf.gen_ref".
200306-13:15:08,77 nipype.workflow INFO:
     [Node] Finished "fmriprep_wf.single_subject_BETTER120018_wf.func_preproc_task_rest_run_2_wf.bold_mni_trans_wf.gen_ref".
200306-13:15:10,814 nipype.workflow INFO:
     [Node] Finished "fmriprep_wf.single_subject_BETTER120018_wf.func_preproc_task_rest_run_1_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.init_aff".
200306-13:15:11,730 nipype.workflow INFO:
     [Node] Setting-up "fmriprep_wf.single_subject_BETTER120018_wf.func_preproc_task_rest_run_1_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.norm" in "/nfsscratch/Users/ariveradompenciel/work/CRESTfmriprep/fmriprep_wf/single_subject_BETTER120018_wf/func_preproc_task_rest_run_1_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/norm".
200306-13:15:11,749 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 [ /nfsscratch/Users/ariveradompenciel/work/CRESTfmriprep/fmriprep_wf/single_subject_BETTER120018_wf/func_preproc_task_rest_run_1_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/init_aff/initialization.mat, 0 ] --initialize-transforms-per-stage 0 --interpolation Linear --output transform --transform Affine[ 0.1 ] --metric Mattes[ /niworkflows_data/tpl-fMRIPrep/tpl-fMRIPrep_space-MNI_res-02_boldref.nii.gz, /nfsscratch/Users/ariveradompenciel/work/CRESTfmriprep/fmriprep_wf/single_subject_BETTER120018_wf/func_preproc_task_rest_run_1_wf/bold_reference_wf/gen_ref/ref_image.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
200306-13:15:12,838 nipype.workflow INFO:
     [Node] Finished "fmriprep_wf.single_subject_BETTER120018_wf.func_preproc_task_rest_run_1_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.norm".
200306-13:15:13,737 nipype.workflow INFO:
     [Node] Setting-up "fmriprep_wf.single_subject_BETTER120018_wf.func_preproc_task_rest_run_1_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.map_brainmask" in "/nfsscratch/Users/ariveradompenciel/work/CRESTfmriprep/fmriprep_wf/single_subject_BETTER120018_wf/func_preproc_task_rest_run_1_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/map_brainmask".
200306-13:15:13,753 nipype.workflow INFO:
     [Node] Running "map_brainmask" ("niworkflows.interfaces.fixes.FixHeaderApplyTransforms"), a CommandLine Interface with command:
antsApplyTransforms --default-value 0 --float 1 --input /niworkflows_data/tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_space-MNI_res-02_brainmask.nii.gz --interpolation MultiLabel --output tpl-MNI152NLin2009cAsym_space-MNI_res-02_brainmask_trans.nii.gz --reference-image /nfsscratch/Users/ariveradompenciel/work/CRESTfmriprep/fmriprep_wf/single_subject_BETTER120018_wf/func_preproc_task_rest_run_1_wf/bold_reference_wf/gen_ref/ref_image.nii.gz --transform [ /nfsscratch/Users/ariveradompenciel/work/CRESTfmriprep/fmriprep_wf/single_subject_BETTER120018_wf/func_preproc_task_rest_run_1_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/norm/transform0GenericAffine.mat, 1 ]
200306-13:15:14,574 nipype.workflow INFO:
     [Node] Setting-up "fmriprep_wf.single_subject_BETTER120018_wf.func_preproc_task_rest_run_2_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.init_aff" in "/nfsscratch/Users/ariveradompenciel/work/CRESTfmriprep/fmriprep_wf/single_subject_BETTER120018_wf/func_preproc_task_rest_run_2_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/init_aff".
200306-13:15:14,592 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 /niworkflows_data/tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_space-MNI_res-02_brainmask.nii.gz -m Mattes[/niworkflows_data/tpl-fMRIPrep/tpl-fMRIPrep_space-MNI_res-02_boldref.nii.gz,/nfsscratch/Users/ariveradompenciel/work/CRESTfmriprep/fmriprep_wf/single_subject_BETTER120018_wf/func_preproc_task_rest_run_2_wf/bold_reference_wf/gen_ref/ref_image.nii.gz,32,Regular,0.200000] -o initialization.mat -p 0 -s [20.000000,0.120000] -t Affine[0.100000] -v 1
200306-13:15:16,874 nipype.workflow INFO:
     [Node] Finished "fmriprep_wf.single_subject_BETTER120018_wf.func_preproc_task_rest_run_1_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.map_brainmask".
200306-13:15:17,299 nipype.workflow INFO:
     [Node] Finished "fmriprep_wf.single_subject_BETTER120018_wf.func_preproc_task_rest_run_2_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.init_aff".
200306-13:15:17,754 nipype.workflow INFO:
     [Node] Setting-up "fmriprep_wf.single_subject_BETTER120018_wf.func_preproc_task_rest_run_1_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.pre_mask_dilate" in "/nfsscratch/Users/ariveradompenciel/work/CRESTfmriprep/fmriprep_wf/single_subject_BETTER120018_wf/func_preproc_task_rest_run_1_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/pre_mask_dilate".
200306-13:15:17,772 nipype.workflow INFO:
     [Node] Running "pre_mask_dilate" ("nipype.interfaces.fsl.maths.DilateImage"), a CommandLine Interface with command:
fslmaths -dt char /nfsscratch/Users/ariveradompenciel/work/CRESTfmriprep/fmriprep_wf/single_subject_BETTER120018_wf/func_preproc_task_rest_run_1_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/map_brainmask/tpl-MNI152NLin2009cAsym_space-MNI_res-02_brainmask_trans.nii.gz -kernel sphere 3.0000 -dilF /nfsscratch/Users/ariveradompenciel/work/CRESTfmriprep/fmriprep_wf/single_subject_BETTER120018_wf/func_preproc_task_rest_run_1_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/pre_mask_dilate/tpl-MNI152NLin2009cAsym_space-MNI_res-02_brainmask_trans_dil.nii.gz
200306-13:15:17,978 nipype.workflow INFO:
     [Node] Finished "fmriprep_wf.single_subject_BETTER120018_wf.func_preproc_task_rest_run_1_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.pre_mask_dilate".
200306-13:15:18,455 nipype.workflow INFO:
     [Node] Setting-up "fmriprep_wf.single_subject_BETTER120018_wf.func_preproc_task_rest_run_2_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.norm" in "/nfsscratch/Users/ariveradompenciel/work/CRESTfmriprep/fmriprep_wf/single_subject_BETTER120018_wf/func_preproc_task_rest_run_2_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/norm".
200306-13:15:18,517 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 [ /nfsscratch/Users/ariveradompenciel/work/CRESTfmriprep/fmriprep_wf/single_subject_BETTER120018_wf/func_preproc_task_rest_run_2_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/init_aff/initialization.mat, 0 ] --initialize-transforms-per-stage 0 --interpolation Linear --output transform --transform Affine[ 0.1 ] --metric Mattes[ /niworkflows_data/tpl-fMRIPrep/tpl-fMRIPrep_space-MNI_res-02_boldref.nii.gz, /nfsscratch/Users/ariveradompenciel/work/CRESTfmriprep/fmriprep_wf/single_subject_BETTER120018_wf/func_preproc_task_rest_run_2_wf/bold_reference_wf/gen_ref/ref_image.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
200306-13:15:20,560 nipype.workflow INFO:
     [Node] Finished "fmriprep_wf.single_subject_BETTER120018_wf.func_preproc_task_rest_run_2_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.norm".
200306-13:15:21,771 nipype.workflow INFO:
     [Node] Setting-up "fmriprep_wf.single_subject_BETTER120018_wf.func_preproc_task_rest_run_1_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.n4_correct" in "/nfsscratch/Users/ariveradompenciel/work/CRESTfmriprep/fmriprep_wf/single_subject_BETTER120018_wf/func_preproc_task_rest_run_1_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/n4_correct".
200306-13:15:21,777 nipype.workflow INFO:
     [Node] Setting-up "fmriprep_wf.single_subject_BETTER120018_wf.func_preproc_task_rest_run_2_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.map_brainmask" in "/nfsscratch/Users/ariveradompenciel/work/CRESTfmriprep/fmriprep_wf/single_subject_BETTER120018_wf/func_preproc_task_rest_run_2_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/map_brainmask".
200306-13:15:21,786 nipype.workflow INFO:
     [Node] Setting-up "fmriprep_wf.single_subject_BETTER120018_wf.anat_preproc_wf.skullstrip_ants_wf.t1_skull_strip" in "/nfsscratch/Users/ariveradompenciel/work/CRESTfmriprep/fmriprep_wf/single_subject_BETTER120018_wf/anat_preproc_wf/skullstrip_ants_wf/t1_skull_strip".
200306-13:15:21,788 nipype.workflow INFO:
     [Node] Running "n4_correct" ("nipype.interfaces.ants.segmentation.N4BiasFieldCorrection"), a CommandLine Interface with command:
N4BiasFieldCorrection -d 3 --input-image /nfsscratch/Users/ariveradompenciel/work/CRESTfmriprep/fmriprep_wf/single_subject_BETTER120018_wf/func_preproc_task_rest_run_1_wf/bold_reference_wf/gen_ref/ref_image.nii.gz --mask-image /nfsscratch/Users/ariveradompenciel/work/CRESTfmriprep/fmriprep_wf/single_subject_BETTER120018_wf/func_preproc_task_rest_run_1_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/check_hdr/tpl-MNI152NLin2009cAsym_space-MNI_res-02_brainmask_trans_dil_hdr.nii.gz --output ref_image_corrected.nii.gz
200306-13:15:21,794 nipype.workflow INFO:
     [Node] Running "map_brainmask" ("niworkflows.interfaces.fixes.FixHeaderApplyTransforms"), a CommandLine Interface with command:
antsApplyTransforms --default-value 0 --float 1 --input /niworkflows_data/tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_space-MNI_res-02_brainmask.nii.gz --interpolation MultiLabel --output tpl-MNI152NLin2009cAsym_space-MNI_res-02_brainmask_trans.nii.gz --reference-image /nfsscratch/Users/ariveradompenciel/work/CRESTfmriprep/fmriprep_wf/single_subject_BETTER120018_wf/func_preproc_task_rest_run_2_wf/bold_reference_wf/gen_ref/ref_image.nii.gz --transform [ /nfsscratch/Users/ariveradompenciel/work/CRESTfmriprep/fmriprep_wf/single_subject_BETTER120018_wf/func_preproc_task_rest_run_2_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/norm/transform0GenericAffine.mat, 1 ]
200306-13:15:21,806 nipype.workflow INFO:
     [Node] Running "t1_skull_strip" ("nipype.interfaces.ants.segmentation.BrainExtraction"), a CommandLine Interface with command:
antsBrainExtraction.sh -a /mnt/Projects/CREST/sub-BETTER120018/anat/sub-BETTER120018_T1w.nii.gz -m /nfsscratch/Users/ariveradompenciel/work/CRESTfmriprep/fmriprep_wf/single_subject_BETTER120018_wf/anat_preproc_wf/skullstrip_ants_wf/t1_skull_strip/T_template0_BrainCerebellumProbabilityMask.nii.gz -e /niworkflows_data/ants_oasis_template_ras/T_template0.nii.gz -d 3 -f /niworkflows_data/ants_oasis_template_ras/T_template0_BrainCerebellumRegistrationMask.nii.gz -s nii.gz -k 1 -o highres001_ -q 1 -u 1
200306-13:15:24,838 nipype.workflow INFO:
     [Node] Finished "fmriprep_wf.single_subject_BETTER120018_wf.func_preproc_task_rest_run_2_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.map_brainmask".
200306-13:15:25,788 nipype.workflow INFO:
     [Node] Setting-up "fmriprep_wf.single_subject_BETTER120018_wf.func_preproc_task_rest_run_2_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.pre_mask_dilate" in "/nfsscratch/Users/ariveradompenciel/work/CRESTfmriprep/fmriprep_wf/single_subject_BETTER120018_wf/func_preproc_task_rest_run_2_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/pre_mask_dilate".
