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1: [WARN] The recommended file /README is missing. See Section 03 (Modality agnostic files) of the BIDS specification. (code: 101 - README_FILE_MISSING)
 Please visit https://neurostars.org/search?q=README_FILE_MISSING for existing conversations about this issue.
Summary: Available Tasks: Available Modalities:
15 Files, 425.93MB Stroop T1w
1 - Subject T2w
1 - Session bold
events
sbref
fieldmap
 If you have any questions, please post on https://neurostars.org/tags/bids.
Making sure the input data is BIDS compliant (warnings can be ignored in most cases).
200322-12:10:37,507 nipype.workflow IMPORTANT:
Running fMRIPREP version 1.5.9:
* BIDS dataset path: /data.
* Participant list: ['01'].
* Run identifier: 20200322-121037_f2dd7abd-e72c-4006-ae01-63c8aa33efb0.
200322-12:10:38,19 nipype.utils INFO:
No new version available.
200322-12:10:41,328 nipype.workflow IMPORTANT:
Creating bold processing workflow for "/data/sub-01/ses-01/func/sub-01_ses-01_task-Stroop_run-01_bold.nii.gz" (0.37 GB / 540 TRs). Memory resampled/largemem=1.49/3.50 GB.
200322-12:10:41,359 nipype.workflow IMPORTANT:
Using single-band reference file sub-01_ses-01_task-Stroop_run-01_sbref.nii.gz
200322-12:10:44,244 nipype.workflow IMPORTANT:
Slice-timing correction will be included.
200322-12:10:45,871 nipype.workflow IMPORTANT:
Creating BOLD surface-sampling workflow.
200322-12:10:51,576 nipype.workflow IMPORTANT:
Works derived from this fMRIPrep execution should include the following boilerplate:
Results included in this manuscript come from preprocessing
performed using *fMRIPrep* 1.5.9
(@fmriprep1; @fmriprep2; RRID:SCR_016216),
which is based on *Nipype* 1.4.2
(@nipype1; @nipype2; RRID:SCR_002502).
Anatomical data preprocessing
: The T1-weighted (T1w) image was corrected for intensity non-uniformity (INU)
with `N4BiasFieldCorrection` [@n4], distributed with ANTs 2.2.0 [@ants, RRID:SCR_004757], and used as T1w-reference throughout the workflow.
The T1w-reference was then skull-stripped with a *Nipype* implementation of
the `antsBrainExtraction.sh` workflow (from ANTs), using OASIS30ANTs
as target template.
Brain tissue segmentation of cerebrospinal fluid (CSF),
white-matter (WM) and gray-matter (GM) was performed on
the brain-extracted T1w using `fast` [FSL 5.0.9, RRID:SCR_002823,
@fsl_fast].
Brain surfaces were reconstructed using `recon-all` [FreeSurfer 6.0.1,
RRID:SCR_001847, @fs_reconall], and the brain mask estimated
previously was refined with a custom variation of the method to reconcile
ANTs-derived and FreeSurfer-derived segmentations of the cortical
gray-matter of Mindboggle [RRID:SCR_002438, @mindboggle].
Volume-based spatial normalization to one standard space (MNI152NLin2009cAsym) was performed through
nonlinear registration with `antsRegistration` (ANTs 2.2.0),
using brain-extracted versions of both T1w reference and the T1w template.
The following template was selected for spatial normalization:
*ICBM 152 Nonlinear Asymmetrical template version 2009c* [@mni152nlin2009casym, RRID:SCR_008796; TemplateFlow ID: MNI152NLin2009cAsym].
Functional data preprocessing
: For each of the 1 BOLD runs found per subject (across all
tasks and sessions), the following preprocessing was performed.
First, a reference volume and its skull-stripped version were generated
using a custom methodology of *fMRIPrep*.
A B0-nonuniformity map (or *fieldmap*) was estimated based on two (or more)
echo-planar imaging (EPI) references with opposing phase-encoding
directions, with `3dQwarp` @afni (AFNI 20160207).
Based on the estimated susceptibility distortion, a corrected
EPI (echo-planar imaging) reference was calculated for a more
accurate co-registration with the anatomical reference.
The BOLD reference was then co-registered to the T1w reference using
`bbregister` (FreeSurfer) which implements boundary-based registration [@bbr].
Co-registration was configured with six degrees of freedom.
Head-motion parameters with respect to the BOLD reference
(transformation matrices, and six corresponding rotation and translation
parameters) are estimated before any spatiotemporal filtering using
`mcflirt` [FSL 5.0.9, @mcflirt].
BOLD runs were slice-time corrected using `3dTshift` from
AFNI 20160207 [@afni, RRID:SCR_005927].
The BOLD time-series, were resampled to surfaces on the following
spaces: *fsaverage5*.
*Grayordinates* files [@hcppipelines], which combine surface-sampled
data and volume-sampled data, were also generated.
The BOLD time-series (including slice-timing correction when applied)
were resampled onto their original, native space by applying
a single, composite transform to correct for head-motion and
susceptibility distortions.
These resampled BOLD time-series will be referred to as *preprocessed
BOLD in original space*, or just *preprocessed BOLD*.
The BOLD time-series were resampled into standard space,
generating a *preprocessed BOLD run in ['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).
tCompCor components are then calculated from the top 5% variable
voxels within a mask covering the subcortical regions.
This subcortical mask is obtained by heavily eroding the brain mask,
which ensures it does not include cortical GM regions.
For aCompCor, components are calculated within the intersection of
the aforementioned mask and the union of CSF and WM masks calculated
in T1w space, after their projection to the native space of each
functional run (using the inverse BOLD-to-T1w transformation). Components
are also calculated separately within the WM and CSF masks.
For each CompCor decomposition, the *k* components with the largest singular
values are retained, such that the retained components' time series are
sufficient to explain 50 percent of variance across the nuisance mask (CSF,
WM, combined, or temporal). The remaining components are dropped from
consideration.
The head-motion estimates calculated in the correction step were also
placed within the corresponding confounds file.
The confound time series derived from head motion estimates and global
signals were expanded with the inclusion of temporal derivatives and
quadratic terms for each [@confounds_satterthwaite_2013].
Frames that exceeded a threshold of 0.5 mm FD or 1.5 standardised DVARS
were annotated as motion outliers.
All resamplings can be performed with *a single interpolation
step* by composing all the pertinent transformations (i.e. head-motion
transform matrices, susceptibility distortion correction when available,
and co-registrations to anatomical and output spaces).
Gridded (volumetric) resamplings were performed using `antsApplyTransforms` (ANTs),
configured with Lanczos interpolation to minimize the smoothing
effects of other kernels [@lanczos].
Non-gridded (surface) resamplings were performed using `mri_vol2surf`
(FreeSurfer).
Many internal operations of *fMRIPrep* use
*Nilearn* 0.6.1 [@nilearn, RRID:SCR_001362],
mostly within the functional processing workflow.
For more details of the pipeline, see [the section corresponding
to workflows in *fMRIPrep*'s documentation](https://fmriprep.readthedocs.io/en/latest/workflows.html "FMRIPrep's documentation").
### Copyright Waiver
The above boilerplate text was automatically generated by fMRIPrep
with the express intention that users should copy and paste this
text into their manuscripts *unchanged*.
It is released under the [CC0](https://creativecommons.org/publicdomain/zero/1.0/) license.
### References
200322-12:11:02,323 nipype.workflow INFO:
[Node] Setting-up "fmriprep_wf.single_subject_01_wf.func_preproc_ses_01_task_Stroop_run_01_wf.func_derivatives_wf.raw_sources" in "/gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/func_derivatives_wf/raw_sources".
200322-12:11:02,323 nipype.workflow INFO:
[Node] Setting-up "fmriprep_wf.single_subject_01_wf.func_preproc_ses_01_task_Stroop_run_01_wf.sdc_estimate_wf.pepolar_unwarp_wf.prepare_epi_wf.split" in "/gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/sdc_estimate_wf/pepolar_unwarp_wf/prepare_epi_wf/split".
200322-12:11:02,329 nipype.workflow INFO:
[Node] Running "raw_sources" ("nipype.interfaces.utility.wrappers.Function")
200322-12:11:02,334 nipype.workflow INFO:
[Node] Finished "fmriprep_wf.single_subject_01_wf.func_preproc_ses_01_task_Stroop_run_01_wf.func_derivatives_wf.raw_sources".
200322-12:11:02,342 nipype.workflow INFO:
[Node] Running "split" ("nipype.interfaces.utility.wrappers.Function")
200322-12:11:02,944 nipype.workflow INFO:
[Node] Finished "fmriprep_wf.single_subject_01_wf.func_preproc_ses_01_task_Stroop_run_01_wf.sdc_estimate_wf.pepolar_unwarp_wf.prepare_epi_wf.split".
200322-12:11:04,176 nipype.workflow INFO:
[Node] Setting-up "fmriprep_wf.single_subject_01_wf.func_preproc_ses_01_task_Stroop_run_01_wf.bold_reference_wf.validate" in "/gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/bold_reference_wf/validate".
200322-12:11:04,178 nipype.workflow INFO:
[Node] Running "validate" ("niworkflows.interfaces.images.ValidateImage")
200322-12:11:04,180 nipype.workflow INFO:
[Node] Setting-up "fmriprep_wf.single_subject_01_wf.func_preproc_ses_01_task_Stroop_run_01_wf.val_sbref" in "/gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/val_sbref".
200322-12:11:04,182 nipype.workflow INFO:
[Node] Running "val_sbref" ("niworkflows.interfaces.images.ValidateImage")
200322-12:11:04,456 nipype.workflow INFO:
[Node] Finished "fmriprep_wf.single_subject_01_wf.func_preproc_ses_01_task_Stroop_run_01_wf.bold_reference_wf.validate".
200322-12:11:04,458 nipype.workflow INFO:
[Node] Finished "fmriprep_wf.single_subject_01_wf.func_preproc_ses_01_task_Stroop_run_01_wf.val_sbref".
200322-12:11:05,883 nipype.workflow INFO:
[Node] Setting-up "fmriprep_wf.single_subject_01_wf.func_preproc_ses_01_task_Stroop_run_01_wf.bold_reference_wf.gen_ref" in "/gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/bold_reference_wf/gen_ref".
200322-12:11:05,889 nipype.workflow INFO:
[Node] Setting-up "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.brain_extraction_wf.lap_tmpl" in "/gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/brain_extraction_wf/lap_tmpl".
200322-12:11:05,893 nipype.workflow INFO:
[Node] Running "lap_tmpl" ("niworkflows.interfaces.ants.ImageMath"), a CommandLine Interface with command:
ImageMath 3 tpl-OASIS30ANTs_res-01_T1w_maths.nii.gz Laplacian /home/jac18015/.cache/templateflow/tpl-OASIS30ANTs/tpl-OASIS30ANTs_res-01_T1w.nii.gz 1.5 1
200322-12:11:05,894 nipype.workflow INFO:
[Node] Running "gen_ref" ("niworkflows.interfaces.registration.EstimateReferenceImage")
200322-12:11:06,602 nipype.workflow INFO:
[Node] Setting-up "fmriprep_wf.single_subject_01_wf.func_preproc_ses_01_task_Stroop_run_01_wf.sdc_estimate_wf.pepolar_unwarp_wf.prepare_epi_wf.merge_op" in "/gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/sdc_estimate_wf/pepolar_unwarp_wf/prepare_epi_wf/merge_op".