200306-13:15:25,804 nipype.workflow INFO:
     [Node] Running "pre_mask_dilate" ("nipype.interfaces.fsl.maths.DilateImage"), a CommandLine Interface with command:
fslmaths -dt char /nfsscratch/Users/ariveradompenciel/work/CRESTfmriprep/fmriprep_wf/single_subject_BETTER120018_wf/func_preproc_task_rest_run_2_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/map_brainmask/tpl-MNI152NLin2009cAsym_space-MNI_res-02_brainmask_trans.nii.gz -kernel sphere 3.0000 -dilF /nfsscratch/Users/ariveradompenciel/work/CRESTfmriprep/fmriprep_wf/single_subject_BETTER120018_wf/func_preproc_task_rest_run_2_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/pre_mask_dilate/tpl-MNI152NLin2009cAsym_space-MNI_res-02_brainmask_trans_dil.nii.gz
200306-13:15:26,25 nipype.workflow INFO:
     [Node] Finished "fmriprep_wf.single_subject_BETTER120018_wf.func_preproc_task_rest_run_2_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.pre_mask_dilate".
200306-13:15:26,346 nipype.workflow INFO:
     [Node] Finished "fmriprep_wf.single_subject_BETTER120018_wf.func_preproc_task_rest_run_1_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.n4_correct".
200306-13:15:27,803 nipype.workflow INFO:
     [Node] Setting-up "fmriprep_wf.single_subject_BETTER120018_wf.func_preproc_task_rest_run_1_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_pass" in "/nfsscratch/Users/ariveradompenciel/work/CRESTfmriprep/fmriprep_wf/single_subject_BETTER120018_wf/func_preproc_task_rest_run_1_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_pass".
200306-13:15:27,821 nipype.workflow INFO:
     [Node] Running "skullstrip_first_pass" ("nipype.interfaces.fsl.preprocess.BET"), a CommandLine Interface with command:
bet /nfsscratch/Users/ariveradompenciel/work/CRESTfmriprep/fmriprep_wf/single_subject_BETTER120018_wf/func_preproc_task_rest_run_1_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/n4_correct/ref_image_corrected.nii.gz /nfsscratch/Users/ariveradompenciel/work/CRESTfmriprep/fmriprep_wf/single_subject_BETTER120018_wf/func_preproc_task_rest_run_1_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_pass/ref_image_corrected_brain.nii.gz -f 0.20 -m
200306-13:15:29,810 nipype.workflow INFO:
     [Node] Setting-up "fmriprep_wf.single_subject_BETTER120018_wf.func_preproc_task_rest_run_2_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.n4_correct" in "/nfsscratch/Users/ariveradompenciel/work/CRESTfmriprep/fmriprep_wf/single_subject_BETTER120018_wf/func_preproc_task_rest_run_2_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/n4_correct".
200306-13:15:29,826 nipype.workflow INFO:
     [Node] Running "n4_correct" ("nipype.interfaces.ants.segmentation.N4BiasFieldCorrection"), a CommandLine Interface with command:
N4BiasFieldCorrection -d 3 --input-image /nfsscratch/Users/ariveradompenciel/work/CRESTfmriprep/fmriprep_wf/single_subject_BETTER120018_wf/func_preproc_task_rest_run_2_wf/bold_reference_wf/gen_ref/ref_image.nii.gz --mask-image /nfsscratch/Users/ariveradompenciel/work/CRESTfmriprep/fmriprep_wf/single_subject_BETTER120018_wf/func_preproc_task_rest_run_2_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/check_hdr/tpl-MNI152NLin2009cAsym_space-MNI_res-02_brainmask_trans_dil_hdr.nii.gz --output ref_image_corrected.nii.gz
200306-13:15:29,876 nipype.workflow INFO:
     [Node] Finished "fmriprep_wf.single_subject_BETTER120018_wf.func_preproc_task_rest_run_1_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_pass".
200306-13:15:31,225 nipype.workflow INFO:
     [Node] Finished "fmriprep_wf.single_subject_BETTER120018_wf.func_preproc_task_rest_run_2_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.n4_correct".
200306-13:15:31,898 nipype.workflow INFO:
     [Node] Setting-up "fmriprep_wf.single_subject_BETTER120018_wf.func_preproc_task_rest_run_1_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_dilate" in "/nfsscratch/Users/ariveradompenciel/work/CRESTfmriprep/fmriprep_wf/single_subject_BETTER120018_wf/func_preproc_task_rest_run_1_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_dilate".
200306-13:15:31,900 nipype.workflow INFO:
     [Node] Setting-up "fmriprep_wf.single_subject_BETTER120018_wf.func_preproc_task_rest_run_2_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_pass" in "/nfsscratch/Users/ariveradompenciel/work/CRESTfmriprep/fmriprep_wf/single_subject_BETTER120018_wf/func_preproc_task_rest_run_2_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_pass".
200306-13:15:31,915 nipype.workflow INFO:
     [Node] Running "skullstrip_first_dilate" ("nipype.interfaces.fsl.maths.DilateImage"), a CommandLine Interface with command:
fslmaths -dt char /nfsscratch/Users/ariveradompenciel/work/CRESTfmriprep/fmriprep_wf/single_subject_BETTER120018_wf/func_preproc_task_rest_run_1_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_pass/ref_image_corrected_brain_mask.nii.gz -kernel sphere 6.0000 -dilF /nfsscratch/Users/ariveradompenciel/work/CRESTfmriprep/fmriprep_wf/single_subject_BETTER120018_wf/func_preproc_task_rest_run_1_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_dilate/ref_image_corrected_brain_mask_dil.nii.gz
200306-13:15:31,918 nipype.workflow INFO:
     [Node] Running "skullstrip_first_pass" ("nipype.interfaces.fsl.preprocess.BET"), a CommandLine Interface with command:
bet /nfsscratch/Users/ariveradompenciel/work/CRESTfmriprep/fmriprep_wf/single_subject_BETTER120018_wf/func_preproc_task_rest_run_2_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/n4_correct/ref_image_corrected.nii.gz /nfsscratch/Users/ariveradompenciel/work/CRESTfmriprep/fmriprep_wf/single_subject_BETTER120018_wf/func_preproc_task_rest_run_2_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_pass/ref_image_corrected_brain.nii.gz -f 0.20 -m
200306-13:15:32,521 nipype.workflow INFO:
     [Node] Finished "fmriprep_wf.single_subject_BETTER120018_wf.func_preproc_task_rest_run_1_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_dilate".
200306-13:15:33,831 nipype.workflow INFO:
     [Node] Setting-up "fmriprep_wf.single_subject_BETTER120018_wf.func_preproc_task_rest_run_1_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_mask" in "/nfsscratch/Users/ariveradompenciel/work/CRESTfmriprep/fmriprep_wf/single_subject_BETTER120018_wf/func_preproc_task_rest_run_1_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_mask".
200306-13:15:33,862 nipype.workflow INFO:
     [Node] Running "skullstrip_first_mask" ("nipype.interfaces.fsl.maths.ApplyMask"), a CommandLine Interface with command:
fslmaths /nfsscratch/Users/ariveradompenciel/work/CRESTfmriprep/fmriprep_wf/single_subject_BETTER120018_wf/func_preproc_task_rest_run_1_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_pass/ref_image_corrected_brain.nii.gz -mas /nfsscratch/Users/ariveradompenciel/work/CRESTfmriprep/fmriprep_wf/single_subject_BETTER120018_wf/func_preproc_task_rest_run_1_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_dilate/ref_image_corrected_brain_mask_dil.nii.gz /nfsscratch/Users/ariveradompenciel/work/CRESTfmriprep/fmriprep_wf/single_subject_BETTER120018_wf/func_preproc_task_rest_run_1_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_mask/ref_image_corrected_brain_masked.nii.gz
200306-13:15:33,889 nipype.workflow INFO:
     [Node] Finished "fmriprep_wf.single_subject_BETTER120018_wf.func_preproc_task_rest_run_2_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_pass".
200306-13:15:34,208 nipype.workflow INFO:
     [Node] Finished "fmriprep_wf.single_subject_BETTER120018_wf.func_preproc_task_rest_run_1_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_mask".
200306-13:15:35,837 nipype.workflow INFO:
     [Node] Setting-up "fmriprep_wf.single_subject_BETTER120018_wf.func_preproc_task_rest_run_1_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.unifize" in "/nfsscratch/Users/ariveradompenciel/work/CRESTfmriprep/fmriprep_wf/single_subject_BETTER120018_wf/func_preproc_task_rest_run_1_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/unifize".
200306-13:15:35,840 nipype.workflow INFO:
     [Node] Setting-up "fmriprep_wf.single_subject_BETTER120018_wf.func_preproc_task_rest_run_2_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_dilate" in "/nfsscratch/Users/ariveradompenciel/work/CRESTfmriprep/fmriprep_wf/single_subject_BETTER120018_wf/func_preproc_task_rest_run_2_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_dilate".
200306-13:15:35,955 nipype.workflow INFO:
     [Node] Running "skullstrip_first_dilate" ("nipype.interfaces.fsl.maths.DilateImage"), a CommandLine Interface with command:
fslmaths -dt char /nfsscratch/Users/ariveradompenciel/work/CRESTfmriprep/fmriprep_wf/single_subject_BETTER120018_wf/func_preproc_task_rest_run_2_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_pass/ref_image_corrected_brain_mask.nii.gz -kernel sphere 6.0000 -dilF /nfsscratch/Users/ariveradompenciel/work/CRESTfmriprep/fmriprep_wf/single_subject_BETTER120018_wf/func_preproc_task_rest_run_2_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_dilate/ref_image_corrected_brain_mask_dil.nii.gz
200306-13:15:35,958 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 /nfsscratch/Users/ariveradompenciel/work/CRESTfmriprep/fmriprep_wf/single_subject_BETTER120018_wf/func_preproc_task_rest_run_1_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/unifize/ref_image_corrected_brain_masked.nii.gz
200306-13:15:36,486 nipype.workflow INFO:
     [Node] Finished "fmriprep_wf.single_subject_BETTER120018_wf.func_preproc_task_rest_run_2_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_dilate".
200306-13:15:37,753 nipype.workflow INFO:
     [Node] Finished "fmriprep_wf.single_subject_BETTER120018_wf.func_preproc_task_rest_run_1_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.unifize".
200306-13:15:37,849 nipype.workflow INFO:
     [Node] Setting-up "fmriprep_wf.single_subject_BETTER120018_wf.func_preproc_task_rest_run_2_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_mask" in "/nfsscratch/Users/ariveradompenciel/work/CRESTfmriprep/fmriprep_wf/single_subject_BETTER120018_wf/func_preproc_task_rest_run_2_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_mask".
200306-13:15:37,866 nipype.workflow INFO:
     [Node] Running "skullstrip_first_mask" ("nipype.interfaces.fsl.maths.ApplyMask"), a CommandLine Interface with command:
fslmaths /nfsscratch/Users/ariveradompenciel/work/CRESTfmriprep/fmriprep_wf/single_subject_BETTER120018_wf/func_preproc_task_rest_run_2_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_pass/ref_image_corrected_brain.nii.gz -mas /nfsscratch/Users/ariveradompenciel/work/CRESTfmriprep/fmriprep_wf/single_subject_BETTER120018_wf/func_preproc_task_rest_run_2_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_dilate/ref_image_corrected_brain_mask_dil.nii.gz /nfsscratch/Users/ariveradompenciel/work/CRESTfmriprep/fmriprep_wf/single_subject_BETTER120018_wf/func_preproc_task_rest_run_2_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_mask/ref_image_corrected_brain_masked.nii.gz
200306-13:15:38,42 nipype.workflow INFO:
     [Node] Finished "fmriprep_wf.single_subject_BETTER120018_wf.func_preproc_task_rest_run_2_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_mask".
200306-13:15:39,862 nipype.workflow INFO:
     [Node] Setting-up "fmriprep_wf.single_subject_BETTER120018_wf.func_preproc_task_rest_run_2_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.unifize" in "/nfsscratch/Users/ariveradompenciel/work/CRESTfmriprep/fmriprep_wf/single_subject_BETTER120018_wf/func_preproc_task_rest_run_2_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/unifize".