200322-12:11:06,612 nipype.workflow INFO:
[Node] Running "merge_op" ("niworkflows.interfaces.freesurfer.StructuralReference"), a CommandLine Interface with command:
mri_robust_template --satit --fixtp --mov /gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/sdc_estimate_wf/pepolar_unwarp_wf/prepare_epi_wf/split/dir-j_tstep-001_pe-000.nii.gz /gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/sdc_estimate_wf/pepolar_unwarp_wf/prepare_epi_wf/split/dir-j_tstep-001_pe-001.nii.gz /gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/sdc_estimate_wf/pepolar_unwarp_wf/prepare_epi_wf/split/dir-j_tstep-001_pe-002.nii.gz --inittp 1 --iscale --noit --template template.nii.gz --subsample 200
200322-12:11:06,633 nipype.workflow INFO:
[Node] Setting-up "fmriprep_wf.single_subject_01_wf.func_preproc_ses_01_task_Stroop_run_01_wf.sdc_estimate_wf.pepolar_unwarp_wf.prepare_epi_wf.merge_ma" in "/gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/sdc_estimate_wf/pepolar_unwarp_wf/prepare_epi_wf/merge_ma".
200322-12:11:06,640 nipype.workflow INFO:
[Node] Running "merge_ma" ("niworkflows.interfaces.freesurfer.StructuralReference"), a CommandLine Interface with command:
mri_robust_template --satit --fixtp --mov /gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/sdc_estimate_wf/pepolar_unwarp_wf/prepare_epi_wf/split/dir-j-_tstep-000_pe-000.nii.gz /gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/sdc_estimate_wf/pepolar_unwarp_wf/prepare_epi_wf/split/dir-j-_tstep-000_pe-001.nii.gz /gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/sdc_estimate_wf/pepolar_unwarp_wf/prepare_epi_wf/split/dir-j-_tstep-000_pe-002.nii.gz --inittp 1 --iscale --noit --template template.nii.gz --subsample 200
200322-12:11:06,681 nipype.workflow INFO:
[Node] Finished "fmriprep_wf.single_subject_01_wf.func_preproc_ses_01_task_Stroop_run_01_wf.bold_reference_wf.gen_ref".
200322-12:11:07,757 nipype.workflow INFO:
[Node] Setting-up "fmriprep_wf.single_subject_01_wf.func_preproc_ses_01_task_Stroop_run_01_wf.bold_hmc_wf.mcflirt" in "/gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/bold_hmc_wf/mcflirt".
200322-12:11:07,768 nipype.workflow INFO:
[Node] Running "mcflirt" ("nipype.interfaces.fsl.preprocess.MCFLIRT"), a CommandLine Interface with command:
mcflirt -in /data/sub-01/ses-01/func/sub-01_ses-01_task-Stroop_run-01_bold.nii.gz -out /gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/bold_hmc_wf/mcflirt/sub-01_ses-01_task-Stroop_run-01_bold_mcf.nii.gz -reffile /gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/bold_reference_wf/gen_ref/ref_sbref.nii.gz -mats -plots
200322-12:11:15,856 nipype.workflow INFO:
[Node] Finished "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.brain_extraction_wf.lap_tmpl".
200322-12:11:17,900 nipype.workflow INFO:
[Node] Setting-up "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.brain_extraction_wf.mrg_tmpl" in "/gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/brain_extraction_wf/mrg_tmpl".
200322-12:11:17,911 nipype.workflow INFO:
[Node] Running "mrg_tmpl" ("nipype.interfaces.utility.base.Merge")
200322-12:11:17,914 nipype.workflow INFO:
[Node] Finished "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.brain_extraction_wf.mrg_tmpl".
200322-12:11:18,349 nipype.workflow INFO:
[Node] Finished "fmriprep_wf.single_subject_01_wf.func_preproc_ses_01_task_Stroop_run_01_wf.sdc_estimate_wf.pepolar_unwarp_wf.prepare_epi_wf.merge_ma".
200322-12:11:19,769 nipype.workflow INFO:
[Node] Setting-up "fmriprep_wf.single_subject_01_wf.func_preproc_ses_01_task_Stroop_run_01_wf.bold_stc_wf.slice_timing_correction" in "/gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/bold_stc_wf/slice_timing_correction".
200322-12:11:19,777 nipype.workflow INFO:
[Node] Setting-up "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.brain_extraction_wf.res_tmpl" in "/gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/brain_extraction_wf/res_tmpl".
200322-12:11:19,800 nipype.workflow INFO:
[Node] Running "res_tmpl" ("niworkflows.interfaces.ants.ResampleImageBySpacing"), a CommandLine Interface with command:
ResampleImageBySpacing 3 /home/jac18015/.cache/templateflow/tpl-OASIS30ANTs/tpl-OASIS30ANTs_res-01_T1w.nii.gz tpl-OASIS30ANTs_res-01_T1w_resampled.nii.gz 4 4 4 1
200322-12:11:19,804 nipype.workflow INFO:
[Node] Finished "fmriprep_wf.single_subject_01_wf.func_preproc_ses_01_task_Stroop_run_01_wf.sdc_estimate_wf.pepolar_unwarp_wf.prepare_epi_wf.merge_op".
200322-12:11:19,805 nipype.workflow INFO:
[Node] Running "slice_timing_correction" ("nipype.interfaces.afni.preprocess.TShift"), a CommandLine Interface with command:
3dTshift -ignore 1 -prefix sub-01_ses-01_task-Stroop_run-01_bold_tshift.nii.gz -tpattern @slice_timing.1D -TR 1.2s /gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/bold_stc_wf/slice_timing_correction/sub-01_ses-01_task-Stroop_run-01_bold.nii.gz
200322-12:11:21,811 nipype.workflow INFO:
[Node] Finished "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.brain_extraction_wf.res_tmpl".
200322-12:11:22,21 nipype.workflow INFO:
[Node] Setting-up "fmriprep_wf.single_subject_01_wf.bidssrc" in "/gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/bidssrc".
200322-12:11:22,28 nipype.workflow INFO:
[Node] Running "bidssrc" ("niworkflows.interfaces.bids.BIDSDataGrabber")
200322-12:11:22,29 nipype.interface WARNING:
No "flair" images found for sub-<undefined>
200322-12:11:22,29 nipype.interface WARNING:
No "roi" images found for sub-<undefined>
200322-12:11:22,32 nipype.workflow INFO:
[Node] Finished "fmriprep_wf.single_subject_01_wf.bidssrc".
200322-12:11:23,778 nipype.workflow INFO:
[Node] Setting-up "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.anat_template_wf.t1w_ref_dimensions" in "/gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/anat_template_wf/t1w_ref_dimensions".
200322-12:11:23,909 nipype.workflow INFO:
[Node] Setting-up "fmriprep_wf.single_subject_01_wf.bids_info" in "/gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/bids_info".
200322-12:11:23,912 nipype.workflow INFO:
[Node] Running "bids_info" ("niworkflows.interfaces.bids.BIDSInfo")
200322-12:11:23,961 nipype.workflow INFO:
[Node] Running "t1w_ref_dimensions" ("niworkflows.interfaces.images.TemplateDimensions")
200322-12:11:24,69 nipype.workflow INFO:
[Node] Finished "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.anat_template_wf.t1w_ref_dimensions".
200322-12:11:24,106 nipype.workflow INFO:
[Node] Finished "fmriprep_wf.single_subject_01_wf.bids_info".
200322-12:11:25,767 nipype.workflow INFO:
[Node] Setting-up "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.anat_derivatives_wf.raw_sources" in "/gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/anat_derivatives_wf/raw_sources".
200322-12:11:25,768 nipype.workflow INFO:
[Node] Setting-up "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.anat_derivatives_wf.t1w_name" in "/gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/anat_derivatives_wf/t1w_name".
200322-12:11:25,788 nipype.workflow INFO:
[Node] Running "t1w_name" ("nipype.interfaces.utility.wrappers.Function")
200322-12:11:25,790 nipype.workflow INFO:
[Node] Running "raw_sources" ("nipype.interfaces.utility.wrappers.Function")
200322-12:11:25,794 nipype.workflow INFO:
[Node] Finished "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.anat_derivatives_wf.raw_sources".
200322-12:11:25,795 nipype.workflow INFO:
[Node] Finished "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.anat_derivatives_wf.t1w_name".
200322-12:11:27,889 nipype.workflow INFO:
[Node] Setting-up "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.anat_template_wf.t1w_conform" in "/gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/anat_template_wf/t1w_conform".
200322-12:11:27,893 nipype.workflow INFO:
[Node] Setting-up "_t1w_conform0" in "/gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/anat_template_wf/t1w_conform/mapflow/_t1w_conform0".
200322-12:11:27,895 nipype.workflow INFO:
[Node] Running "_t1w_conform0" ("niworkflows.interfaces.images.Conform")
200322-12:11:27,982 nipype.workflow INFO:
[Node] Finished "_t1w_conform0".
200322-12:11:27,984 nipype.workflow INFO:
[Node] Finished "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.anat_template_wf.t1w_conform".
200322-12:11:32,354 nipype.workflow INFO:
[Node] Setting-up "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.anat_template_wf.get1st" in "/gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/anat_template_wf/get1st".
200322-12:11:32,363 nipype.workflow INFO:
[Node] Running "get1st" ("nipype.interfaces.utility.base.Select")
200322-12:11:32,368 nipype.workflow INFO:
[Node] Finished "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.anat_template_wf.get1st".
200322-12:11:36,356 nipype.workflow INFO:
[Node] Setting-up "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.surface_recon_wf.fov_check" in "/gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/surface_recon_wf/fov_check".
200322-12:11:36,356 nipype.workflow INFO:
[Node] Setting-up "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.surface_recon_wf.recon_config" in "/gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/surface_recon_wf/recon_config".
200322-12:11:36,366 nipype.workflow INFO:
[Node] Running "fov_check" ("nipype.interfaces.utility.wrappers.Function")
200322-12:11:36,367 nipype.workflow INFO:
[Node] Running "recon_config" ("niworkflows.interfaces.freesurfer.FSDetectInputs")
200322-12:11:36,457 nipype.workflow INFO:
[Node] Finished "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.surface_recon_wf.recon_config".
200322-12:11:36,835 nipype.workflow INFO:
[Node] Finished "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.surface_recon_wf.fov_check".
200322-12:11:38,368 nipype.workflow INFO:
[Node] Setting-up "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.brain_extraction_wf.truncate_images" in "/gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/brain_extraction_wf/truncate_images".
200322-12:11:38,374 nipype.workflow INFO:
[Node] Setting-up "_truncate_images0" in "/gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/brain_extraction_wf/truncate_images/mapflow/_truncate_images0".
200322-12:11:38,377 nipype.workflow INFO:
[Node] Running "_truncate_images0" ("niworkflows.interfaces.ants.ImageMath"), a CommandLine Interface with command:
ImageMath 3 sub-01_ses-01_T1w_maths.nii.gz TruncateImageIntensity /data/sub-01/ses-01/anat/sub-01_ses-01_T1w.nii.gz 0.01 0.999 256
200322-12:11:53,144 nipype.workflow INFO:
[Node] Finished "_truncate_images0".
200322-12:11:53,147 nipype.workflow INFO:
[Node] Finished "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.brain_extraction_wf.truncate_images".
200322-12:12:15,451 nipype.workflow INFO:
[Node] Finished "fmriprep_wf.single_subject_01_wf.func_preproc_ses_01_task_Stroop_run_01_wf.bold_stc_wf.slice_timing_correction".
200322-12:12:16,391 nipype.workflow INFO:
[Node] Setting-up "fmriprep_wf.single_subject_01_wf.func_preproc_ses_01_task_Stroop_run_01_wf.bold_stc_wf.copy_xform" in "/gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/bold_stc_wf/copy_xform".
200322-12:12:16,408 nipype.workflow INFO:
[Node] Running "copy_xform" ("niworkflows.interfaces.utils.CopyXForm")
200322-12:12:35,659 nipype.workflow INFO:
[Node] Finished "fmriprep_wf.single_subject_01_wf.func_preproc_ses_01_task_Stroop_run_01_wf.bold_stc_wf.copy_xform".