200306-13:15:40,461 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 /nfsscratch/Users/ariveradompenciel/work/CRESTfmriprep/fmriprep_wf/single_subject_BETTER120018_wf/func_preproc_task_rest_run_2_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/unifize/ref_image_corrected_brain_masked.nii.gz
200306-13:15:40,649 nipype.workflow INFO:
     [Node] Setting-up "fmriprep_wf.single_subject_BETTER120018_wf.func_preproc_task_rest_run_1_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.fixhdr_unifize" in "/nfsscratch/Users/ariveradompenciel/work/CRESTfmriprep/fmriprep_wf/single_subject_BETTER120018_wf/func_preproc_task_rest_run_1_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/fixhdr_unifize".
200306-13:15:40,663 nipype.workflow INFO:
     [Node] Running "fixhdr_unifize" ("niworkflows.interfaces.utils.CopyXForm")
200306-13:15:41,738 nipype.workflow INFO:
     [Node] Finished "fmriprep_wf.single_subject_BETTER120018_wf.func_preproc_task_rest_run_2_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.unifize".
200306-13:15:41,865 nipype.workflow INFO:
     [Node] Setting-up "fmriprep_wf.single_subject_BETTER120018_wf.func_preproc_task_rest_run_2_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.fixhdr_unifize" in "/nfsscratch/Users/ariveradompenciel/work/CRESTfmriprep/fmriprep_wf/single_subject_BETTER120018_wf/func_preproc_task_rest_run_2_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/fixhdr_unifize".
200306-13:15:41,886 nipype.workflow INFO:
     [Node] Running "fixhdr_unifize" ("niworkflows.interfaces.utils.CopyXForm")
200306-13:15:45,311 nipype.workflow INFO:
     [Node] Finished "fmriprep_wf.single_subject_BETTER120018_wf.func_preproc_task_rest_run_1_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.fixhdr_unifize".
200306-13:15:45,311 nipype.workflow INFO:
     [Node] Finished "fmriprep_wf.single_subject_BETTER120018_wf.func_preproc_task_rest_run_2_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.fixhdr_unifize".
200306-13:15:45,884 nipype.workflow INFO:
     [Node] Setting-up "fmriprep_wf.single_subject_BETTER120018_wf.func_preproc_task_rest_run_1_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.skullstrip_second_pass" in "/nfsscratch/Users/ariveradompenciel/work/CRESTfmriprep/fmriprep_wf/single_subject_BETTER120018_wf/func_preproc_task_rest_run_1_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_second_pass".
200306-13:15:45,887 nipype.workflow INFO:
     [Node] Setting-up "fmriprep_wf.single_subject_BETTER120018_wf.func_preproc_task_rest_run_2_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.skullstrip_second_pass" in "/nfsscratch/Users/ariveradompenciel/work/CRESTfmriprep/fmriprep_wf/single_subject_BETTER120018_wf/func_preproc_task_rest_run_2_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_second_pass".
200306-13:15:45,902 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 /nfsscratch/Users/ariveradompenciel/work/CRESTfmriprep/fmriprep_wf/single_subject_BETTER120018_wf/func_preproc_task_rest_run_1_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_second_pass/uni_xform.nii.gz
200306-13:15:45,904 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 /nfsscratch/Users/ariveradompenciel/work/CRESTfmriprep/fmriprep_wf/single_subject_BETTER120018_wf/func_preproc_task_rest_run_2_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_second_pass/uni_xform.nii.gz
200306-13:15:50,40 nipype.workflow INFO:
     [Node] Finished "fmriprep_wf.single_subject_BETTER120018_wf.func_preproc_task_rest_run_1_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.skullstrip_second_pass".
200306-13:15:50,40 nipype.workflow INFO:
     [Node] Finished "fmriprep_wf.single_subject_BETTER120018_wf.func_preproc_task_rest_run_2_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.skullstrip_second_pass".
200306-13:15:51,925 nipype.workflow INFO:
     [Node] Setting-up "fmriprep_wf.single_subject_BETTER120018_wf.func_preproc_task_rest_run_1_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.fixhdr_skullstrip2" in "/nfsscratch/Users/ariveradompenciel/work/CRESTfmriprep/fmriprep_wf/single_subject_BETTER120018_wf/func_preproc_task_rest_run_1_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/fixhdr_skullstrip2".
200306-13:15:51,928 nipype.workflow INFO:
     [Node] Setting-up "fmriprep_wf.single_subject_BETTER120018_wf.func_preproc_task_rest_run_2_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.fixhdr_skullstrip2" in "/nfsscratch/Users/ariveradompenciel/work/CRESTfmriprep/fmriprep_wf/single_subject_BETTER120018_wf/func_preproc_task_rest_run_2_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/fixhdr_skullstrip2".
200306-13:15:51,939 nipype.workflow INFO:
     [Node] Running "fixhdr_skullstrip2" ("niworkflows.interfaces.utils.CopyXForm")
200306-13:15:51,942 nipype.workflow INFO:
     [Node] Running "fixhdr_skullstrip2" ("niworkflows.interfaces.utils.CopyXForm")
200306-13:15:57,364 nipype.workflow INFO:
     [Node] Finished "fmriprep_wf.single_subject_BETTER120018_wf.func_preproc_task_rest_run_2_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.fixhdr_skullstrip2".
200306-13:15:57,364 nipype.workflow INFO:
     [Node] Finished "fmriprep_wf.single_subject_BETTER120018_wf.func_preproc_task_rest_run_1_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.fixhdr_skullstrip2".
200306-13:15:57,943 nipype.workflow INFO:
     [Node] Setting-up "fmriprep_wf.single_subject_BETTER120018_wf.func_preproc_task_rest_run_1_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.combine_masks" in "/nfsscratch/Users/ariveradompenciel/work/CRESTfmriprep/fmriprep_wf/single_subject_BETTER120018_wf/func_preproc_task_rest_run_1_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/combine_masks".
200306-13:15:57,947 nipype.workflow INFO:
     [Node] Setting-up "fmriprep_wf.single_subject_BETTER120018_wf.func_preproc_task_rest_run_2_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.combine_masks" in "/nfsscratch/Users/ariveradompenciel/work/CRESTfmriprep/fmriprep_wf/single_subject_BETTER120018_wf/func_preproc_task_rest_run_2_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/combine_masks".
200306-13:15:57,970 nipype.workflow INFO:
     [Node] Running "combine_masks" ("nipype.interfaces.fsl.maths.BinaryMaths"), a CommandLine Interface with command:
fslmaths /nfsscratch/Users/ariveradompenciel/work/CRESTfmriprep/fmriprep_wf/single_subject_BETTER120018_wf/func_preproc_task_rest_run_2_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_pass/ref_image_corrected_brain_mask.nii.gz -mul /nfsscratch/Users/ariveradompenciel/work/CRESTfmriprep/fmriprep_wf/single_subject_BETTER120018_wf/func_preproc_task_rest_run_2_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/fixhdr_skullstrip2/uni_xform_mask_xform.nii.gz /nfsscratch/Users/ariveradompenciel/work/CRESTfmriprep/fmriprep_wf/single_subject_BETTER120018_wf/func_preproc_task_rest_run_2_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/combine_masks/ref_image_corrected_brain_mask_maths.nii.gz
200306-13:15:57,970 nipype.workflow INFO:
     [Node] Running "combine_masks" ("nipype.interfaces.fsl.maths.BinaryMaths"), a CommandLine Interface with command:
fslmaths /nfsscratch/Users/ariveradompenciel/work/CRESTfmriprep/fmriprep_wf/single_subject_BETTER120018_wf/func_preproc_task_rest_run_1_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_pass/ref_image_corrected_brain_mask.nii.gz -mul /nfsscratch/Users/ariveradompenciel/work/CRESTfmriprep/fmriprep_wf/single_subject_BETTER120018_wf/func_preproc_task_rest_run_1_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/fixhdr_skullstrip2/uni_xform_mask_xform.nii.gz /nfsscratch/Users/ariveradompenciel/work/CRESTfmriprep/fmriprep_wf/single_subject_BETTER120018_wf/func_preproc_task_rest_run_1_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/combine_masks/ref_image_corrected_brain_mask_maths.nii.gz
200306-13:15:58,185 nipype.workflow INFO:
     [Node] Finished "fmriprep_wf.single_subject_BETTER120018_wf.func_preproc_task_rest_run_1_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.combine_masks".
200306-13:15:58,185 nipype.workflow INFO:
     [Node] Finished "fmriprep_wf.single_subject_BETTER120018_wf.func_preproc_task_rest_run_2_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.combine_masks".
200306-13:15:59,954 nipype.workflow INFO:
     [Node] Setting-up "fmriprep_wf.single_subject_BETTER120018_wf.func_preproc_task_rest_run_1_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.apply_mask" in "/nfsscratch/Users/ariveradompenciel/work/CRESTfmriprep/fmriprep_wf/single_subject_BETTER120018_wf/func_preproc_task_rest_run_1_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/apply_mask".
200306-13:15:59,958 nipype.workflow INFO:
     [Node] Setting-up "fmriprep_wf.single_subject_BETTER120018_wf.func_preproc_task_rest_run_2_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.apply_mask" in "/nfsscratch/Users/ariveradompenciel/work/CRESTfmriprep/fmriprep_wf/single_subject_BETTER120018_wf/func_preproc_task_rest_run_2_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/apply_mask".
200306-13:16:01,992 nipype.workflow INFO:
     [Node] Running "apply_mask" ("nipype.interfaces.fsl.maths.ApplyMask"), a CommandLine Interface with command:
fslmaths /nfsscratch/Users/ariveradompenciel/work/CRESTfmriprep/fmriprep_wf/single_subject_BETTER120018_wf/func_preproc_task_rest_run_1_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/fixhdr_unifize/uni_xform.nii.gz -mas /nfsscratch/Users/ariveradompenciel/work/CRESTfmriprep/fmriprep_wf/single_subject_BETTER120018_wf/func_preproc_task_rest_run_1_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/combine_masks/ref_image_corrected_brain_mask_maths.nii.gz /nfsscratch/Users/ariveradompenciel/work/CRESTfmriprep/fmriprep_wf/single_subject_BETTER120018_wf/func_preproc_task_rest_run_1_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/apply_mask/uni_xform_masked.nii.gz
200306-13:16:01,994 nipype.workflow INFO:
     [Node] Running "apply_mask" ("nipype.interfaces.fsl.maths.ApplyMask"), a CommandLine Interface with command:
fslmaths /nfsscratch/Users/ariveradompenciel/work/CRESTfmriprep/fmriprep_wf/single_subject_BETTER120018_wf/func_preproc_task_rest_run_2_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/fixhdr_unifize/uni_xform.nii.gz -mas /nfsscratch/Users/ariveradompenciel/work/CRESTfmriprep/fmriprep_wf/single_subject_BETTER120018_wf/func_preproc_task_rest_run_2_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/combine_masks/ref_image_corrected_brain_mask_maths.nii.gz /nfsscratch/Users/ariveradompenciel/work/CRESTfmriprep/fmriprep_wf/single_subject_BETTER120018_wf/func_preproc_task_rest_run_2_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/apply_mask/uni_xform_masked.nii.gz
200306-13:16:02,230 nipype.workflow INFO:
     [Node] Finished "fmriprep_wf.single_subject_BETTER120018_wf.func_preproc_task_rest_run_1_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.apply_mask".
200306-13:16:02,280 nipype.workflow INFO:
     [Node] Finished "fmriprep_wf.single_subject_BETTER120018_wf.func_preproc_task_rest_run_2_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.apply_mask".
200306-13:16:06,412 nipype.workflow INFO:
     [Node] Finished "fmriprep_wf.single_subject_BETTER120018_wf.func_preproc_task_rest_run_2_wf.bold_hmc_wf.mcflirt".
200306-13:16:07,981 nipype.workflow INFO:
     [Node] Setting-up "fmriprep_wf.single_subject_BETTER120018_wf.func_preproc_task_rest_run_2_wf.bold_hmc_wf.normalize_motion" in "/nfsscratch/Users/ariveradompenciel/work/CRESTfmriprep/fmriprep_wf/single_subject_BETTER120018_wf/func_preproc_task_rest_run_2_wf/bold_hmc_wf/normalize_motion".
200306-13:16:07,998 nipype.workflow INFO:
     [Node] Running "normalize_motion" ("niworkflows.interfaces.utils.NormalizeMotionParams")
200306-13:16:08,27 nipype.workflow INFO:
     [Node] Finished "fmriprep_wf.single_subject_BETTER120018_wf.func_preproc_task_rest_run_2_wf.bold_hmc_wf.normalize_motion".
200306-13:16:10,179 nipype.workflow INFO:
     [Node] Setting-up "fmriprep_wf.single_subject_BETTER120018_wf.func_preproc_task_rest_run_2_wf.bold_confounds_wf.fdisp" in "/nfsscratch/Users/ariveradompenciel/work/CRESTfmriprep/fmriprep_wf/single_subject_BETTER120018_wf/func_preproc_task_rest_run_2_wf/bold_confounds_wf/fdisp".
200306-13:16:10,195 nipype.workflow INFO:
     [Node] Running "fdisp" ("nipype.algorithms.confounds.FramewiseDisplacement")
200306-13:16:10,223 nipype.workflow INFO:
     [Node] Finished "fmriprep_wf.single_subject_BETTER120018_wf.func_preproc_task_rest_run_2_wf.bold_confounds_wf.fdisp".
200306-13:16:10,659 nipype.workflow INFO:
     [Node] Finished "fmriprep_wf.single_subject_BETTER120018_wf.func_preproc_task_rest_run_1_wf.bold_hmc_wf.mcflirt".
200306-13:16:12,3 nipype.workflow INFO:
     [Node] Setting-up "fmriprep_wf.single_subject_BETTER120018_wf.func_preproc_task_rest_run_1_wf.bold_hmc_wf.normalize_motion" in "/nfsscratch/Users/ariveradompenciel/work/CRESTfmriprep/fmriprep_wf/single_subject_BETTER120018_wf/func_preproc_task_rest_run_1_wf/bold_hmc_wf/normalize_motion".
200306-13:16:12,18 nipype.workflow INFO:
     [Node] Running "normalize_motion" ("niworkflows.interfaces.utils.NormalizeMotionParams")
200306-13:16:12,45 nipype.workflow INFO:
     [Node] Finished "fmriprep_wf.single_subject_BETTER120018_wf.func_preproc_task_rest_run_1_wf.bold_hmc_wf.normalize_motion".
200306-13:16:14,158 nipype.workflow INFO:
     [Node] Setting-up "fmriprep_wf.single_subject_BETTER120018_wf.func_preproc_task_rest_run_1_wf.bold_confounds_wf.fdisp" in "/nfsscratch/Users/ariveradompenciel/work/CRESTfmriprep/fmriprep_wf/single_subject_BETTER120018_wf/func_preproc_task_rest_run_1_wf/bold_confounds_wf/fdisp".
200306-13:16:14,172 nipype.workflow INFO:
     [Node] Running "fdisp" ("nipype.algorithms.confounds.FramewiseDisplacement")
200306-13:16:14,198 nipype.workflow INFO:
     [Node] Finished "fmriprep_wf.single_subject_BETTER120018_wf.func_preproc_task_rest_run_1_wf.bold_confounds_wf.fdisp".
200306-13:31:43,642 nipype.workflow INFO:
     [Node] Finished "fmriprep_wf.single_subject_BETTER120018_wf.anat_preproc_wf.skullstrip_ants_wf.t1_skull_strip".
200306-13:31:44,624 nipype.workflow INFO:
     [Node] Setting-up "fmriprep_wf.single_subject_BETTER120018_wf.func_preproc_task_rest_run_1_wf.bold_hmc_wf.fsl2itk" in "/nfsscratch/Users/ariveradompenciel/work/CRESTfmriprep/fmriprep_wf/single_subject_BETTER120018_wf/func_preproc_task_rest_run_1_wf/bold_hmc_wf/fsl2itk".
200306-13:31:44,674 nipype.workflow INFO:
     [Node] Running "fsl2itk" ("fmriprep.interfaces.itk.MCFLIRT2ITK")
200306-13:33:10,907 nipype.workflow INFO:
     [Node] Finished "fmriprep_wf.single_subject_BETTER120018_wf.func_preproc_task_rest_run_1_wf.bold_hmc_wf.fsl2itk".
200306-13:33:13,203 nipype.workflow INFO:
     [Node] Setting-up "fmriprep_wf.single_subject_BETTER120018_wf.func_preproc_task_rest_run_2_wf.bold_hmc_wf.fsl2itk" in "/nfsscratch/Users/ariveradompenciel/work/CRESTfmriprep/fmriprep_wf/single_subject_BETTER120018_wf/func_preproc_task_rest_run_2_wf/bold_hmc_wf/fsl2itk".
200306-13:33:13,248 nipype.workflow INFO:
     [Node] Running "fsl2itk" ("fmriprep.interfaces.itk.MCFLIRT2ITK")
200306-13:34:42,514 nipype.workflow INFO:
     [Node] Finished "fmriprep_wf.single_subject_BETTER120018_wf.func_preproc_task_rest_run_2_wf.bold_hmc_wf.fsl2itk".
200306-13:34:43,192 nipype.workflow INFO:
     [Node] Setting-up "fmriprep_wf.single_subject_BETTER120018_wf.func_preproc_task_rest_run_1_wf.bold_bold_trans_wf.bold_transform" in "/nfsscratch/Users/ariveradompenciel/work/CRESTfmriprep/fmriprep_wf/single_subject_BETTER120018_wf/func_preproc_task_rest_run_1_wf/bold_bold_trans_wf/bold_transform".
200306-13:34:43,219 nipype.workflow INFO:
     [Node] Running "bold_transform" ("fmriprep.interfaces.itk.MultiApplyTransforms")
200306-13:36:28,428 nipype.workflow INFO:
     [Node] Finished "fmriprep_wf.single_subject_BETTER120018_wf.func_preproc_task_rest_run_1_wf.bold_bold_trans_wf.bold_transform".
200306-13:36:29,510 nipype.workflow INFO:
     [Node] Setting-up "fmriprep_wf.single_subject_BETTER120018_wf.func_preproc_task_rest_run_1_wf.bold_bold_trans_wf.merge" in "/nfsscratch/Users/ariveradompenciel/work/CRESTfmriprep/fmriprep_wf/single_subject_BETTER120018_wf/func_preproc_task_rest_run_1_wf/bold_bold_trans_wf/merge".
200306-13:36:29,536 nipype.workflow INFO:
     [Node] Running "merge" ("fmriprep.interfaces.nilearn.Merge")
200306-13:36:29,701 nipype.workflow INFO:
     [Node] Setting-up "fmriprep_wf.single_subject_BETTER120018_wf.func_preproc_task_rest_run_2_wf.bold_bold_trans_wf.bold_transform" in "/nfsscratch/Users/ariveradompenciel/work/CRESTfmriprep/fmriprep_wf/single_subject_BETTER120018_wf/func_preproc_task_rest_run_2_wf/bold_bold_trans_wf/bold_transform".
200306-13:36:29,733 nipype.workflow INFO:
     [Node] Running "bold_transform" ("fmriprep.interfaces.itk.MultiApplyTransforms")
200306-13:36:42,978 nipype.workflow INFO:
     [Node] Finished "fmriprep_wf.single_subject_BETTER120018_wf.func_preproc_task_rest_run_1_wf.bold_bold_trans_wf.merge".
200306-13:36:43,688 nipype.workflow INFO:
     [Node] Setting-up "fmriprep_wf.single_subject_BETTER120018_wf.func_preproc_task_rest_run_1_wf.bold_bold_trans_wf.bold_reference_wf.validate" in "/nfsscratch/Users/ariveradompenciel/work/CRESTfmriprep/fmriprep_wf/single_subject_BETTER120018_wf/func_preproc_task_rest_run_1_wf/bold_bold_trans_wf/bold_reference_wf/validate".
200306-13:36:43,706 nipype.workflow INFO:
     [Node] Running "validate" ("fmriprep.interfaces.images.ValidateImage")
200306-13:36:47,114 nipype.workflow INFO:
     [Node] Finished "fmriprep_wf.single_subject_BETTER120018_wf.func_preproc_task_rest_run_1_wf.bold_bold_trans_wf.bold_reference_wf.validate".
200306-13:36:47,553 nipype.workflow INFO:
     [Node] Setting-up "fmriprep_wf.single_subject_BETTER120018_wf.func_preproc_task_rest_run_1_wf.bold_bold_trans_wf.bold_reference_wf.gen_ref" in "/nfsscratch/Users/ariveradompenciel/work/CRESTfmriprep/fmriprep_wf/single_subject_BETTER120018_wf/func_preproc_task_rest_run_1_wf/bold_bold_trans_wf/bold_reference_wf/gen_ref".
200306-13:36:47,567 nipype.workflow INFO:
     [Node] Running "gen_ref" ("niworkflows.interfaces.registration.EstimateReferenceImage")
200306-13:36:48,28 nipype.workflow INFO:
     [Node] Finished "fmriprep_wf.single_subject_BETTER120018_wf.func_preproc_task_rest_run_1_wf.bold_bold_trans_wf.bold_reference_wf.gen_ref".
200306-13:36:49,567 nipype.workflow INFO:
     [Node] Setting-up "fmriprep_wf.single_subject_BETTER120018_wf.func_preproc_task_rest_run_1_wf.bold_bold_trans_wf.bold_reference_wf.validate_ref" in "/nfsscratch/Users/ariveradompenciel/work/CRESTfmriprep/fmriprep_wf/single_subject_BETTER120018_wf/func_preproc_task_rest_run_1_wf/bold_bold_trans_wf/bold_reference_wf/validate_ref".
200306-13:36:49,627 nipype.workflow INFO:
     [Node] Running "validate_ref" ("fmriprep.interfaces.images.ValidateImage")
200306-13:36:53,868 nipype.workflow INFO:
     [Node] Finished "fmriprep_wf.single_subject_BETTER120018_wf.func_preproc_task_rest_run_1_wf.bold_bold_trans_wf.bold_reference_wf.validate_ref".
200306-13:38:07,217 nipype.workflow INFO:
     [Node] Finished "fmriprep_wf.single_subject_BETTER120018_wf.func_preproc_task_rest_run_2_wf.bold_bold_trans_wf.bold_transform".
200306-13:38:07,897 nipype.workflow INFO:
     [Node] Setting-up "fmriprep_wf.single_subject_BETTER120018_wf.func_preproc_task_rest_run_1_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.init_aff" in "/nfsscratch/Users/ariveradompenciel/work/CRESTfmriprep/fmriprep_wf/single_subject_BETTER120018_wf/func_preproc_task_rest_run_1_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/init_aff".
200306-13:38:07,916 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 /niworkflows_data/tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_space-MNI_res-02_brainmask.nii.gz -m Mattes[/niworkflows_data/tpl-fMRIPrep/tpl-fMRIPrep_space-MNI_res-02_boldref.nii.gz,/nfsscratch/Users/ariveradompenciel/work/CRESTfmriprep/fmriprep_wf/single_subject_BETTER120018_wf/func_preproc_task_rest_run_1_wf/bold_bold_trans_wf/bold_reference_wf/validate_ref/ref_image_valid.nii.gz,32,Regular,0.200000] -o initialization.mat -p 0 -s [20.000000,0.120000] -t Affine[0.100000] -v 1
200306-13:38:07,927 nipype.workflow INFO:
     [Node] Setting-up "fmriprep_wf.single_subject_BETTER120018_wf.func_preproc_task_rest_run_2_wf.bold_bold_trans_wf.merge" in "/nfsscratch/Users/ariveradompenciel/work/CRESTfmriprep/fmriprep_wf/single_subject_BETTER120018_wf/func_preproc_task_rest_run_2_wf/bold_bold_trans_wf/merge".
200306-13:38:07,953 nipype.workflow INFO:
     [Node] Running "merge" ("fmriprep.interfaces.nilearn.Merge")
200306-13:38:10,735 nipype.workflow INFO:
     [Node] Finished "fmriprep_wf.single_subject_BETTER120018_wf.func_preproc_task_rest_run_1_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.init_aff".