200322-12:12:36,410 nipype.workflow INFO:
[Node] Setting-up "fmriprep_wf.single_subject_01_wf.func_preproc_ses_01_task_Stroop_run_01_wf.bold_split" in "/gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/bold_split".
200322-12:12:36,417 nipype.workflow INFO:
[Node] Running "bold_split" ("nipype.interfaces.fsl.utils.Split"), a CommandLine Interface with command:
fslsplit /gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/bold_stc_wf/copy_xform/sub-01_ses-01_task-Stroop_run-01_bold_tshift_xform.nii.gz -t
200322-12:13:17,717 nipype.workflow INFO:
[Node] Finished "fmriprep_wf.single_subject_01_wf.func_preproc_ses_01_task_Stroop_run_01_wf.bold_split".
200322-12:13:39,453 nipype.workflow INFO:
[Node] Finished "fmriprep_wf.single_subject_01_wf.func_preproc_ses_01_task_Stroop_run_01_wf.bold_hmc_wf.mcflirt".
200322-12:13:40,466 nipype.workflow INFO:
[Node] Setting-up "fmriprep_wf.single_subject_01_wf.func_preproc_ses_01_task_Stroop_run_01_wf.sdc_estimate_wf.pepolar_unwarp_wf.prepare_epi_wf.ref_ma_wf.init_aff" in "/gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/sdc_estimate_wf/pepolar_unwarp_wf/prepare_epi_wf/ref_ma_wf/init_aff".
200322-12:13:40,522 nipype.workflow INFO:
[Node] Running "init_aff" ("niworkflows.interfaces.ants.AI"), a CommandLine Interface with command:
antsAI -c [10,0.000001,10] -d 3 -x /home/jac18015/.cache/templateflow/tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_res-02_desc-brain_mask.nii.gz -m Mattes[/home/jac18015/.cache/templateflow/tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_res-02_desc-fMRIPrep_boldref.nii.gz,/gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/sdc_estimate_wf/pepolar_unwarp_wf/prepare_epi_wf/merge_ma/template.nii.gz,32,Regular,0.200000] -o initialization.mat -p 0 -s [20.000000,0.120000] -t Affine[0.100000] -v 1
200322-12:13:45,208 nipype.workflow INFO:
[Node] Finished "fmriprep_wf.single_subject_01_wf.func_preproc_ses_01_task_Stroop_run_01_wf.sdc_estimate_wf.pepolar_unwarp_wf.prepare_epi_wf.ref_ma_wf.init_aff".
200322-12:13:46,487 nipype.workflow INFO:
[Node] Setting-up "fmriprep_wf.single_subject_01_wf.func_preproc_ses_01_task_Stroop_run_01_wf.sdc_estimate_wf.pepolar_unwarp_wf.prepare_epi_wf.ref_ma_wf.norm" in "/gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/sdc_estimate_wf/pepolar_unwarp_wf/prepare_epi_wf/ref_ma_wf/norm".
200322-12:13:46,533 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 [ /gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/sdc_estimate_wf/pepolar_unwarp_wf/prepare_epi_wf/ref_ma_wf/init_aff/initialization.mat, 0 ] --initialize-transforms-per-stage 0 --interpolation Linear --output transform --transform Affine[ 0.1 ] --metric Mattes[ /home/jac18015/.cache/templateflow/tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_res-02_desc-fMRIPrep_boldref.nii.gz, /gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/sdc_estimate_wf/pepolar_unwarp_wf/prepare_epi_wf/merge_ma/template.nii.gz, 1, 64, Random, 0.2 ] --convergence [ 200, 1e-09, 10 ] --smoothing-sigmas 2.0mm --shrink-factors 2 --use-estimate-learning-rate-once 1 --use-histogram-matching 1 --winsorize-image-intensities [ 0.05, 0.98 ] --write-composite-transform 0
200322-12:13:47,717 nipype.workflow INFO:
[Node] Finished "fmriprep_wf.single_subject_01_wf.func_preproc_ses_01_task_Stroop_run_01_wf.sdc_estimate_wf.pepolar_unwarp_wf.prepare_epi_wf.ref_ma_wf.norm".
200322-12:13:48,467 nipype.workflow INFO:
[Node] Setting-up "fmriprep_wf.single_subject_01_wf.func_preproc_ses_01_task_Stroop_run_01_wf.sdc_estimate_wf.pepolar_unwarp_wf.prepare_epi_wf.ref_ma_wf.map_brainmask" in "/gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/sdc_estimate_wf/pepolar_unwarp_wf/prepare_epi_wf/ref_ma_wf/map_brainmask".
200322-12:13:48,468 nipype.workflow INFO:
[Node] Setting-up "fmriprep_wf.single_subject_01_wf.func_preproc_ses_01_task_Stroop_run_01_wf.bold_hmc_wf.normalize_motion" in "/gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/bold_hmc_wf/normalize_motion".
200322-12:13:48,475 nipype.workflow INFO:
[Node] Running "map_brainmask" ("niworkflows.interfaces.fixes.FixHeaderApplyTransforms"), a CommandLine Interface with command:
antsApplyTransforms --default-value 0 --float 1 --input /home/jac18015/.cache/templateflow/tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_res-02_desc-brain_mask.nii.gz --interpolation MultiLabel --output tpl-MNI152NLin2009cAsym_res-02_desc-brain_mask_trans.nii.gz --reference-image /gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/sdc_estimate_wf/pepolar_unwarp_wf/prepare_epi_wf/merge_ma/template.nii.gz --transform [ /gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/sdc_estimate_wf/pepolar_unwarp_wf/prepare_epi_wf/ref_ma_wf/norm/transform0GenericAffine.mat, 1 ]
200322-12:13:48,728 nipype.workflow INFO:
[Node] Running "normalize_motion" ("niworkflows.interfaces.utils.NormalizeMotionParams")
200322-12:13:48,755 nipype.workflow INFO:
[Node] Finished "fmriprep_wf.single_subject_01_wf.func_preproc_ses_01_task_Stroop_run_01_wf.bold_hmc_wf.normalize_motion".
200322-12:13:50,587 nipype.workflow INFO:
[Node] Setting-up "fmriprep_wf.single_subject_01_wf.func_preproc_ses_01_task_Stroop_run_01_wf.bold_confounds_wf.fdisp" in "/gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/bold_confounds_wf/fdisp".
200322-12:13:50,593 nipype.workflow INFO:
[Node] Running "fdisp" ("nipype.algorithms.confounds.FramewiseDisplacement")
200322-12:13:50,604 nipype.workflow INFO:
[Node] Finished "fmriprep_wf.single_subject_01_wf.func_preproc_ses_01_task_Stroop_run_01_wf.bold_confounds_wf.fdisp".
200322-12:13:54,115 nipype.workflow INFO:
[Node] Finished "fmriprep_wf.single_subject_01_wf.func_preproc_ses_01_task_Stroop_run_01_wf.sdc_estimate_wf.pepolar_unwarp_wf.prepare_epi_wf.ref_ma_wf.map_brainmask".
200322-12:13:54,472 nipype.workflow INFO:
[Node] Setting-up "fmriprep_wf.single_subject_01_wf.func_preproc_ses_01_task_Stroop_run_01_wf.sdc_estimate_wf.pepolar_unwarp_wf.prepare_epi_wf.ref_ma_wf.pre_mask_dilate" in "/gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/sdc_estimate_wf/pepolar_unwarp_wf/prepare_epi_wf/ref_ma_wf/pre_mask_dilate".
200322-12:13:54,479 nipype.workflow INFO:
[Node] Running "pre_mask_dilate" ("nipype.interfaces.fsl.maths.DilateImage"), a CommandLine Interface with command:
fslmaths -dt char /gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/sdc_estimate_wf/pepolar_unwarp_wf/prepare_epi_wf/ref_ma_wf/map_brainmask/tpl-MNI152NLin2009cAsym_res-02_desc-brain_mask_trans.nii.gz -kernel sphere 3.0000 -dilF /gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/sdc_estimate_wf/pepolar_unwarp_wf/prepare_epi_wf/ref_ma_wf/pre_mask_dilate/tpl-MNI152NLin2009cAsym_res-02_desc-brain_mask_trans_dil.nii.gz
200322-12:13:54,869 nipype.workflow INFO:
[Node] Finished "fmriprep_wf.single_subject_01_wf.func_preproc_ses_01_task_Stroop_run_01_wf.sdc_estimate_wf.pepolar_unwarp_wf.prepare_epi_wf.ref_ma_wf.pre_mask_dilate".
200322-12:13:56,513 nipype.interface WARNING:
q-forms of reference and mask are substantially different
200322-12:13:56,650 nipype.workflow INFO:
[Node] Setting-up "fmriprep_wf.single_subject_01_wf.func_preproc_ses_01_task_Stroop_run_01_wf.sdc_estimate_wf.pepolar_unwarp_wf.prepare_epi_wf.ref_op_wf.init_aff" in "/gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/sdc_estimate_wf/pepolar_unwarp_wf/prepare_epi_wf/ref_op_wf/init_aff".
200322-12:13:56,704 nipype.workflow INFO:
[Node] Running "init_aff" ("niworkflows.interfaces.ants.AI"), a CommandLine Interface with command:
antsAI -c [10,0.000001,10] -d 3 -x /home/jac18015/.cache/templateflow/tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_res-02_desc-brain_mask.nii.gz -m Mattes[/home/jac18015/.cache/templateflow/tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_res-02_desc-fMRIPrep_boldref.nii.gz,/gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/sdc_estimate_wf/pepolar_unwarp_wf/prepare_epi_wf/merge_op/template.nii.gz,32,Regular,0.200000] -o initialization.mat -p 0 -s [20.000000,0.120000] -t Affine[0.100000] -v 1
200322-12:14:00,933 nipype.workflow INFO:
[Node] Finished "fmriprep_wf.single_subject_01_wf.func_preproc_ses_01_task_Stroop_run_01_wf.sdc_estimate_wf.pepolar_unwarp_wf.prepare_epi_wf.ref_op_wf.init_aff".
200322-12:14:02,480 nipype.workflow INFO:
[Node] Setting-up "fmriprep_wf.single_subject_01_wf.func_preproc_ses_01_task_Stroop_run_01_wf.sdc_estimate_wf.pepolar_unwarp_wf.prepare_epi_wf.ref_ma_wf.n4_correct" in "/gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/sdc_estimate_wf/pepolar_unwarp_wf/prepare_epi_wf/ref_ma_wf/n4_correct".
200322-12:14:02,566 nipype.workflow INFO:
[Node] Running "n4_correct" ("niworkflows.interfaces.fixes.FixN4BiasFieldCorrection"), a CommandLine Interface with command:
N4BiasFieldCorrection --bspline-fitting [ 200 ] -d 3 --input-image /gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/sdc_estimate_wf/pepolar_unwarp_wf/prepare_epi_wf/merge_ma/template.nii.gz --mask-image /gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/sdc_estimate_wf/pepolar_unwarp_wf/prepare_epi_wf/ref_ma_wf/check_hdr/tpl-MNI152NLin2009cAsym_res-02_desc-brain_mask_trans_dil_hdr.nii.gz --output template_corrected.nii.gz -r
200322-12:14:08,781 nipype.workflow INFO:
[Node] Finished "fmriprep_wf.single_subject_01_wf.func_preproc_ses_01_task_Stroop_run_01_wf.sdc_estimate_wf.pepolar_unwarp_wf.prepare_epi_wf.ref_ma_wf.n4_correct".