200306-13:38:11,919 nipype.workflow INFO:
     [Node] Setting-up "fmriprep_wf.single_subject_BETTER120018_wf.func_preproc_task_rest_run_1_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.norm" in "/nfsscratch/Users/ariveradompenciel/work/CRESTfmriprep/fmriprep_wf/single_subject_BETTER120018_wf/func_preproc_task_rest_run_1_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/norm".
200306-13:38:11,947 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 [ /nfsscratch/Users/ariveradompenciel/work/CRESTfmriprep/fmriprep_wf/single_subject_BETTER120018_wf/func_preproc_task_rest_run_1_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/init_aff/initialization.mat, 0 ] --initialize-transforms-per-stage 0 --interpolation Linear --output transform --transform Affine[ 0.1 ] --metric Mattes[ /niworkflows_data/tpl-fMRIPrep/tpl-fMRIPrep_space-MNI_res-02_boldref.nii.gz, /nfsscratch/Users/ariveradompenciel/work/CRESTfmriprep/fmriprep_wf/single_subject_BETTER120018_wf/func_preproc_task_rest_run_1_wf/bold_bold_trans_wf/bold_reference_wf/validate_ref/ref_image_valid.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
200306-13:38:12,660 nipype.workflow INFO:
     [Node] Finished "fmriprep_wf.single_subject_BETTER120018_wf.func_preproc_task_rest_run_1_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.norm".
200306-13:38:13,929 nipype.workflow INFO:
     [Node] Setting-up "fmriprep_wf.single_subject_BETTER120018_wf.func_preproc_task_rest_run_1_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.map_brainmask" in "/nfsscratch/Users/ariveradompenciel/work/CRESTfmriprep/fmriprep_wf/single_subject_BETTER120018_wf/func_preproc_task_rest_run_1_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/map_brainmask".
200306-13:38:13,944 nipype.workflow INFO:
     [Node] Setting-up "fmriprep_wf.single_subject_BETTER120018_wf.anat_preproc_wf.surface_recon_wf.autorecon1" in "/nfsscratch/Users/ariveradompenciel/work/CRESTfmriprep/fmriprep_wf/single_subject_BETTER120018_wf/anat_preproc_wf/surface_recon_wf/autorecon1".
200306-13:38:13,961 nipype.workflow INFO:
     [Node] Running "map_brainmask" ("niworkflows.interfaces.fixes.FixHeaderApplyTransforms"), a CommandLine Interface with command:
antsApplyTransforms --default-value 0 --float 1 --input /niworkflows_data/tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_space-MNI_res-02_brainmask.nii.gz --interpolation MultiLabel --output tpl-MNI152NLin2009cAsym_space-MNI_res-02_brainmask_trans.nii.gz --reference-image /nfsscratch/Users/ariveradompenciel/work/CRESTfmriprep/fmriprep_wf/single_subject_BETTER120018_wf/func_preproc_task_rest_run_1_wf/bold_bold_trans_wf/bold_reference_wf/validate_ref/ref_image_valid.nii.gz --transform [ /nfsscratch/Users/ariveradompenciel/work/CRESTfmriprep/fmriprep_wf/single_subject_BETTER120018_wf/func_preproc_task_rest_run_1_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/norm/transform0GenericAffine.mat, 1 ]
200306-13:38:13,966 nipype.workflow INFO:
     [Node] Running "autorecon1" ("nipype.interfaces.freesurfer.preprocess.ReconAll"), a CommandLine Interface with command:
recon-all -autorecon1 -i /mnt/Projects/CREST/sub-BETTER120018/anat/sub-BETTER120018_T1w.nii.gz -noskullstrip -openmp 10 -subjid sub-BETTER120018 -sd /mnt/Projects/CREST/derivatives/freesurfer
200306-13:38:18,69 nipype.workflow INFO:
     [Node] Finished "fmriprep_wf.single_subject_BETTER120018_wf.func_preproc_task_rest_run_1_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.map_brainmask".
200306-13:38:19,952 nipype.workflow INFO:
     [Node] Setting-up "fmriprep_wf.single_subject_BETTER120018_wf.func_preproc_task_rest_run_1_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.pre_mask_dilate" in "/nfsscratch/Users/ariveradompenciel/work/CRESTfmriprep/fmriprep_wf/single_subject_BETTER120018_wf/func_preproc_task_rest_run_1_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/pre_mask_dilate".
200306-13:38:19,970 nipype.workflow INFO:
     [Node] Running "pre_mask_dilate" ("nipype.interfaces.fsl.maths.DilateImage"), a CommandLine Interface with command:
fslmaths -dt char /nfsscratch/Users/ariveradompenciel/work/CRESTfmriprep/fmriprep_wf/single_subject_BETTER120018_wf/func_preproc_task_rest_run_1_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/map_brainmask/tpl-MNI152NLin2009cAsym_space-MNI_res-02_brainmask_trans.nii.gz -kernel sphere 3.0000 -dilF /nfsscratch/Users/ariveradompenciel/work/CRESTfmriprep/fmriprep_wf/single_subject_BETTER120018_wf/func_preproc_task_rest_run_1_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/pre_mask_dilate/tpl-MNI152NLin2009cAsym_space-MNI_res-02_brainmask_trans_dil.nii.gz
200306-13:38:20,202 nipype.workflow INFO:
     [Node] Finished "fmriprep_wf.single_subject_BETTER120018_wf.func_preproc_task_rest_run_1_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.pre_mask_dilate".
200306-13:38:21,991 nipype.interface WARNING:
     q-forms of reference and mask are substantially different
200306-13:38:22,944 nipype.workflow INFO:
     [Node] Finished "fmriprep_wf.single_subject_BETTER120018_wf.func_preproc_task_rest_run_2_wf.bold_bold_trans_wf.merge".
200306-13:38:23,967 nipype.workflow INFO:
     [Node] Setting-up "fmriprep_wf.single_subject_BETTER120018_wf.func_preproc_task_rest_run_1_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.n4_correct" in "/nfsscratch/Users/ariveradompenciel/work/CRESTfmriprep/fmriprep_wf/single_subject_BETTER120018_wf/func_preproc_task_rest_run_1_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/n4_correct".
200306-13:38:23,969 nipype.workflow INFO:
     [Node] Setting-up "fmriprep_wf.single_subject_BETTER120018_wf.func_preproc_task_rest_run_2_wf.bold_bold_trans_wf.bold_reference_wf.validate" in "/nfsscratch/Users/ariveradompenciel/work/CRESTfmriprep/fmriprep_wf/single_subject_BETTER120018_wf/func_preproc_task_rest_run_2_wf/bold_bold_trans_wf/bold_reference_wf/validate".
200306-13:38:23,983 nipype.workflow INFO:
     [Node] Running "n4_correct" ("nipype.interfaces.ants.segmentation.N4BiasFieldCorrection"), a CommandLine Interface with command:
N4BiasFieldCorrection -d 3 --input-image /nfsscratch/Users/ariveradompenciel/work/CRESTfmriprep/fmriprep_wf/single_subject_BETTER120018_wf/func_preproc_task_rest_run_1_wf/bold_bold_trans_wf/bold_reference_wf/validate_ref/ref_image_valid.nii.gz --mask-image /nfsscratch/Users/ariveradompenciel/work/CRESTfmriprep/fmriprep_wf/single_subject_BETTER120018_wf/func_preproc_task_rest_run_1_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/check_hdr/tpl-MNI152NLin2009cAsym_space-MNI_res-02_brainmask_trans_dil_hdr.nii.gz --output ref_image_valid_corrected.nii.gz
200306-13:38:23,985 nipype.workflow INFO:
     [Node] Running "validate" ("fmriprep.interfaces.images.ValidateImage")
200306-13:38:25,152 nipype.workflow INFO:
     [Node] Finished "fmriprep_wf.single_subject_BETTER120018_wf.func_preproc_task_rest_run_1_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.n4_correct".
200306-13:38:25,977 nipype.workflow INFO:
     [Node] Setting-up "fmriprep_wf.single_subject_BETTER120018_wf.func_preproc_task_rest_run_1_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_pass" in "/nfsscratch/Users/ariveradompenciel/work/CRESTfmriprep/fmriprep_wf/single_subject_BETTER120018_wf/func_preproc_task_rest_run_1_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_pass".
200306-13:38:25,998 nipype.workflow INFO:
     [Node] Running "skullstrip_first_pass" ("nipype.interfaces.fsl.preprocess.BET"), a CommandLine Interface with command:
bet /nfsscratch/Users/ariveradompenciel/work/CRESTfmriprep/fmriprep_wf/single_subject_BETTER120018_wf/func_preproc_task_rest_run_1_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/n4_correct/ref_image_valid_corrected.nii.gz /nfsscratch/Users/ariveradompenciel/work/CRESTfmriprep/fmriprep_wf/single_subject_BETTER120018_wf/func_preproc_task_rest_run_1_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_pass/ref_image_valid_corrected_brain.nii.gz -f 0.20 -m
200306-13:38:27,256 nipype.workflow INFO:
     [Node] Finished "fmriprep_wf.single_subject_BETTER120018_wf.func_preproc_task_rest_run_2_wf.bold_bold_trans_wf.bold_reference_wf.validate".
200306-13:38:27,932 nipype.workflow INFO:
     [Node] Finished "fmriprep_wf.single_subject_BETTER120018_wf.func_preproc_task_rest_run_1_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_pass".
200306-13:38:27,988 nipype.workflow INFO:
     [Node] Setting-up "fmriprep_wf.single_subject_BETTER120018_wf.func_preproc_task_rest_run_2_wf.bold_bold_trans_wf.bold_reference_wf.gen_ref" in "/nfsscratch/Users/ariveradompenciel/work/CRESTfmriprep/fmriprep_wf/single_subject_BETTER120018_wf/func_preproc_task_rest_run_2_wf/bold_bold_trans_wf/bold_reference_wf/gen_ref".
200306-13:38:28,3 nipype.workflow INFO:
     [Node] Running "gen_ref" ("niworkflows.interfaces.registration.EstimateReferenceImage")
200306-13:38:28,473 nipype.workflow INFO:
     [Node] Finished "fmriprep_wf.single_subject_BETTER120018_wf.func_preproc_task_rest_run_2_wf.bold_bold_trans_wf.bold_reference_wf.gen_ref".
200306-13:38:29,995 nipype.workflow INFO:
     [Node] Setting-up "fmriprep_wf.single_subject_BETTER120018_wf.func_preproc_task_rest_run_1_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_dilate" in "/nfsscratch/Users/ariveradompenciel/work/CRESTfmriprep/fmriprep_wf/single_subject_BETTER120018_wf/func_preproc_task_rest_run_1_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_dilate".
200306-13:38:29,997 nipype.workflow INFO:
     [Node] Setting-up "fmriprep_wf.single_subject_BETTER120018_wf.func_preproc_task_rest_run_2_wf.bold_bold_trans_wf.bold_reference_wf.validate_ref" in "/nfsscratch/Users/ariveradompenciel/work/CRESTfmriprep/fmriprep_wf/single_subject_BETTER120018_wf/func_preproc_task_rest_run_2_wf/bold_bold_trans_wf/bold_reference_wf/validate_ref".
200306-13:38:30,13 nipype.workflow INFO:
     [Node] Running "validate_ref" ("fmriprep.interfaces.images.ValidateImage")
200306-13:38:30,14 nipype.workflow INFO:
     [Node] Running "skullstrip_first_dilate" ("nipype.interfaces.fsl.maths.DilateImage"), a CommandLine Interface with command:
fslmaths -dt char /nfsscratch/Users/ariveradompenciel/work/CRESTfmriprep/fmriprep_wf/single_subject_BETTER120018_wf/func_preproc_task_rest_run_1_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_pass/ref_image_valid_corrected_brain_mask.nii.gz -kernel sphere 6.0000 -dilF /nfsscratch/Users/ariveradompenciel/work/CRESTfmriprep/fmriprep_wf/single_subject_BETTER120018_wf/func_preproc_task_rest_run_1_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_dilate/ref_image_valid_corrected_brain_mask_dil.nii.gz
200306-13:38:30,427 nipype.workflow INFO:
     [Node] Finished "fmriprep_wf.single_subject_BETTER120018_wf.func_preproc_task_rest_run_1_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_dilate".
200306-13:38:32,5 nipype.workflow INFO:
     [Node] Setting-up "fmriprep_wf.single_subject_BETTER120018_wf.func_preproc_task_rest_run_1_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_mask" in "/nfsscratch/Users/ariveradompenciel/work/CRESTfmriprep/fmriprep_wf/single_subject_BETTER120018_wf/func_preproc_task_rest_run_1_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_mask".
200306-13:38:32,23 nipype.workflow INFO:
     [Node] Running "skullstrip_first_mask" ("nipype.interfaces.fsl.maths.ApplyMask"), a CommandLine Interface with command:
fslmaths /nfsscratch/Users/ariveradompenciel/work/CRESTfmriprep/fmriprep_wf/single_subject_BETTER120018_wf/func_preproc_task_rest_run_1_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_pass/ref_image_valid_corrected_brain.nii.gz -mas /nfsscratch/Users/ariveradompenciel/work/CRESTfmriprep/fmriprep_wf/single_subject_BETTER120018_wf/func_preproc_task_rest_run_1_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_dilate/ref_image_valid_corrected_brain_mask_dil.nii.gz /nfsscratch/Users/ariveradompenciel/work/CRESTfmriprep/fmriprep_wf/single_subject_BETTER120018_wf/func_preproc_task_rest_run_1_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_mask/ref_image_valid_corrected_brain_masked.nii.gz
200306-13:38:32,214 nipype.workflow INFO:
     [Node] Finished "fmriprep_wf.single_subject_BETTER120018_wf.func_preproc_task_rest_run_1_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_mask".
200306-13:38:33,511 nipype.workflow INFO:
     [Node] Finished "fmriprep_wf.single_subject_BETTER120018_wf.func_preproc_task_rest_run_2_wf.bold_bold_trans_wf.bold_reference_wf.validate_ref".
200306-13:38:34,20 nipype.workflow INFO:
     [Node] Setting-up "fmriprep_wf.single_subject_BETTER120018_wf.func_preproc_task_rest_run_1_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.unifize" in "/nfsscratch/Users/ariveradompenciel/work/CRESTfmriprep/fmriprep_wf/single_subject_BETTER120018_wf/func_preproc_task_rest_run_1_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/unifize".
200306-13:38:34,40 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 /nfsscratch/Users/ariveradompenciel/work/CRESTfmriprep/fmriprep_wf/single_subject_BETTER120018_wf/func_preproc_task_rest_run_1_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/unifize/ref_image_valid_corrected_brain_masked.nii.gz
200306-13:38:35,264 nipype.workflow INFO:
     [Node] Finished "fmriprep_wf.single_subject_BETTER120018_wf.func_preproc_task_rest_run_1_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.unifize".
200306-13:38:36,22 nipype.workflow INFO:
     [Node] Setting-up "fmriprep_wf.single_subject_BETTER120018_wf.func_preproc_task_rest_run_1_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.fixhdr_unifize" in "/nfsscratch/Users/ariveradompenciel/work/CRESTfmriprep/fmriprep_wf/single_subject_BETTER120018_wf/func_preproc_task_rest_run_1_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/fixhdr_unifize".
200306-13:38:36,38 nipype.workflow INFO:
     [Node] Running "fixhdr_unifize" ("niworkflows.interfaces.utils.CopyXForm")
200306-13:38:37,565 nipype.workflow INFO:
     [Node] Finished "fmriprep_wf.single_subject_BETTER120018_wf.func_preproc_task_rest_run_1_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.fixhdr_unifize".
200306-13:38:38,33 nipype.workflow INFO:
     [Node] Setting-up "fmriprep_wf.single_subject_BETTER120018_wf.func_preproc_task_rest_run_1_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.skullstrip_second_pass" in "/nfsscratch/Users/ariveradompenciel/work/CRESTfmriprep/fmriprep_wf/single_subject_BETTER120018_wf/func_preproc_task_rest_run_1_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_second_pass".
200306-13:38:38,71 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 /nfsscratch/Users/ariveradompenciel/work/CRESTfmriprep/fmriprep_wf/single_subject_BETTER120018_wf/func_preproc_task_rest_run_1_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_second_pass/uni_xform.nii.gz
200306-13:38:41,701 nipype.workflow INFO:
     [Node] Finished "fmriprep_wf.single_subject_BETTER120018_wf.func_preproc_task_rest_run_1_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.skullstrip_second_pass".
200306-13:38:42,58 nipype.workflow INFO:
     [Node] Setting-up "fmriprep_wf.single_subject_BETTER120018_wf.func_preproc_task_rest_run_1_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.fixhdr_skullstrip2" in "/nfsscratch/Users/ariveradompenciel/work/CRESTfmriprep/fmriprep_wf/single_subject_BETTER120018_wf/func_preproc_task_rest_run_1_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/fixhdr_skullstrip2".
200306-13:38:42,75 nipype.workflow INFO:
     [Node] Running "fixhdr_skullstrip2" ("niworkflows.interfaces.utils.CopyXForm")
200306-13:38:42,185 nipype.workflow INFO:
     [Node] Finished "fmriprep_wf.single_subject_BETTER120018_wf.func_preproc_task_rest_run_1_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.fixhdr_skullstrip2".
200306-13:38:44,63 nipype.workflow INFO:
     [Node] Setting-up "fmriprep_wf.single_subject_BETTER120018_wf.func_preproc_task_rest_run_1_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.combine_masks" in "/nfsscratch/Users/ariveradompenciel/work/CRESTfmriprep/fmriprep_wf/single_subject_BETTER120018_wf/func_preproc_task_rest_run_1_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/combine_masks".
200306-13:38:44,79 nipype.workflow INFO:
     [Node] Running "combine_masks" ("nipype.interfaces.fsl.maths.BinaryMaths"), a CommandLine Interface with command:
fslmaths /nfsscratch/Users/ariveradompenciel/work/CRESTfmriprep/fmriprep_wf/single_subject_BETTER120018_wf/func_preproc_task_rest_run_1_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_pass/ref_image_valid_corrected_brain_mask.nii.gz -mul /nfsscratch/Users/ariveradompenciel/work/CRESTfmriprep/fmriprep_wf/single_subject_BETTER120018_wf/func_preproc_task_rest_run_1_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/fixhdr_skullstrip2/uni_xform_mask_xform.nii.gz /nfsscratch/Users/ariveradompenciel/work/CRESTfmriprep/fmriprep_wf/single_subject_BETTER120018_wf/func_preproc_task_rest_run_1_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/combine_masks/ref_image_valid_corrected_brain_mask_maths.nii.gz
200306-13:38:44,290 nipype.workflow INFO:
     [Node] Finished "fmriprep_wf.single_subject_BETTER120018_wf.func_preproc_task_rest_run_1_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.combine_masks".
200306-13:38:46,85 nipype.workflow INFO:
     [Node] Setting-up "fmriprep_wf.single_subject_BETTER120018_wf.func_preproc_task_rest_run_1_wf.bold_confounds_wf.dvars" in "/nfsscratch/Users/ariveradompenciel/work/CRESTfmriprep/fmriprep_wf/single_subject_BETTER120018_wf/func_preproc_task_rest_run_1_wf/bold_confounds_wf/dvars".
200306-13:38:46,89 nipype.workflow INFO:
     [Node] Setting-up "fmriprep_wf.single_subject_BETTER120018_wf.func_preproc_task_rest_run_1_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.apply_mask" in "/nfsscratch/Users/ariveradompenciel/work/CRESTfmriprep/fmriprep_wf/single_subject_BETTER120018_wf/func_preproc_task_rest_run_1_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/apply_mask".
200306-13:38:46,100 nipype.workflow INFO:
     [Node] Running "dvars" ("nipype.algorithms.confounds.ComputeDVARS")
200306-13:38:46,106 nipype.workflow INFO:
     [Node] Running "apply_mask" ("nipype.interfaces.fsl.maths.ApplyMask"), a CommandLine Interface with command:
fslmaths /nfsscratch/Users/ariveradompenciel/work/CRESTfmriprep/fmriprep_wf/single_subject_BETTER120018_wf/func_preproc_task_rest_run_1_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/fixhdr_unifize/uni_xform.nii.gz -mas /nfsscratch/Users/ariveradompenciel/work/CRESTfmriprep/fmriprep_wf/single_subject_BETTER120018_wf/func_preproc_task_rest_run_1_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/combine_masks/ref_image_valid_corrected_brain_mask_maths.nii.gz /nfsscratch/Users/ariveradompenciel/work/CRESTfmriprep/fmriprep_wf/single_subject_BETTER120018_wf/func_preproc_task_rest_run_1_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/apply_mask/uni_xform_masked.nii.gz
200306-13:38:46,309 nipype.workflow INFO:
     [Node] Finished "fmriprep_wf.single_subject_BETTER120018_wf.func_preproc_task_rest_run_1_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.apply_mask".
200306-13:38:57,907 nipype.workflow INFO:
     [Node] Finished "fmriprep_wf.single_subject_BETTER120018_wf.func_preproc_task_rest_run_1_wf.bold_confounds_wf.dvars".
200306-13:43:27,933 nipype.workflow INFO:
     [Node] Finished "fmriprep_wf.single_subject_BETTER120018_wf.anat_preproc_wf.surface_recon_wf.autorecon1".
200306-13:43:29,429 nipype.workflow INFO:
     [Node] Setting-up "fmriprep_wf.single_subject_BETTER120018_wf.func_preproc_task_rest_run_2_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.init_aff" in "/nfsscratch/Users/ariveradompenciel/work/CRESTfmriprep/fmriprep_wf/single_subject_BETTER120018_wf/func_preproc_task_rest_run_2_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/init_aff".
200306-13:43:29,440 nipype.workflow INFO:
     [Node] Setting-up "fmriprep_wf.single_subject_BETTER120018_wf.anat_preproc_wf.surface_recon_wf.skull_strip_extern" in "/nfsscratch/Users/ariveradompenciel/work/CRESTfmriprep/fmriprep_wf/single_subject_BETTER120018_wf/anat_preproc_wf/surface_recon_wf/skull_strip_extern".
200306-13:43:29,468 nipype.workflow INFO:
     [Node] Running "skull_strip_extern" ("fmriprep.interfaces.freesurfer.FSInjectBrainExtracted")
200306-13:43:29,473 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 /niworkflows_data/tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_space-MNI_res-02_brainmask.nii.gz -m Mattes[/niworkflows_data/tpl-fMRIPrep/tpl-fMRIPrep_space-MNI_res-02_boldref.nii.gz,/nfsscratch/Users/ariveradompenciel/work/CRESTfmriprep/fmriprep_wf/single_subject_BETTER120018_wf/func_preproc_task_rest_run_2_wf/bold_bold_trans_wf/bold_reference_wf/validate_ref/ref_image_valid.nii.gz,32,Regular,0.200000] -o initialization.mat -p 0 -s [20.000000,0.120000] -t Affine[0.100000] -v 1
200306-13:43:29,604 nipype.workflow INFO:
     [Node] Setting-up "fmriprep_wf.single_subject_BETTER120018_wf.anat_preproc_wf.surface_recon_wf.fsnative_2_t1_xfm" in "/nfsscratch/Users/ariveradompenciel/work/CRESTfmriprep/fmriprep_wf/single_subject_BETTER120018_wf/anat_preproc_wf/surface_recon_wf/fsnative_2_t1_xfm".
200306-13:43:29,628 nipype.workflow INFO:
     [Node] Running "fsnative_2_t1_xfm" ("fmriprep.interfaces.freesurfer.PatchedRobustRegister"), a CommandLine Interface with command:
mri_robust_register --satit --iscale --lta /nfsscratch/Users/ariveradompenciel/work/CRESTfmriprep/fmriprep_wf/single_subject_BETTER120018_wf/anat_preproc_wf/surface_recon_wf/fsnative_2_t1_xfm/T1_robustreg.lta --mov /mnt/Projects/CREST/derivatives/freesurfer/sub-BETTER120018/mri/T1.mgz --dst /mnt/Projects/CREST/sub-BETTER120018/anat/sub-BETTER120018_T1w.nii.gz
200306-13:43:32,254 nipype.workflow INFO:
     [Node] Finished "fmriprep_wf.single_subject_BETTER120018_wf.func_preproc_task_rest_run_2_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.init_aff".