200322-12:14:10,484 nipype.workflow INFO:
[Node] Setting-up "fmriprep_wf.single_subject_01_wf.func_preproc_ses_01_task_Stroop_run_01_wf.sdc_estimate_wf.pepolar_unwarp_wf.prepare_epi_wf.ref_ma_wf.skullstrip_first_pass" in "/gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/sdc_estimate_wf/pepolar_unwarp_wf/prepare_epi_wf/ref_ma_wf/skullstrip_first_pass".
200322-12:14:10,492 nipype.workflow INFO:
[Node] Running "skullstrip_first_pass" ("nipype.interfaces.fsl.preprocess.BET"), a CommandLine Interface with command:
bet /gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/sdc_estimate_wf/pepolar_unwarp_wf/prepare_epi_wf/ref_ma_wf/n4_correct/template_corrected.nii.gz /gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/sdc_estimate_wf/pepolar_unwarp_wf/prepare_epi_wf/ref_ma_wf/skullstrip_first_pass/template_corrected_brain.nii.gz -f 0.20 -m
200322-12:14:12,158 nipype.workflow INFO:
[Node] Finished "fmriprep_wf.single_subject_01_wf.func_preproc_ses_01_task_Stroop_run_01_wf.sdc_estimate_wf.pepolar_unwarp_wf.prepare_epi_wf.ref_ma_wf.skullstrip_first_pass".
200322-12:14:12,486 nipype.workflow INFO:
[Node] Setting-up "fmriprep_wf.single_subject_01_wf.func_preproc_ses_01_task_Stroop_run_01_wf.sdc_estimate_wf.pepolar_unwarp_wf.prepare_epi_wf.ref_ma_wf.skullstrip_first_dilate" in "/gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/sdc_estimate_wf/pepolar_unwarp_wf/prepare_epi_wf/ref_ma_wf/skullstrip_first_dilate".
200322-12:14:12,492 nipype.workflow INFO:
[Node] Running "skullstrip_first_dilate" ("nipype.interfaces.fsl.maths.DilateImage"), a CommandLine Interface with command:
fslmaths -dt char /gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/sdc_estimate_wf/pepolar_unwarp_wf/prepare_epi_wf/ref_ma_wf/skullstrip_first_pass/template_corrected_brain_mask.nii.gz -kernel sphere 6.0000 -dilF /gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/sdc_estimate_wf/pepolar_unwarp_wf/prepare_epi_wf/ref_ma_wf/skullstrip_first_dilate/template_corrected_brain_mask_dil.nii.gz
200322-12:14:14,675 nipype.workflow INFO:
[Node] Finished "fmriprep_wf.single_subject_01_wf.func_preproc_ses_01_task_Stroop_run_01_wf.sdc_estimate_wf.pepolar_unwarp_wf.prepare_epi_wf.ref_ma_wf.skullstrip_first_dilate".
200322-12:14:16,499 nipype.workflow INFO:
[Node] Setting-up "fmriprep_wf.single_subject_01_wf.func_preproc_ses_01_task_Stroop_run_01_wf.sdc_estimate_wf.pepolar_unwarp_wf.prepare_epi_wf.ref_ma_wf.skullstrip_first_mask" in "/gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/sdc_estimate_wf/pepolar_unwarp_wf/prepare_epi_wf/ref_ma_wf/skullstrip_first_mask".
200322-12:14:16,509 nipype.workflow INFO:
[Node] Running "skullstrip_first_mask" ("nipype.interfaces.fsl.maths.ApplyMask"), a CommandLine Interface with command:
fslmaths /gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/sdc_estimate_wf/pepolar_unwarp_wf/prepare_epi_wf/ref_ma_wf/skullstrip_first_pass/template_corrected_brain.nii.gz -mas /gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/sdc_estimate_wf/pepolar_unwarp_wf/prepare_epi_wf/ref_ma_wf/skullstrip_first_dilate/template_corrected_brain_mask_dil.nii.gz /gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/sdc_estimate_wf/pepolar_unwarp_wf/prepare_epi_wf/ref_ma_wf/skullstrip_first_mask/template_corrected_brain_masked.nii.gz
200322-12:14:16,655 nipype.workflow INFO:
[Node] Finished "fmriprep_wf.single_subject_01_wf.func_preproc_ses_01_task_Stroop_run_01_wf.sdc_estimate_wf.pepolar_unwarp_wf.prepare_epi_wf.ref_ma_wf.skullstrip_first_mask".
200322-12:14:18,497 nipype.workflow INFO:
[Node] Setting-up "fmriprep_wf.single_subject_01_wf.func_preproc_ses_01_task_Stroop_run_01_wf.sdc_estimate_wf.pepolar_unwarp_wf.prepare_epi_wf.ref_ma_wf.unifize" in "/gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/sdc_estimate_wf/pepolar_unwarp_wf/prepare_epi_wf/ref_ma_wf/unifize".
200322-12:14:18,505 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 /gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/sdc_estimate_wf/pepolar_unwarp_wf/prepare_epi_wf/ref_ma_wf/unifize/template_corrected_brain_masked.nii.gz
200322-12:14:21,648 nipype.workflow INFO:
[Node] Finished "fmriprep_wf.single_subject_01_wf.func_preproc_ses_01_task_Stroop_run_01_wf.sdc_estimate_wf.pepolar_unwarp_wf.prepare_epi_wf.ref_ma_wf.unifize".
200322-12:14:22,498 nipype.workflow INFO:
[Node] Setting-up "fmriprep_wf.single_subject_01_wf.func_preproc_ses_01_task_Stroop_run_01_wf.sdc_estimate_wf.pepolar_unwarp_wf.prepare_epi_wf.ref_ma_wf.fixhdr_unifize" in "/gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/sdc_estimate_wf/pepolar_unwarp_wf/prepare_epi_wf/ref_ma_wf/fixhdr_unifize".
200322-12:14:22,506 nipype.workflow INFO:
[Node] Running "fixhdr_unifize" ("niworkflows.interfaces.utils.CopyXForm")
200322-12:14:22,598 nipype.workflow INFO:
[Node] Finished "fmriprep_wf.single_subject_01_wf.func_preproc_ses_01_task_Stroop_run_01_wf.sdc_estimate_wf.pepolar_unwarp_wf.prepare_epi_wf.ref_ma_wf.fixhdr_unifize".
200322-12:14:24,501 nipype.workflow INFO:
[Node] Setting-up "fmriprep_wf.single_subject_01_wf.func_preproc_ses_01_task_Stroop_run_01_wf.sdc_estimate_wf.pepolar_unwarp_wf.prepare_epi_wf.ref_ma_wf.skullstrip_second_pass" in "/gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/sdc_estimate_wf/pepolar_unwarp_wf/prepare_epi_wf/ref_ma_wf/skullstrip_second_pass".
200322-12:14:24,509 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 /gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/sdc_estimate_wf/pepolar_unwarp_wf/prepare_epi_wf/ref_ma_wf/skullstrip_second_pass/uni_xform.nii.gz
200322-12:14:24,746 nipype.workflow INFO:
[Node] Finished "fmriprep_wf.single_subject_01_wf.func_preproc_ses_01_task_Stroop_run_01_wf.sdc_estimate_wf.pepolar_unwarp_wf.prepare_epi_wf.ref_ma_wf.skullstrip_second_pass".
200322-12:14:26,511 nipype.workflow INFO:
[Node] Setting-up "fmriprep_wf.single_subject_01_wf.func_preproc_ses_01_task_Stroop_run_01_wf.sdc_estimate_wf.pepolar_unwarp_wf.prepare_epi_wf.ref_ma_wf.fixhdr_skullstrip2" in "/gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/sdc_estimate_wf/pepolar_unwarp_wf/prepare_epi_wf/ref_ma_wf/fixhdr_skullstrip2".
200322-12:14:26,523 nipype.workflow INFO:
[Node] Running "fixhdr_skullstrip2" ("niworkflows.interfaces.utils.CopyXForm")
200322-12:14:26,586 nipype.workflow INFO:
[Node] Finished "fmriprep_wf.single_subject_01_wf.func_preproc_ses_01_task_Stroop_run_01_wf.sdc_estimate_wf.pepolar_unwarp_wf.prepare_epi_wf.ref_ma_wf.fixhdr_skullstrip2".
200322-12:14:28,504 nipype.workflow INFO:
[Node] Setting-up "fmriprep_wf.single_subject_01_wf.func_preproc_ses_01_task_Stroop_run_01_wf.sdc_estimate_wf.pepolar_unwarp_wf.prepare_epi_wf.ref_ma_wf.combine_masks" in "/gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/sdc_estimate_wf/pepolar_unwarp_wf/prepare_epi_wf/ref_ma_wf/combine_masks".
200322-12:14:28,527 nipype.workflow INFO:
[Node] Running "combine_masks" ("nipype.interfaces.fsl.maths.BinaryMaths"), a CommandLine Interface with command:
fslmaths /gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/sdc_estimate_wf/pepolar_unwarp_wf/prepare_epi_wf/ref_ma_wf/skullstrip_first_pass/template_corrected_brain_mask.nii.gz -mul /gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/sdc_estimate_wf/pepolar_unwarp_wf/prepare_epi_wf/ref_ma_wf/fixhdr_skullstrip2/uni_xform_mask_xform.nii.gz /gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/sdc_estimate_wf/pepolar_unwarp_wf/prepare_epi_wf/ref_ma_wf/combine_masks/template_corrected_brain_mask_maths.nii.gz
200322-12:14:28,644 nipype.workflow INFO:
[Node] Finished "fmriprep_wf.single_subject_01_wf.func_preproc_ses_01_task_Stroop_run_01_wf.sdc_estimate_wf.pepolar_unwarp_wf.prepare_epi_wf.ref_ma_wf.combine_masks".
200322-12:14:30,506 nipype.workflow INFO:
[Node] Setting-up "fmriprep_wf.single_subject_01_wf.func_preproc_ses_01_task_Stroop_run_01_wf.sdc_estimate_wf.pepolar_unwarp_wf.prepare_epi_wf.ref_ma_wf.apply_mask" in "/gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/sdc_estimate_wf/pepolar_unwarp_wf/prepare_epi_wf/ref_ma_wf/apply_mask".
200322-12:14:30,516 nipype.workflow INFO:
[Node] Running "apply_mask" ("nipype.interfaces.fsl.maths.ApplyMask"), a CommandLine Interface with command:
fslmaths /gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/sdc_estimate_wf/pepolar_unwarp_wf/prepare_epi_wf/ref_ma_wf/fixhdr_unifize/uni_xform.nii.gz -mas /gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/sdc_estimate_wf/pepolar_unwarp_wf/prepare_epi_wf/ref_ma_wf/combine_masks/template_corrected_brain_mask_maths.nii.gz /gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/sdc_estimate_wf/pepolar_unwarp_wf/prepare_epi_wf/ref_ma_wf/apply_mask/uni_xform_masked.nii.gz
200322-12:14:30,657 nipype.workflow INFO:
[Node] Finished "fmriprep_wf.single_subject_01_wf.func_preproc_ses_01_task_Stroop_run_01_wf.sdc_estimate_wf.pepolar_unwarp_wf.prepare_epi_wf.ref_ma_wf.apply_mask".
200322-12:14:32,514 nipype.workflow INFO:
[Node] Setting-up "fmriprep_wf.single_subject_01_wf.func_preproc_ses_01_task_Stroop_run_01_wf.sdc_estimate_wf.pepolar_unwarp_wf.prepare_epi_wf.ref_op_wf.norm" in "/gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/sdc_estimate_wf/pepolar_unwarp_wf/prepare_epi_wf/ref_op_wf/norm".