200306-13:43:32,929 nipype.workflow INFO:
     [Node] Finished "fmriprep_wf.single_subject_BETTER120018_wf.anat_preproc_wf.surface_recon_wf.skull_strip_extern".
200306-13:43:33,493 nipype.workflow INFO:
     [Node] Setting-up "fmriprep_wf.single_subject_BETTER120018_wf.func_preproc_task_rest_run_2_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.norm" in "/nfsscratch/Users/ariveradompenciel/work/CRESTfmriprep/fmriprep_wf/single_subject_BETTER120018_wf/func_preproc_task_rest_run_2_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/norm".
200306-13:43:33,515 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 [ /nfsscratch/Users/ariveradompenciel/work/CRESTfmriprep/fmriprep_wf/single_subject_BETTER120018_wf/func_preproc_task_rest_run_2_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[ /niworkflows_data/tpl-fMRIPrep/tpl-fMRIPrep_space-MNI_res-02_boldref.nii.gz, /nfsscratch/Users/ariveradompenciel/work/CRESTfmriprep/fmriprep_wf/single_subject_BETTER120018_wf/func_preproc_task_rest_run_2_wf/bold_bold_trans_wf/bold_reference_wf/validate_ref/ref_image_valid.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
200306-13:43:34,637 nipype.workflow INFO:
     [Node] Finished "fmriprep_wf.single_subject_BETTER120018_wf.func_preproc_task_rest_run_2_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.norm".
200306-13:43:35,492 nipype.workflow INFO:
     [Node] Setting-up "fmriprep_wf.single_subject_BETTER120018_wf.func_preproc_task_rest_run_2_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.map_brainmask" in "/nfsscratch/Users/ariveradompenciel/work/CRESTfmriprep/fmriprep_wf/single_subject_BETTER120018_wf/func_preproc_task_rest_run_2_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/map_brainmask".
200306-13:43:35,496 nipype.workflow INFO:
     [Node] Setting-up "fmriprep_wf.single_subject_BETTER120018_wf.anat_preproc_wf.surface_recon_wf.autorecon_resume_wf.autorecon2_vol" in "/nfsscratch/Users/ariveradompenciel/work/CRESTfmriprep/fmriprep_wf/single_subject_BETTER120018_wf/anat_preproc_wf/surface_recon_wf/autorecon_resume_wf/autorecon2_vol".
200306-13:43:35,510 nipype.workflow INFO:
     [Node] Running "map_brainmask" ("niworkflows.interfaces.fixes.FixHeaderApplyTransforms"), a CommandLine Interface with command:
antsApplyTransforms --default-value 0 --float 1 --input /niworkflows_data/tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_space-MNI_res-02_brainmask.nii.gz --interpolation MultiLabel --output tpl-MNI152NLin2009cAsym_space-MNI_res-02_brainmask_trans.nii.gz --reference-image /nfsscratch/Users/ariveradompenciel/work/CRESTfmriprep/fmriprep_wf/single_subject_BETTER120018_wf/func_preproc_task_rest_run_2_wf/bold_bold_trans_wf/bold_reference_wf/validate_ref/ref_image_valid.nii.gz --transform [ /nfsscratch/Users/ariveradompenciel/work/CRESTfmriprep/fmriprep_wf/single_subject_BETTER120018_wf/func_preproc_task_rest_run_2_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/norm/transform0GenericAffine.mat, 1 ]
200306-13:43:35,519 nipype.interface INFO:
     resume recon-all : recon-all -autorecon2-volonly -openmp 10 -subjid sub-BETTER120018 -sd /mnt/Projects/CREST/derivatives/freesurfer 
200306-13:43:35,521 nipype.workflow INFO:
     [Node] Running "autorecon2_vol" ("nipype.interfaces.freesurfer.preprocess.ReconAll"), a CommandLine Interface with command:
recon-all -autorecon2-volonly -openmp 10 -subjid sub-BETTER120018 -sd /mnt/Projects/CREST/derivatives/freesurfer 
200306-13:43:35,528 nipype.interface INFO:
     resume recon-all : recon-all -autorecon2-volonly -openmp 10 -subjid sub-BETTER120018 -sd /mnt/Projects/CREST/derivatives/freesurfer 
200306-13:43:38,64 nipype.workflow INFO:
     [Node] Finished "fmriprep_wf.single_subject_BETTER120018_wf.func_preproc_task_rest_run_2_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.map_brainmask".
200306-13:43:39,500 nipype.workflow INFO:
     [Node] Setting-up "fmriprep_wf.single_subject_BETTER120018_wf.func_preproc_task_rest_run_2_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.pre_mask_dilate" in "/nfsscratch/Users/ariveradompenciel/work/CRESTfmriprep/fmriprep_wf/single_subject_BETTER120018_wf/func_preproc_task_rest_run_2_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/pre_mask_dilate".
200306-13:43:39,517 nipype.workflow INFO:
     [Node] Running "pre_mask_dilate" ("nipype.interfaces.fsl.maths.DilateImage"), a CommandLine Interface with command:
fslmaths -dt char /nfsscratch/Users/ariveradompenciel/work/CRESTfmriprep/fmriprep_wf/single_subject_BETTER120018_wf/func_preproc_task_rest_run_2_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/map_brainmask/tpl-MNI152NLin2009cAsym_space-MNI_res-02_brainmask_trans.nii.gz -kernel sphere 3.0000 -dilF /nfsscratch/Users/ariveradompenciel/work/CRESTfmriprep/fmriprep_wf/single_subject_BETTER120018_wf/func_preproc_task_rest_run_2_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/pre_mask_dilate/tpl-MNI152NLin2009cAsym_space-MNI_res-02_brainmask_trans_dil.nii.gz
200306-13:43:39,747 nipype.workflow INFO:
     [Node] Finished "fmriprep_wf.single_subject_BETTER120018_wf.func_preproc_task_rest_run_2_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.pre_mask_dilate".
200306-13:43:41,488 nipype.interface WARNING:
     q-forms of reference and mask are substantially different
200306-13:43:43,468 nipype.workflow INFO:
     [Node] Setting-up "fmriprep_wf.single_subject_BETTER120018_wf.func_preproc_task_rest_run_2_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.n4_correct" in "/nfsscratch/Users/ariveradompenciel/work/CRESTfmriprep/fmriprep_wf/single_subject_BETTER120018_wf/func_preproc_task_rest_run_2_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/n4_correct".
200306-13:43:43,487 nipype.workflow INFO:
     [Node] Running "n4_correct" ("nipype.interfaces.ants.segmentation.N4BiasFieldCorrection"), a CommandLine Interface with command:
N4BiasFieldCorrection -d 3 --input-image /nfsscratch/Users/ariveradompenciel/work/CRESTfmriprep/fmriprep_wf/single_subject_BETTER120018_wf/func_preproc_task_rest_run_2_wf/bold_bold_trans_wf/bold_reference_wf/validate_ref/ref_image_valid.nii.gz --mask-image /nfsscratch/Users/ariveradompenciel/work/CRESTfmriprep/fmriprep_wf/single_subject_BETTER120018_wf/func_preproc_task_rest_run_2_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/check_hdr/tpl-MNI152NLin2009cAsym_space-MNI_res-02_brainmask_trans_dil_hdr.nii.gz --output ref_image_valid_corrected.nii.gz
200306-13:43:48,43 nipype.workflow INFO:
     [Node] Finished "fmriprep_wf.single_subject_BETTER120018_wf.func_preproc_task_rest_run_2_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.n4_correct".
200306-13:43:49,491 nipype.workflow INFO:
     [Node] Setting-up "fmriprep_wf.single_subject_BETTER120018_wf.func_preproc_task_rest_run_2_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_pass" in "/nfsscratch/Users/ariveradompenciel/work/CRESTfmriprep/fmriprep_wf/single_subject_BETTER120018_wf/func_preproc_task_rest_run_2_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_pass".
200306-13:43:49,509 nipype.workflow INFO:
     [Node] Running "skullstrip_first_pass" ("nipype.interfaces.fsl.preprocess.BET"), a CommandLine Interface with command:
bet /nfsscratch/Users/ariveradompenciel/work/CRESTfmriprep/fmriprep_wf/single_subject_BETTER120018_wf/func_preproc_task_rest_run_2_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/n4_correct/ref_image_valid_corrected.nii.gz /nfsscratch/Users/ariveradompenciel/work/CRESTfmriprep/fmriprep_wf/single_subject_BETTER120018_wf/func_preproc_task_rest_run_2_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_pass/ref_image_valid_corrected_brain.nii.gz -f 0.20 -m
200306-13:44:06,806 nipype.workflow INFO:
     [Node] Finished "fmriprep_wf.single_subject_BETTER120018_wf.func_preproc_task_rest_run_2_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_pass".
200306-13:44:07,588 nipype.workflow INFO:
     [Node] Setting-up "fmriprep_wf.single_subject_BETTER120018_wf.func_preproc_task_rest_run_2_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_dilate" in "/nfsscratch/Users/ariveradompenciel/work/CRESTfmriprep/fmriprep_wf/single_subject_BETTER120018_wf/func_preproc_task_rest_run_2_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_dilate".
200306-13:44:07,612 nipype.workflow INFO:
     [Node] Running "skullstrip_first_dilate" ("nipype.interfaces.fsl.maths.DilateImage"), a CommandLine Interface with command:
fslmaths -dt char /nfsscratch/Users/ariveradompenciel/work/CRESTfmriprep/fmriprep_wf/single_subject_BETTER120018_wf/func_preproc_task_rest_run_2_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_pass/ref_image_valid_corrected_brain_mask.nii.gz -kernel sphere 6.0000 -dilF /nfsscratch/Users/ariveradompenciel/work/CRESTfmriprep/fmriprep_wf/single_subject_BETTER120018_wf/func_preproc_task_rest_run_2_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_dilate/ref_image_valid_corrected_brain_mask_dil.nii.gz
200306-13:44:08,54 nipype.workflow INFO:
     [Node] Finished "fmriprep_wf.single_subject_BETTER120018_wf.func_preproc_task_rest_run_2_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_dilate".
200306-13:44:09,602 nipype.workflow INFO:
     [Node] Setting-up "fmriprep_wf.single_subject_BETTER120018_wf.func_preproc_task_rest_run_2_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_mask" in "/nfsscratch/Users/ariveradompenciel/work/CRESTfmriprep/fmriprep_wf/single_subject_BETTER120018_wf/func_preproc_task_rest_run_2_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_mask".
200306-13:44:09,617 nipype.workflow INFO:
     [Node] Running "skullstrip_first_mask" ("nipype.interfaces.fsl.maths.ApplyMask"), a CommandLine Interface with command:
fslmaths /nfsscratch/Users/ariveradompenciel/work/CRESTfmriprep/fmriprep_wf/single_subject_BETTER120018_wf/func_preproc_task_rest_run_2_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_pass/ref_image_valid_corrected_brain.nii.gz -mas /nfsscratch/Users/ariveradompenciel/work/CRESTfmriprep/fmriprep_wf/single_subject_BETTER120018_wf/func_preproc_task_rest_run_2_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_dilate/ref_image_valid_corrected_brain_mask_dil.nii.gz /nfsscratch/Users/ariveradompenciel/work/CRESTfmriprep/fmriprep_wf/single_subject_BETTER120018_wf/func_preproc_task_rest_run_2_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_mask/ref_image_valid_corrected_brain_masked.nii.gz
200306-13:44:09,861 nipype.workflow INFO:
     [Node] Finished "fmriprep_wf.single_subject_BETTER120018_wf.func_preproc_task_rest_run_2_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_mask".
200306-13:44:11,607 nipype.workflow INFO:
     [Node] Setting-up "fmriprep_wf.single_subject_BETTER120018_wf.func_preproc_task_rest_run_2_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.unifize" in "/nfsscratch/Users/ariveradompenciel/work/CRESTfmriprep/fmriprep_wf/single_subject_BETTER120018_wf/func_preproc_task_rest_run_2_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/unifize".