200322-12:14:32,527 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 [ /gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/sdc_estimate_wf/pepolar_unwarp_wf/prepare_epi_wf/ref_op_wf/init_aff/initialization.mat, 0 ] --initialize-transforms-per-stage 0 --interpolation Linear --output transform --transform Affine[ 0.1 ] --metric Mattes[ /home/jac18015/.cache/templateflow/tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_res-02_desc-fMRIPrep_boldref.nii.gz, /gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/sdc_estimate_wf/pepolar_unwarp_wf/prepare_epi_wf/merge_op/template.nii.gz, 1, 64, Random, 0.2 ] --convergence [ 200, 1e-09, 10 ] --smoothing-sigmas 2.0mm --shrink-factors 2 --use-estimate-learning-rate-once 1 --use-histogram-matching 1 --winsorize-image-intensities [ 0.05, 0.98 ] --write-composite-transform 0
200322-12:14:33,823 nipype.workflow INFO:
[Node] Finished "fmriprep_wf.single_subject_01_wf.func_preproc_ses_01_task_Stroop_run_01_wf.sdc_estimate_wf.pepolar_unwarp_wf.prepare_epi_wf.ref_op_wf.norm".
200322-12:14:34,515 nipype.workflow INFO:
[Node] Setting-up "fmriprep_wf.single_subject_01_wf.func_preproc_ses_01_task_Stroop_run_01_wf.sdc_estimate_wf.pepolar_unwarp_wf.prepare_epi_wf.ref_op_wf.map_brainmask" in "/gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/sdc_estimate_wf/pepolar_unwarp_wf/prepare_epi_wf/ref_op_wf/map_brainmask".
200322-12:14:34,544 nipype.workflow INFO:
[Node] Running "map_brainmask" ("niworkflows.interfaces.fixes.FixHeaderApplyTransforms"), a CommandLine Interface with command:
antsApplyTransforms --default-value 0 --float 1 --input /home/jac18015/.cache/templateflow/tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_res-02_desc-brain_mask.nii.gz --interpolation MultiLabel --output tpl-MNI152NLin2009cAsym_res-02_desc-brain_mask_trans.nii.gz --reference-image /gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/sdc_estimate_wf/pepolar_unwarp_wf/prepare_epi_wf/merge_op/template.nii.gz --transform [ /gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/sdc_estimate_wf/pepolar_unwarp_wf/prepare_epi_wf/ref_op_wf/norm/transform0GenericAffine.mat, 1 ]
200322-12:14:39,955 nipype.workflow INFO:
[Node] Finished "fmriprep_wf.single_subject_01_wf.func_preproc_ses_01_task_Stroop_run_01_wf.sdc_estimate_wf.pepolar_unwarp_wf.prepare_epi_wf.ref_op_wf.map_brainmask".
200322-12:14:40,516 nipype.workflow INFO:
[Node] Setting-up "fmriprep_wf.single_subject_01_wf.func_preproc_ses_01_task_Stroop_run_01_wf.sdc_estimate_wf.pepolar_unwarp_wf.prepare_epi_wf.ref_op_wf.pre_mask_dilate" in "/gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/sdc_estimate_wf/pepolar_unwarp_wf/prepare_epi_wf/ref_op_wf/pre_mask_dilate".
200322-12:14:40,525 nipype.workflow INFO:
[Node] Running "pre_mask_dilate" ("nipype.interfaces.fsl.maths.DilateImage"), a CommandLine Interface with command:
fslmaths -dt char /gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/sdc_estimate_wf/pepolar_unwarp_wf/prepare_epi_wf/ref_op_wf/map_brainmask/tpl-MNI152NLin2009cAsym_res-02_desc-brain_mask_trans.nii.gz -kernel sphere 3.0000 -dilF /gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/sdc_estimate_wf/pepolar_unwarp_wf/prepare_epi_wf/ref_op_wf/pre_mask_dilate/tpl-MNI152NLin2009cAsym_res-02_desc-brain_mask_trans_dil.nii.gz
200322-12:14:40,908 nipype.workflow INFO:
[Node] Finished "fmriprep_wf.single_subject_01_wf.func_preproc_ses_01_task_Stroop_run_01_wf.sdc_estimate_wf.pepolar_unwarp_wf.prepare_epi_wf.ref_op_wf.pre_mask_dilate".
200322-12:14:42,588 nipype.interface WARNING:
q-forms of reference and mask are substantially different
200322-12:14:42,717 nipype.workflow INFO:
[Node] Setting-up "fmriprep_wf.single_subject_01_wf.func_preproc_ses_01_task_Stroop_run_01_wf.bold_hmc_wf.fsl2itk" in "/gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/bold_hmc_wf/fsl2itk".
200322-12:14:43,97 nipype.workflow INFO:
[Node] Running "fsl2itk" ("niworkflows.interfaces.itk.MCFLIRT2ITK")
200322-12:15:27,355 nipype.workflow INFO:
[Node] Finished "fmriprep_wf.single_subject_01_wf.func_preproc_ses_01_task_Stroop_run_01_wf.bold_hmc_wf.fsl2itk".
200322-12:15:28,590 nipype.workflow INFO:
[Node] Setting-up "fmriprep_wf.single_subject_01_wf.func_preproc_ses_01_task_Stroop_run_01_wf.sdc_estimate_wf.pepolar_unwarp_wf.prepare_epi_wf.ref_op_wf.n4_correct" in "/gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/sdc_estimate_wf/pepolar_unwarp_wf/prepare_epi_wf/ref_op_wf/n4_correct".
200322-12:15:28,675 nipype.workflow INFO:
[Node] Running "n4_correct" ("niworkflows.interfaces.fixes.FixN4BiasFieldCorrection"), a CommandLine Interface with command:
N4BiasFieldCorrection --bspline-fitting [ 200 ] -d 3 --input-image /gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/sdc_estimate_wf/pepolar_unwarp_wf/prepare_epi_wf/merge_op/template.nii.gz --mask-image /gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/sdc_estimate_wf/pepolar_unwarp_wf/prepare_epi_wf/ref_op_wf/check_hdr/tpl-MNI152NLin2009cAsym_res-02_desc-brain_mask_trans_dil_hdr.nii.gz --output template_corrected.nii.gz -r
200322-12:15:34,700 nipype.workflow INFO:
[Node] Finished "fmriprep_wf.single_subject_01_wf.func_preproc_ses_01_task_Stroop_run_01_wf.sdc_estimate_wf.pepolar_unwarp_wf.prepare_epi_wf.ref_op_wf.n4_correct".
200322-12:15:36,570 nipype.workflow INFO:
[Node] Setting-up "fmriprep_wf.single_subject_01_wf.func_preproc_ses_01_task_Stroop_run_01_wf.sdc_estimate_wf.pepolar_unwarp_wf.prepare_epi_wf.ref_op_wf.skullstrip_first_pass" in "/gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/sdc_estimate_wf/pepolar_unwarp_wf/prepare_epi_wf/ref_op_wf/skullstrip_first_pass".
200322-12:15:36,577 nipype.workflow INFO:
[Node] Running "skullstrip_first_pass" ("nipype.interfaces.fsl.preprocess.BET"), a CommandLine Interface with command:
bet /gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/sdc_estimate_wf/pepolar_unwarp_wf/prepare_epi_wf/ref_op_wf/n4_correct/template_corrected.nii.gz /gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/sdc_estimate_wf/pepolar_unwarp_wf/prepare_epi_wf/ref_op_wf/skullstrip_first_pass/template_corrected_brain.nii.gz -f 0.20 -m
200322-12:15:38,219 nipype.workflow INFO:
[Node] Finished "fmriprep_wf.single_subject_01_wf.func_preproc_ses_01_task_Stroop_run_01_wf.sdc_estimate_wf.pepolar_unwarp_wf.prepare_epi_wf.ref_op_wf.skullstrip_first_pass".
200322-12:15:38,571 nipype.workflow INFO:
[Node] Setting-up "fmriprep_wf.single_subject_01_wf.func_preproc_ses_01_task_Stroop_run_01_wf.sdc_estimate_wf.pepolar_unwarp_wf.prepare_epi_wf.ref_op_wf.skullstrip_first_dilate" in "/gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/sdc_estimate_wf/pepolar_unwarp_wf/prepare_epi_wf/ref_op_wf/skullstrip_first_dilate".
200322-12:15:38,589 nipype.workflow INFO:
[Node] Running "skullstrip_first_dilate" ("nipype.interfaces.fsl.maths.DilateImage"), a CommandLine Interface with command:
fslmaths -dt char /gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/sdc_estimate_wf/pepolar_unwarp_wf/prepare_epi_wf/ref_op_wf/skullstrip_first_pass/template_corrected_brain_mask.nii.gz -kernel sphere 6.0000 -dilF /gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/sdc_estimate_wf/pepolar_unwarp_wf/prepare_epi_wf/ref_op_wf/skullstrip_first_dilate/template_corrected_brain_mask_dil.nii.gz
200322-12:15:40,781 nipype.workflow INFO:
[Node] Finished "fmriprep_wf.single_subject_01_wf.func_preproc_ses_01_task_Stroop_run_01_wf.sdc_estimate_wf.pepolar_unwarp_wf.prepare_epi_wf.ref_op_wf.skullstrip_first_dilate".
200322-12:15:42,575 nipype.workflow INFO:
[Node] Setting-up "fmriprep_wf.single_subject_01_wf.func_preproc_ses_01_task_Stroop_run_01_wf.sdc_estimate_wf.pepolar_unwarp_wf.prepare_epi_wf.ref_op_wf.skullstrip_first_mask" in "/gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/sdc_estimate_wf/pepolar_unwarp_wf/prepare_epi_wf/ref_op_wf/skullstrip_first_mask".
200322-12:15:42,584 nipype.workflow INFO:
[Node] Running "skullstrip_first_mask" ("nipype.interfaces.fsl.maths.ApplyMask"), a CommandLine Interface with command:
fslmaths /gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/sdc_estimate_wf/pepolar_unwarp_wf/prepare_epi_wf/ref_op_wf/skullstrip_first_pass/template_corrected_brain.nii.gz -mas /gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/sdc_estimate_wf/pepolar_unwarp_wf/prepare_epi_wf/ref_op_wf/skullstrip_first_dilate/template_corrected_brain_mask_dil.nii.gz /gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/sdc_estimate_wf/pepolar_unwarp_wf/prepare_epi_wf/ref_op_wf/skullstrip_first_mask/template_corrected_brain_masked.nii.gz
200322-12:15:42,743 nipype.workflow INFO:
[Node] Finished "fmriprep_wf.single_subject_01_wf.func_preproc_ses_01_task_Stroop_run_01_wf.sdc_estimate_wf.pepolar_unwarp_wf.prepare_epi_wf.ref_op_wf.skullstrip_first_mask".
200322-12:15:44,599 nipype.workflow INFO:
[Node] Setting-up "fmriprep_wf.single_subject_01_wf.func_preproc_ses_01_task_Stroop_run_01_wf.sdc_estimate_wf.pepolar_unwarp_wf.prepare_epi_wf.ref_op_wf.unifize" in "/gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/sdc_estimate_wf/pepolar_unwarp_wf/prepare_epi_wf/ref_op_wf/unifize".
200322-12:15:44,626 nipype.workflow INFO:
[Node] Running "unifize" ("nipype.interfaces.afni.utils.Unifize"), a CommandLine Interface with command:
3dUnifize -clfrac 0.2 -rbt 18.3 65.0 90.0 -prefix uni.nii.gz -T2 -input /gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/sdc_estimate_wf/pepolar_unwarp_wf/prepare_epi_wf/ref_op_wf/unifize/template_corrected_brain_masked.nii.gz
200322-12:15:47,725 nipype.workflow INFO:
[Node] Finished "fmriprep_wf.single_subject_01_wf.func_preproc_ses_01_task_Stroop_run_01_wf.sdc_estimate_wf.pepolar_unwarp_wf.prepare_epi_wf.ref_op_wf.unifize".
200322-12:15:48,576 nipype.workflow INFO:
[Node] Setting-up "fmriprep_wf.single_subject_01_wf.func_preproc_ses_01_task_Stroop_run_01_wf.sdc_estimate_wf.pepolar_unwarp_wf.prepare_epi_wf.ref_op_wf.fixhdr_unifize" in "/gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/sdc_estimate_wf/pepolar_unwarp_wf/prepare_epi_wf/ref_op_wf/fixhdr_unifize".
200322-12:15:48,583 nipype.workflow INFO:
[Node] Running "fixhdr_unifize" ("niworkflows.interfaces.utils.CopyXForm")
200322-12:15:48,680 nipype.workflow INFO:
[Node] Finished "fmriprep_wf.single_subject_01_wf.func_preproc_ses_01_task_Stroop_run_01_wf.sdc_estimate_wf.pepolar_unwarp_wf.prepare_epi_wf.ref_op_wf.fixhdr_unifize".
200322-12:15:50,581 nipype.workflow INFO:
[Node] Setting-up "fmriprep_wf.single_subject_01_wf.func_preproc_ses_01_task_Stroop_run_01_wf.sdc_estimate_wf.pepolar_unwarp_wf.prepare_epi_wf.ref_op_wf.skullstrip_second_pass" in "/gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/sdc_estimate_wf/pepolar_unwarp_wf/prepare_epi_wf/ref_op_wf/skullstrip_second_pass".
200322-12:15:50,589 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 /gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/sdc_estimate_wf/pepolar_unwarp_wf/prepare_epi_wf/ref_op_wf/skullstrip_second_pass/uni_xform.nii.gz
200322-12:15:50,810 nipype.workflow INFO:
[Node] Finished "fmriprep_wf.single_subject_01_wf.func_preproc_ses_01_task_Stroop_run_01_wf.sdc_estimate_wf.pepolar_unwarp_wf.prepare_epi_wf.ref_op_wf.skullstrip_second_pass".
200322-12:15:52,582 nipype.workflow INFO:
[Node] Setting-up "fmriprep_wf.single_subject_01_wf.func_preproc_ses_01_task_Stroop_run_01_wf.sdc_estimate_wf.pepolar_unwarp_wf.prepare_epi_wf.ref_op_wf.fixhdr_skullstrip2" in "/gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/sdc_estimate_wf/pepolar_unwarp_wf/prepare_epi_wf/ref_op_wf/fixhdr_skullstrip2".
200322-12:15:52,589 nipype.workflow INFO:
[Node] Running "fixhdr_skullstrip2" ("niworkflows.interfaces.utils.CopyXForm")
200322-12:15:52,661 nipype.workflow INFO:
[Node] Finished "fmriprep_wf.single_subject_01_wf.func_preproc_ses_01_task_Stroop_run_01_wf.sdc_estimate_wf.pepolar_unwarp_wf.prepare_epi_wf.ref_op_wf.fixhdr_skullstrip2".
200322-12:15:54,590 nipype.workflow INFO:
[Node] Setting-up "fmriprep_wf.single_subject_01_wf.func_preproc_ses_01_task_Stroop_run_01_wf.sdc_estimate_wf.pepolar_unwarp_wf.prepare_epi_wf.ref_op_wf.combine_masks" in "/gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/sdc_estimate_wf/pepolar_unwarp_wf/prepare_epi_wf/ref_op_wf/combine_masks".
200322-12:15:54,599 nipype.workflow INFO:
[Node] Running "combine_masks" ("nipype.interfaces.fsl.maths.BinaryMaths"), a CommandLine Interface with command:
fslmaths /gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/sdc_estimate_wf/pepolar_unwarp_wf/prepare_epi_wf/ref_op_wf/skullstrip_first_pass/template_corrected_brain_mask.nii.gz -mul /gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/sdc_estimate_wf/pepolar_unwarp_wf/prepare_epi_wf/ref_op_wf/fixhdr_skullstrip2/uni_xform_mask_xform.nii.gz /gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/sdc_estimate_wf/pepolar_unwarp_wf/prepare_epi_wf/ref_op_wf/combine_masks/template_corrected_brain_mask_maths.nii.gz
200322-12:15:54,716 nipype.workflow INFO:
[Node] Finished "fmriprep_wf.single_subject_01_wf.func_preproc_ses_01_task_Stroop_run_01_wf.sdc_estimate_wf.pepolar_unwarp_wf.prepare_epi_wf.ref_op_wf.combine_masks".
200322-12:15:56,589 nipype.workflow INFO:
[Node] Setting-up "fmriprep_wf.single_subject_01_wf.func_preproc_ses_01_task_Stroop_run_01_wf.sdc_estimate_wf.pepolar_unwarp_wf.prepare_epi_wf.ref_op_wf.apply_mask" in "/gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/sdc_estimate_wf/pepolar_unwarp_wf/prepare_epi_wf/ref_op_wf/apply_mask".
200322-12:15:56,598 nipype.workflow INFO:
[Node] Running "apply_mask" ("nipype.interfaces.fsl.maths.ApplyMask"), a CommandLine Interface with command:
fslmaths /gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/sdc_estimate_wf/pepolar_unwarp_wf/prepare_epi_wf/ref_op_wf/fixhdr_unifize/uni_xform.nii.gz -mas /gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/sdc_estimate_wf/pepolar_unwarp_wf/prepare_epi_wf/ref_op_wf/combine_masks/template_corrected_brain_mask_maths.nii.gz /gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/sdc_estimate_wf/pepolar_unwarp_wf/prepare_epi_wf/ref_op_wf/apply_mask/uni_xform_masked.nii.gz
200322-12:15:56,740 nipype.workflow INFO:
[Node] Finished "fmriprep_wf.single_subject_01_wf.func_preproc_ses_01_task_Stroop_run_01_wf.sdc_estimate_wf.pepolar_unwarp_wf.prepare_epi_wf.ref_op_wf.apply_mask".
200322-12:15:58,601 nipype.workflow INFO:
[Node] Setting-up "fmriprep_wf.single_subject_01_wf.func_preproc_ses_01_task_Stroop_run_01_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.init_aff" in "/gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/init_aff".
200322-12:15:58,630 nipype.workflow INFO:
[Node] Running "init_aff" ("niworkflows.interfaces.ants.AI"), a CommandLine Interface with command:
antsAI -c [10,0.000001,10] -d 3 -x /home/jac18015/.cache/templateflow/tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_res-02_desc-brain_mask.nii.gz -m Mattes[/home/jac18015/.cache/templateflow/tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_res-02_desc-fMRIPrep_boldref.nii.gz,/gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/bold_reference_wf/gen_ref/ref_sbref.nii.gz,32,Regular,0.200000] -o initialization.mat -p 0 -s [20.000000,0.120000] -t Affine[0.100000] -v 1
200322-12:16:02,794 nipype.workflow INFO:
[Node] Finished "fmriprep_wf.single_subject_01_wf.func_preproc_ses_01_task_Stroop_run_01_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.init_aff".
200322-12:16:04,603 nipype.workflow INFO:
[Node] Setting-up "fmriprep_wf.single_subject_01_wf.func_preproc_ses_01_task_Stroop_run_01_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.norm" in "/gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/norm".
200322-12:16:04,616 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 [ /gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/init_aff/initialization.mat, 0 ] --initialize-transforms-per-stage 0 --interpolation Linear --output transform --transform Affine[ 0.1 ] --metric Mattes[ /home/jac18015/.cache/templateflow/tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_res-02_desc-fMRIPrep_boldref.nii.gz, /gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/bold_reference_wf/gen_ref/ref_sbref.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
200322-12:16:06,135 nipype.workflow INFO:
[Node] Finished "fmriprep_wf.single_subject_01_wf.func_preproc_ses_01_task_Stroop_run_01_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.norm".
200322-12:16:06,596 nipype.workflow INFO:
[Node] Setting-up "fmriprep_wf.single_subject_01_wf.func_preproc_ses_01_task_Stroop_run_01_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.map_brainmask" in "/gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/map_brainmask".
200322-12:16:06,604 nipype.workflow INFO:
[Node] Running "map_brainmask" ("niworkflows.interfaces.fixes.FixHeaderApplyTransforms"), a CommandLine Interface with command:
antsApplyTransforms --default-value 0 --float 1 --input /home/jac18015/.cache/templateflow/tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_res-02_desc-brain_mask.nii.gz --interpolation MultiLabel --output tpl-MNI152NLin2009cAsym_res-02_desc-brain_mask_trans.nii.gz --reference-image /gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/bold_reference_wf/gen_ref/ref_sbref.nii.gz --transform [ /gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/norm/transform0GenericAffine.mat, 1 ]
200322-12:16:11,839 nipype.workflow INFO:
[Node] Finished "fmriprep_wf.single_subject_01_wf.func_preproc_ses_01_task_Stroop_run_01_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.map_brainmask".
200322-12:16:12,604 nipype.workflow INFO:
[Node] Setting-up "fmriprep_wf.single_subject_01_wf.func_preproc_ses_01_task_Stroop_run_01_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.pre_mask_dilate" in "/gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/pre_mask_dilate".
200322-12:16:12,609 nipype.workflow INFO:
[Node] Running "pre_mask_dilate" ("nipype.interfaces.fsl.maths.DilateImage"), a CommandLine Interface with command:
fslmaths -dt char /gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/map_brainmask/tpl-MNI152NLin2009cAsym_res-02_desc-brain_mask_trans.nii.gz -kernel sphere 3.0000 -dilF /gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/pre_mask_dilate/tpl-MNI152NLin2009cAsym_res-02_desc-brain_mask_trans_dil.nii.gz
200322-12:16:12,990 nipype.workflow INFO:
[Node] Finished "fmriprep_wf.single_subject_01_wf.func_preproc_ses_01_task_Stroop_run_01_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.pre_mask_dilate".
200322-12:16:14,769 nipype.workflow INFO:
[Node] Setting-up "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.brain_extraction_wf.inu_n4" in "/gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/brain_extraction_wf/inu_n4".
200322-12:16:14,777 nipype.workflow INFO:
[Node] Setting-up "_inu_n40" in "/gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/brain_extraction_wf/inu_n4/mapflow/_inu_n40".
200322-12:16:14,781 nipype.workflow INFO:
[Node] Running "_inu_n40" ("nipype.interfaces.ants.segmentation.N4BiasFieldCorrection"), a CommandLine Interface with command:
N4BiasFieldCorrection --bspline-fitting [ 200 ] -d 3 --input-image /gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/brain_extraction_wf/truncate_images/mapflow/_truncate_images0/sub-01_ses-01_T1w_maths.nii.gz --convergence [ 50x50x50x50, 1e-07 ] --output sub-01_ses-01_T1w_maths_corrected.nii.gz --shrink-factor 4
200322-12:18:46,703 nipype.workflow INFO:
[Node] Finished "_inu_n40".
200322-12:18:46,712 nipype.workflow INFO:
[Node] Finished "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.brain_extraction_wf.inu_n4".
200322-12:18:48,755 nipype.workflow INFO:
[Node] Setting-up "fmriprep_wf.single_subject_01_wf.func_preproc_ses_01_task_Stroop_run_01_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.n4_correct" in "/gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/n4_correct".
200322-12:18:48,757 nipype.workflow INFO:
[Node] Setting-up "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.brain_extraction_wf.lap_target" in "/gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/brain_extraction_wf/lap_target".
200322-12:18:48,757 nipype.workflow INFO:
[Node] Setting-up "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.brain_extraction_wf.res_target" in "/gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/brain_extraction_wf/res_target".