200306-13:44:11,632 nipype.workflow INFO:
     [Node] Running "unifize" ("nipype.interfaces.afni.utils.Unifize"), a CommandLine Interface with command:
3dUnifize -clfrac 0.2 -rbt 18.3 65.0 90.0 -prefix uni.nii.gz -T2 -input /nfsscratch/Users/ariveradompenciel/work/CRESTfmriprep/fmriprep_wf/single_subject_BETTER120018_wf/func_preproc_task_rest_run_2_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/unifize/ref_image_valid_corrected_brain_masked.nii.gz
200306-13:44:12,985 nipype.workflow INFO:
     [Node] Finished "fmriprep_wf.single_subject_BETTER120018_wf.func_preproc_task_rest_run_2_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.unifize".
200306-13:44:13,617 nipype.workflow INFO:
     [Node] Setting-up "fmriprep_wf.single_subject_BETTER120018_wf.func_preproc_task_rest_run_2_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.fixhdr_unifize" in "/nfsscratch/Users/ariveradompenciel/work/CRESTfmriprep/fmriprep_wf/single_subject_BETTER120018_wf/func_preproc_task_rest_run_2_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/fixhdr_unifize".
200306-13:44:13,632 nipype.workflow INFO:
     [Node] Running "fixhdr_unifize" ("niworkflows.interfaces.utils.CopyXForm")
200306-13:44:13,863 nipype.workflow INFO:
     [Node] Finished "fmriprep_wf.single_subject_BETTER120018_wf.func_preproc_task_rest_run_2_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.fixhdr_unifize".
200306-13:44:15,625 nipype.workflow INFO:
     [Node] Setting-up "fmriprep_wf.single_subject_BETTER120018_wf.func_preproc_task_rest_run_2_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.skullstrip_second_pass" in "/nfsscratch/Users/ariveradompenciel/work/CRESTfmriprep/fmriprep_wf/single_subject_BETTER120018_wf/func_preproc_task_rest_run_2_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_second_pass".
200306-13:44:15,645 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 /nfsscratch/Users/ariveradompenciel/work/CRESTfmriprep/fmriprep_wf/single_subject_BETTER120018_wf/func_preproc_task_rest_run_2_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_second_pass/uni_xform.nii.gz
200306-13:44:18,547 nipype.workflow INFO:
     [Node] Finished "fmriprep_wf.single_subject_BETTER120018_wf.func_preproc_task_rest_run_2_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.skullstrip_second_pass".
200306-13:44:19,645 nipype.workflow INFO:
     [Node] Setting-up "fmriprep_wf.single_subject_BETTER120018_wf.func_preproc_task_rest_run_2_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.fixhdr_skullstrip2" in "/nfsscratch/Users/ariveradompenciel/work/CRESTfmriprep/fmriprep_wf/single_subject_BETTER120018_wf/func_preproc_task_rest_run_2_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/fixhdr_skullstrip2".
200306-13:44:19,659 nipype.workflow INFO:
     [Node] Running "fixhdr_skullstrip2" ("niworkflows.interfaces.utils.CopyXForm")
200306-13:44:22,452 nipype.workflow INFO:
     [Node] Finished "fmriprep_wf.single_subject_BETTER120018_wf.func_preproc_task_rest_run_2_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.fixhdr_skullstrip2".
200306-13:44:23,667 nipype.workflow INFO:
     [Node] Setting-up "fmriprep_wf.single_subject_BETTER120018_wf.func_preproc_task_rest_run_2_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.combine_masks" in "/nfsscratch/Users/ariveradompenciel/work/CRESTfmriprep/fmriprep_wf/single_subject_BETTER120018_wf/func_preproc_task_rest_run_2_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/combine_masks".
200306-13:44:23,696 nipype.workflow INFO:
     [Node] Running "combine_masks" ("nipype.interfaces.fsl.maths.BinaryMaths"), a CommandLine Interface with command:
fslmaths /nfsscratch/Users/ariveradompenciel/work/CRESTfmriprep/fmriprep_wf/single_subject_BETTER120018_wf/func_preproc_task_rest_run_2_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_pass/ref_image_valid_corrected_brain_mask.nii.gz -mul /nfsscratch/Users/ariveradompenciel/work/CRESTfmriprep/fmriprep_wf/single_subject_BETTER120018_wf/func_preproc_task_rest_run_2_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/fixhdr_skullstrip2/uni_xform_mask_xform.nii.gz /nfsscratch/Users/ariveradompenciel/work/CRESTfmriprep/fmriprep_wf/single_subject_BETTER120018_wf/func_preproc_task_rest_run_2_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/combine_masks/ref_image_valid_corrected_brain_mask_maths.nii.gz
200306-13:44:23,877 nipype.workflow INFO:
     [Node] Finished "fmriprep_wf.single_subject_BETTER120018_wf.func_preproc_task_rest_run_2_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.combine_masks".
200306-13:44:25,680 nipype.workflow INFO:
     [Node] Setting-up "fmriprep_wf.single_subject_BETTER120018_wf.func_preproc_task_rest_run_2_wf.bold_confounds_wf.dvars" in "/nfsscratch/Users/ariveradompenciel/work/CRESTfmriprep/fmriprep_wf/single_subject_BETTER120018_wf/func_preproc_task_rest_run_2_wf/bold_confounds_wf/dvars".
200306-13:44:25,681 nipype.workflow INFO:
     [Node] Setting-up "fmriprep_wf.single_subject_BETTER120018_wf.func_preproc_task_rest_run_2_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.apply_mask" in "/nfsscratch/Users/ariveradompenciel/work/CRESTfmriprep/fmriprep_wf/single_subject_BETTER120018_wf/func_preproc_task_rest_run_2_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/apply_mask".
200306-13:44:25,695 nipype.workflow INFO:
     [Node] Running "dvars" ("nipype.algorithms.confounds.ComputeDVARS")
200306-13:44:25,697 nipype.workflow INFO:
     [Node] Running "apply_mask" ("nipype.interfaces.fsl.maths.ApplyMask"), a CommandLine Interface with command:
fslmaths /nfsscratch/Users/ariveradompenciel/work/CRESTfmriprep/fmriprep_wf/single_subject_BETTER120018_wf/func_preproc_task_rest_run_2_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/fixhdr_unifize/uni_xform.nii.gz -mas /nfsscratch/Users/ariveradompenciel/work/CRESTfmriprep/fmriprep_wf/single_subject_BETTER120018_wf/func_preproc_task_rest_run_2_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/combine_masks/ref_image_valid_corrected_brain_mask_maths.nii.gz /nfsscratch/Users/ariveradompenciel/work/CRESTfmriprep/fmriprep_wf/single_subject_BETTER120018_wf/func_preproc_task_rest_run_2_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/apply_mask/uni_xform_masked.nii.gz
200306-13:44:25,931 nipype.workflow INFO:
     [Node] Finished "fmriprep_wf.single_subject_BETTER120018_wf.func_preproc_task_rest_run_2_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.apply_mask".
200306-13:44:27,663 nipype.workflow INFO:
     [Node] Finished "fmriprep_wf.single_subject_BETTER120018_wf.func_preproc_task_rest_run_2_wf.bold_confounds_wf.dvars".
200306-13:44:27,916 nipype.workflow INFO:
     [Node] Finished "fmriprep_wf.single_subject_BETTER120018_wf.anat_preproc_wf.surface_recon_wf.fsnative_2_t1_xfm".
200306-13:44:29,993 nipype.workflow INFO:
     [Node] Setting-up "fmriprep_wf.single_subject_BETTER120018_wf.anat_preproc_wf.surface_recon_wf.t1_2_fsnative_xfm" in "/nfsscratch/Users/ariveradompenciel/work/CRESTfmriprep/fmriprep_wf/single_subject_BETTER120018_wf/anat_preproc_wf/surface_recon_wf/t1_2_fsnative_xfm".
200306-13:44:30,27 nipype.workflow INFO:
     [Node] Running "t1_2_fsnative_xfm" ("fmriprep.interfaces.freesurfer.PatchedLTAConvert"), a CommandLine Interface with command:
lta_convert --inlta /nfsscratch/Users/ariveradompenciel/work/CRESTfmriprep/fmriprep_wf/single_subject_BETTER120018_wf/anat_preproc_wf/surface_recon_wf/fsnative_2_t1_xfm/T1_robustreg.lta --invert --outlta /nfsscratch/Users/ariveradompenciel/work/CRESTfmriprep/fmriprep_wf/single_subject_BETTER120018_wf/anat_preproc_wf/surface_recon_wf/t1_2_fsnative_xfm/out.lta
200306-13:44:30,221 nipype.workflow INFO:
     [Node] Finished "fmriprep_wf.single_subject_BETTER120018_wf.anat_preproc_wf.surface_recon_wf.t1_2_fsnative_xfm".
200306-13:44:31,702 nipype.workflow INFO:
     [Node] Setting-up "fmriprep_wf.single_subject_BETTER120018_wf.anat_preproc_wf.anat_derivatives_wf.lta_2_itk" in "/nfsscratch/Users/ariveradompenciel/work/CRESTfmriprep/fmriprep_wf/single_subject_BETTER120018_wf/anat_preproc_wf/anat_derivatives_wf/lta_2_itk".
200306-13:44:31,720 nipype.workflow INFO:
     [Node] Running "lta_2_itk" ("fmriprep.interfaces.freesurfer.PatchedLTAConvert"), a CommandLine Interface with command:
lta_convert --inlta /nfsscratch/Users/ariveradompenciel/work/CRESTfmriprep/fmriprep_wf/single_subject_BETTER120018_wf/anat_preproc_wf/surface_recon_wf/t1_2_fsnative_xfm/out.lta --outitk /nfsscratch/Users/ariveradompenciel/work/CRESTfmriprep/fmriprep_wf/single_subject_BETTER120018_wf/anat_preproc_wf/anat_derivatives_wf/lta_2_itk/out.txt
200306-13:44:31,876 nipype.workflow INFO:
     [Node] Finished "fmriprep_wf.single_subject_BETTER120018_wf.anat_preproc_wf.anat_derivatives_wf.lta_2_itk".

Error (stderr file)

/usr/local/miniconda/lib/python3.6/site-packages/bids/grabbids/__init__.py:6: FutureWarning: grabbids has been renamed to layout in version 0.6.5, and will be removed in version 0.8
  warnings.warn("grabbids has been renamed to layout in version 0.6.5, and will be removed in version 0.8", FutureWarning)
[WARNING] This document format requires a nonempty <title> element.
  Please specify either 'title' or 'pagetitle' in the metadata.
  Falling back to 'CITATION'
/usr/local/miniconda/lib/python3.6/site-packages/bids/grabbids/__init__.py:6: FutureWarning: grabbids has been renamed to layout in version 0.6.5, and will be removed in version 0.8
  warnings.warn("grabbids has been renamed to layout in version 0.6.5, and will be removed in version 0.8", FutureWarning)
/usr/local/miniconda/lib/python3.6/site-packages/bids/layout/bids_layout.py:116: UserWarning: 'dataset_description.json' file is missing from project root. You may want to set the root path to a valid BIDS project.
  warnings.warn("'dataset_description.json' file is missing from "

Potential Solution

deleted the following directories: /nfsscratch/Users/ariveradompenciel/work/CRESTfmriprep/fmriprep_wf/single_subject_BETTER120018_wf/anat_preproc_wf/surface_recon_wf/segs_to_native_aseg

/Shared/vosslabhpc/Projects/CREST/derivatives/freesurfer/sub-BETTER120018

ariveradompenciel commented 4 years ago

Exit status of 1 remains.

jdkent commented 4 years ago

I don't see anything that gives a good clue... I would delete the entire anatomical preprocessing working directory and the freesurfer directory again (if it exists):

rm -rf /nfsscratch/Users/ariveradompenciel/work/CRESTfmriprep/fmriprep_wf/single_subject_BETTER120018_wf
rm -rf /Shared/vosslabhpc/Projects/CREST/derivatives/freesurfer/sub-BETTER120018