200322-12:18:48,766 nipype.workflow INFO:
[Node] Running "lap_target" ("niworkflows.interfaces.ants.ImageMath"), a CommandLine Interface with command:
ImageMath 3 sub-01_ses-01_T1w_maths_corrected_maths.nii.gz Laplacian /gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/brain_extraction_wf/inu_n4/mapflow/_inu_n40/sub-01_ses-01_T1w_maths_corrected.nii.gz 1.5 1
200322-12:18:48,766 nipype.workflow INFO:
[Node] Running "res_target" ("niworkflows.interfaces.ants.ResampleImageBySpacing"), a CommandLine Interface with command:
ResampleImageBySpacing 3 /gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/brain_extraction_wf/inu_n4/mapflow/_inu_n40/sub-01_ses-01_T1w_maths_corrected.nii.gz sub-01_ses-01_T1w_maths_corrected_resampled.nii.gz 4 4 4 1
200322-12:18:48,816 nipype.workflow INFO:
[Node] Running "n4_correct" ("niworkflows.interfaces.fixes.FixN4BiasFieldCorrection"), a CommandLine Interface with command:
N4BiasFieldCorrection --bspline-fitting [ 200 ] -d 3 --input-image /gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/bold_reference_wf/gen_ref/ref_sbref.nii.gz --mask-image /gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/check_hdr/tpl-MNI152NLin2009cAsym_res-02_desc-brain_mask_trans_dil_hdr.nii.gz --output ref_sbref_corrected.nii.gz -r
200322-12:18:51,154 nipype.workflow INFO:
[Node] Finished "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.brain_extraction_wf.res_target".
200322-12:18:54,779 nipype.workflow INFO:
[Node] Finished "fmriprep_wf.single_subject_01_wf.func_preproc_ses_01_task_Stroop_run_01_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.n4_correct".
200322-12:18:56,765 nipype.workflow INFO:
[Node] Setting-up "fmriprep_wf.single_subject_01_wf.func_preproc_ses_01_task_Stroop_run_01_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_pass" in "/gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_pass".
200322-12:18:56,772 nipype.workflow INFO:
[Node] Running "skullstrip_first_pass" ("nipype.interfaces.fsl.preprocess.BET"), a CommandLine Interface with command:
bet /gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/n4_correct/ref_sbref_corrected.nii.gz /gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_pass/ref_sbref_corrected_brain.nii.gz -f 0.20 -m
200322-12:18:58,434 nipype.workflow INFO:
[Node] Finished "fmriprep_wf.single_subject_01_wf.func_preproc_ses_01_task_Stroop_run_01_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_pass".
200322-12:18:58,766 nipype.workflow INFO:
[Node] Setting-up "fmriprep_wf.single_subject_01_wf.func_preproc_ses_01_task_Stroop_run_01_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_dilate" in "/gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_dilate".
200322-12:18:58,772 nipype.workflow INFO:
[Node] Running "skullstrip_first_dilate" ("nipype.interfaces.fsl.maths.DilateImage"), a CommandLine Interface with command:
fslmaths -dt char /gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_pass/ref_sbref_corrected_brain_mask.nii.gz -kernel sphere 6.0000 -dilF /gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_dilate/ref_sbref_corrected_brain_mask_dil.nii.gz
200322-12:19:00,959 nipype.workflow INFO:
[Node] Finished "fmriprep_wf.single_subject_01_wf.func_preproc_ses_01_task_Stroop_run_01_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_dilate".
200322-12:19:02,776 nipype.workflow INFO:
[Node] Setting-up "fmriprep_wf.single_subject_01_wf.func_preproc_ses_01_task_Stroop_run_01_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_mask" in "/gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_mask".
200322-12:19:02,799 nipype.workflow INFO:
[Node] Running "skullstrip_first_mask" ("nipype.interfaces.fsl.maths.ApplyMask"), a CommandLine Interface with command:
fslmaths /gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_pass/ref_sbref_corrected_brain.nii.gz -mas /gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_dilate/ref_sbref_corrected_brain_mask_dil.nii.gz /gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_mask/ref_sbref_corrected_brain_masked.nii.gz
200322-12:19:02,964 nipype.workflow INFO:
[Node] Finished "fmriprep_wf.single_subject_01_wf.func_preproc_ses_01_task_Stroop_run_01_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_mask".
200322-12:19:04,773 nipype.workflow INFO:
[Node] Setting-up "fmriprep_wf.single_subject_01_wf.func_preproc_ses_01_task_Stroop_run_01_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.unifize" in "/gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/unifize".
200322-12:19:04,781 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 /gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/unifize/ref_sbref_corrected_brain_masked.nii.gz
200322-12:19:05,160 nipype.workflow INFO:
[Node] Finished "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.brain_extraction_wf.lap_target".
200322-12:19:06,768 nipype.workflow INFO:
[Node] Setting-up "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.brain_extraction_wf.mrg_target" in "/gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/brain_extraction_wf/mrg_target".
200322-12:19:06,777 nipype.workflow INFO:
[Node] Running "mrg_target" ("nipype.interfaces.utility.base.Merge")
200322-12:19:06,780 nipype.workflow INFO:
[Node] Finished "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.brain_extraction_wf.mrg_target".
200322-12:19:07,872 nipype.workflow INFO:
[Node] Finished "fmriprep_wf.single_subject_01_wf.func_preproc_ses_01_task_Stroop_run_01_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.unifize".
200322-12:19:08,774 nipype.workflow INFO:
[Node] Setting-up "fmriprep_wf.single_subject_01_wf.func_preproc_ses_01_task_Stroop_run_01_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.fixhdr_unifize" in "/gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/fixhdr_unifize".
200322-12:19:08,782 nipype.workflow INFO:
[Node] Running "fixhdr_unifize" ("niworkflows.interfaces.utils.CopyXForm")
200322-12:19:08,865 nipype.workflow INFO:
[Node] Finished "fmriprep_wf.single_subject_01_wf.func_preproc_ses_01_task_Stroop_run_01_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.fixhdr_unifize".
200322-12:19:10,783 nipype.workflow INFO:
[Node] Setting-up "fmriprep_wf.single_subject_01_wf.func_preproc_ses_01_task_Stroop_run_01_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.skullstrip_second_pass" in "/gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_second_pass".
200322-12:19:10,811 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 /gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_second_pass/uni_xform.nii.gz
200322-12:19:11,43 nipype.workflow INFO:
[Node] Finished "fmriprep_wf.single_subject_01_wf.func_preproc_ses_01_task_Stroop_run_01_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.skullstrip_second_pass".
200322-12:19:12,776 nipype.workflow INFO:
[Node] Setting-up "fmriprep_wf.single_subject_01_wf.func_preproc_ses_01_task_Stroop_run_01_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.fixhdr_skullstrip2" in "/gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/fixhdr_skullstrip2".
200322-12:19:12,784 nipype.workflow INFO:
[Node] Running "fixhdr_skullstrip2" ("niworkflows.interfaces.utils.CopyXForm")
200322-12:19:12,836 nipype.workflow INFO:
[Node] Finished "fmriprep_wf.single_subject_01_wf.func_preproc_ses_01_task_Stroop_run_01_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.fixhdr_skullstrip2".
200322-12:19:14,781 nipype.workflow INFO:
[Node] Setting-up "fmriprep_wf.single_subject_01_wf.func_preproc_ses_01_task_Stroop_run_01_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.combine_masks" in "/gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/combine_masks".
200322-12:19:14,793 nipype.workflow INFO:
[Node] Running "combine_masks" ("nipype.interfaces.fsl.maths.BinaryMaths"), a CommandLine Interface with command:
fslmaths /gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_pass/ref_sbref_corrected_brain_mask.nii.gz -mul /gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/fixhdr_skullstrip2/uni_xform_mask_xform.nii.gz /gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/combine_masks/ref_sbref_corrected_brain_mask_maths.nii.gz
200322-12:19:14,950 nipype.workflow INFO:
[Node] Finished "fmriprep_wf.single_subject_01_wf.func_preproc_ses_01_task_Stroop_run_01_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.combine_masks".
200322-12:19:16,783 nipype.workflow INFO:
[Node] Setting-up "fmriprep_wf.single_subject_01_wf.func_preproc_ses_01_task_Stroop_run_01_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.apply_mask" in "/gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/apply_mask".
200322-12:19:16,794 nipype.workflow INFO:
[Node] Running "apply_mask" ("nipype.interfaces.fsl.maths.ApplyMask"), a CommandLine Interface with command:
fslmaths /gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/fixhdr_unifize/uni_xform.nii.gz -mas /gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/combine_masks/ref_sbref_corrected_brain_mask_maths.nii.gz /gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/apply_mask/uni_xform_masked.nii.gz
200322-12:19:16,943 nipype.workflow INFO:
[Node] Finished "fmriprep_wf.single_subject_01_wf.func_preproc_ses_01_task_Stroop_run_01_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.apply_mask".
200322-12:19:18,785 nipype.workflow INFO:
[Node] Setting-up "fmriprep_wf.single_subject_01_wf.func_preproc_ses_01_task_Stroop_run_01_wf.sdc_estimate_wf.pepolar_unwarp_wf.prepare_epi_wf.ma2ref_reg" in "/gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/sdc_estimate_wf/pepolar_unwarp_wf/prepare_epi_wf/ma2ref_reg".
200322-12:19:18,801 nipype.workflow INFO:
[Node] Running "ma2ref_reg" ("nipype.interfaces.ants.registration.Registration"), a CommandLine Interface with command:
antsRegistration --collapse-output-transforms 1 --dimensionality 3 --float 1 --initialize-transforms-per-stage 0 --interpolation LanczosWindowedSinc --output [ transform, transform_Warped.nii.gz ] --transform Translation[ 0.05 ] --metric Mattes[ /gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/apply_mask/uni_xform_masked.nii.gz, /gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/sdc_estimate_wf/pepolar_unwarp_wf/prepare_epi_wf/ref_ma_wf/apply_mask/uni_xform_masked.nii.gz, 1, 64, Random, 0.5 ] --convergence [ 500, 1e-07, 200 ] --smoothing-sigmas 8.0mm --shrink-factors 2 --use-estimate-learning-rate-once 1 --use-histogram-matching 1 --transform Rigid[ 0.01 ] --metric Mattes[ /gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/apply_mask/uni_xform_masked.nii.gz, /gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/sdc_estimate_wf/pepolar_unwarp_wf/prepare_epi_wf/ref_ma_wf/apply_mask/uni_xform_masked.nii.gz, 1, 64, Random, 0.5 ] --convergence [ 200, 1e-08, 100 ] --smoothing-sigmas 2.0mm --shrink-factors 1 --use-estimate-learning-rate-once 1 --use-histogram-matching 1 --winsorize-image-intensities [ 0.005, 0.998 ] --write-composite-transform 1
200322-12:20:29,28 nipype.workflow INFO:
[Node] Finished "fmriprep_wf.single_subject_01_wf.func_preproc_ses_01_task_Stroop_run_01_wf.sdc_estimate_wf.pepolar_unwarp_wf.prepare_epi_wf.ma2ref_reg".
200322-12:20:30,855 nipype.workflow INFO:
[Node] Setting-up "fmriprep_wf.single_subject_01_wf.func_preproc_ses_01_task_Stroop_run_01_wf.sdc_estimate_wf.pepolar_unwarp_wf.prepare_epi_wf.op2ref_reg" in "/gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/sdc_estimate_wf/pepolar_unwarp_wf/prepare_epi_wf/op2ref_reg".
200322-12:20:30,924 nipype.workflow INFO:
[Node] Running "op2ref_reg" ("nipype.interfaces.ants.registration.Registration"), a CommandLine Interface with command:
antsRegistration --collapse-output-transforms 1 --dimensionality 3 --float 1 --initialize-transforms-per-stage 0 --interpolation LanczosWindowedSinc --output [ transform, transform_Warped.nii.gz ] --transform Translation[ 0.05 ] --metric Mattes[ /gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/apply_mask/uni_xform_masked.nii.gz, /gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/sdc_estimate_wf/pepolar_unwarp_wf/prepare_epi_wf/ref_op_wf/apply_mask/uni_xform_masked.nii.gz, 1, 64, Random, 0.5 ] --convergence [ 500, 1e-07, 200 ] --smoothing-sigmas 8.0mm --shrink-factors 2 --use-estimate-learning-rate-once 1 --use-histogram-matching 1 --transform Rigid[ 0.01 ] --metric Mattes[ /gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/apply_mask/uni_xform_masked.nii.gz, /gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/sdc_estimate_wf/pepolar_unwarp_wf/prepare_epi_wf/ref_op_wf/apply_mask/uni_xform_masked.nii.gz, 1, 64, Random, 0.5 ] --convergence [ 200, 1e-08, 100 ] --smoothing-sigmas 2.0mm --shrink-factors 1 --use-estimate-learning-rate-once 1 --use-histogram-matching 1 --winsorize-image-intensities [ 0.005, 0.998 ] --write-composite-transform 1
200322-12:21:16,909 nipype.workflow INFO:
[Node] Finished "fmriprep_wf.single_subject_01_wf.func_preproc_ses_01_task_Stroop_run_01_wf.sdc_estimate_wf.pepolar_unwarp_wf.prepare_epi_wf.op2ref_reg".
200322-12:21:18,900 nipype.workflow INFO:
[Node] Setting-up "fmriprep_wf.single_subject_01_wf.func_preproc_ses_01_task_Stroop_run_01_wf.sdc_estimate_wf.pepolar_unwarp_wf.qwarp" in "/gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/sdc_estimate_wf/pepolar_unwarp_wf/qwarp".
200322-12:21:18,914 nipype.workflow INFO:
[Node] Running "qwarp" ("nipype.interfaces.afni.preprocess.QwarpPlusMinus"), a CommandLine Interface with command:
3dQwarp -prefix Qwarp.nii.gz -plusminus -noXdis -noZdis -base /gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/sdc_estimate_wf/pepolar_unwarp_wf/qwarp/transform_Warped.nii.gz -blur -1.0 -1.0 -source /gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/sdc_estimate_wf/pepolar_unwarp_wf/qwarp/transform_Warped_c0000.nii.gz -minpatch 9 -nopadWARP -noweight -pblur 0.05 0.05
200322-12:24:49,164 nipype.workflow INFO:
[Node] Finished "fmriprep_wf.single_subject_01_wf.func_preproc_ses_01_task_Stroop_run_01_wf.sdc_estimate_wf.pepolar_unwarp_wf.qwarp".
200322-12:24:51,110 nipype.workflow INFO:
[Node] Setting-up "fmriprep_wf.single_subject_01_wf.func_preproc_ses_01_task_Stroop_run_01_wf.sdc_estimate_wf.pepolar_unwarp_wf.cphdr_warp" in "/gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/sdc_estimate_wf/pepolar_unwarp_wf/cphdr_warp".
200322-12:24:51,120 nipype.workflow INFO:
[Node] Running "cphdr_warp" ("niworkflows.interfaces.utils.CopyHeader")
200322-12:24:51,316 nipype.workflow INFO:
[Node] Finished "fmriprep_wf.single_subject_01_wf.func_preproc_ses_01_task_Stroop_run_01_wf.sdc_estimate_wf.pepolar_unwarp_wf.cphdr_warp".
200322-12:24:53,110 nipype.workflow INFO:
[Node] Setting-up "fmriprep_wf.single_subject_01_wf.func_preproc_ses_01_task_Stroop_run_01_wf.sdc_estimate_wf.pepolar_unwarp_wf.to_ants" in "/gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/sdc_estimate_wf/pepolar_unwarp_wf/to_ants".
200322-12:24:53,117 nipype.workflow INFO:
[Node] Running "to_ants" ("nipype.interfaces.utility.wrappers.Function")
200322-12:24:53,270 nipype.workflow INFO:
[Node] Finished "fmriprep_wf.single_subject_01_wf.func_preproc_ses_01_task_Stroop_run_01_wf.sdc_estimate_wf.pepolar_unwarp_wf.to_ants".
200322-12:24:55,263 nipype.workflow INFO:
[Node] Setting-up "fmriprep_wf.single_subject_01_wf.func_preproc_ses_01_task_Stroop_run_01_wf.sdc_estimate_wf.pepolar_unwarp_wf.unwarp_reference" in "/gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/sdc_estimate_wf/pepolar_unwarp_wf/unwarp_reference".
200322-12:24:55,272 nipype.workflow INFO:
[Node] Running "unwarp_reference" ("niworkflows.interfaces.registration.ANTSApplyTransformsRPT"), a CommandLine Interface with command:
antsApplyTransforms --default-value 0 --dimensionality 3 --float 1 --input /gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/n4_correct/ref_sbref_corrected.nii.gz --interpolation LanczosWindowedSinc --output ref_sbref_corrected_trans.nii.gz --reference-image /gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/n4_correct/ref_sbref_corrected.nii.gz --transform /gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/sdc_estimate_wf/pepolar_unwarp_wf/cphdr_warp/_warpfieldQwarp_PLUS_WARP_fixhdr.nii.gz
200322-12:24:58,633 nipype.workflow INFO:
[Node] Finished "fmriprep_wf.single_subject_01_wf.func_preproc_ses_01_task_Stroop_run_01_wf.sdc_estimate_wf.pepolar_unwarp_wf.unwarp_reference".
200322-12:24:59,126 nipype.workflow INFO:
[Node] Setting-up "fmriprep_wf.single_subject_01_wf.func_preproc_ses_01_task_Stroop_run_01_wf.sdc_estimate_wf.pepolar_unwarp_wf.enhance_and_skullstrip_bold_wf.init_aff" in "/gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/sdc_estimate_wf/pepolar_unwarp_wf/enhance_and_skullstrip_bold_wf/init_aff".
200322-12:24:59,133 nipype.workflow INFO:
[Node] Running "init_aff" ("niworkflows.interfaces.ants.AI"), a CommandLine Interface with command:
antsAI -c [10,0.000001,10] -d 3 -x /home/jac18015/.cache/templateflow/tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_res-02_desc-brain_mask.nii.gz -m Mattes[/home/jac18015/.cache/templateflow/tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_res-02_desc-fMRIPrep_boldref.nii.gz,/gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/sdc_estimate_wf/pepolar_unwarp_wf/unwarp_reference/ref_sbref_corrected_trans.nii.gz,32,Regular,0.200000] -o initialization.mat -p 0 -s [20.000000,0.120000] -t Affine[0.100000] -v 1
200322-12:25:03,132 nipype.workflow INFO:
[Node] Finished "fmriprep_wf.single_subject_01_wf.func_preproc_ses_01_task_Stroop_run_01_wf.sdc_estimate_wf.pepolar_unwarp_wf.enhance_and_skullstrip_bold_wf.init_aff".
200322-12:25:05,129 nipype.workflow INFO:
[Node] Setting-up "fmriprep_wf.single_subject_01_wf.func_preproc_ses_01_task_Stroop_run_01_wf.sdc_estimate_wf.pepolar_unwarp_wf.enhance_and_skullstrip_bold_wf.norm" in "/gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/sdc_estimate_wf/pepolar_unwarp_wf/enhance_and_skullstrip_bold_wf/norm".
200322-12:25:05,143 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 [ /gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/sdc_estimate_wf/pepolar_unwarp_wf/enhance_and_skullstrip_bold_wf/init_aff/initialization.mat, 0 ] --initialize-transforms-per-stage 0 --interpolation Linear --output transform --transform Affine[ 0.1 ] --metric Mattes[ /home/jac18015/.cache/templateflow/tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_res-02_desc-fMRIPrep_boldref.nii.gz, /gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/sdc_estimate_wf/pepolar_unwarp_wf/unwarp_reference/ref_sbref_corrected_trans.nii.gz, 1, 64, Random, 0.2 ] --convergence [ 200, 1e-09, 10 ] --smoothing-sigmas 2.0mm --shrink-factors 2 --use-estimate-learning-rate-once 1 --use-histogram-matching 1 --winsorize-image-intensities [ 0.05, 0.98 ] --write-composite-transform 0
200322-12:25:07,376 nipype.workflow INFO:
[Node] Finished "fmriprep_wf.single_subject_01_wf.func_preproc_ses_01_task_Stroop_run_01_wf.sdc_estimate_wf.pepolar_unwarp_wf.enhance_and_skullstrip_bold_wf.norm".
200322-12:25:09,129 nipype.workflow INFO:
[Node] Setting-up "fmriprep_wf.single_subject_01_wf.func_preproc_ses_01_task_Stroop_run_01_wf.sdc_estimate_wf.pepolar_unwarp_wf.enhance_and_skullstrip_bold_wf.map_brainmask" in "/gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/sdc_estimate_wf/pepolar_unwarp_wf/enhance_and_skullstrip_bold_wf/map_brainmask".
200322-12:25:09,140 nipype.workflow INFO:
[Node] Running "map_brainmask" ("niworkflows.interfaces.fixes.FixHeaderApplyTransforms"), a CommandLine Interface with command:
antsApplyTransforms --default-value 0 --float 1 --input /home/jac18015/.cache/templateflow/tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_res-02_desc-brain_mask.nii.gz --interpolation MultiLabel --output tpl-MNI152NLin2009cAsym_res-02_desc-brain_mask_trans.nii.gz --reference-image /gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/sdc_estimate_wf/pepolar_unwarp_wf/unwarp_reference/ref_sbref_corrected_trans.nii.gz --transform [ /gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/sdc_estimate_wf/pepolar_unwarp_wf/enhance_and_skullstrip_bold_wf/norm/transform0GenericAffine.mat, 1 ]
200322-12:25:13,986 nipype.workflow INFO:
[Node] Finished "fmriprep_wf.single_subject_01_wf.func_preproc_ses_01_task_Stroop_run_01_wf.sdc_estimate_wf.pepolar_unwarp_wf.enhance_and_skullstrip_bold_wf.map_brainmask".
200322-12:25:15,133 nipype.workflow INFO:
[Node] Setting-up "fmriprep_wf.single_subject_01_wf.func_preproc_ses_01_task_Stroop_run_01_wf.sdc_estimate_wf.pepolar_unwarp_wf.enhance_and_skullstrip_bold_wf.pre_mask_dilate" in "/gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/sdc_estimate_wf/pepolar_unwarp_wf/enhance_and_skullstrip_bold_wf/pre_mask_dilate".
200322-12:25:15,140 nipype.workflow INFO:
[Node] Running "pre_mask_dilate" ("nipype.interfaces.fsl.maths.DilateImage"), a CommandLine Interface with command:
fslmaths -dt char /gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/sdc_estimate_wf/pepolar_unwarp_wf/enhance_and_skullstrip_bold_wf/map_brainmask/tpl-MNI152NLin2009cAsym_res-02_desc-brain_mask_trans.nii.gz -kernel sphere 3.0000 -dilF /gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/sdc_estimate_wf/pepolar_unwarp_wf/enhance_and_skullstrip_bold_wf/pre_mask_dilate/tpl-MNI152NLin2009cAsym_res-02_desc-brain_mask_trans_dil.nii.gz
200322-12:25:15,508 nipype.workflow INFO:
[Node] Finished "fmriprep_wf.single_subject_01_wf.func_preproc_ses_01_task_Stroop_run_01_wf.sdc_estimate_wf.pepolar_unwarp_wf.enhance_and_skullstrip_bold_wf.pre_mask_dilate".
200322-12:25:17,341 nipype.workflow INFO:
[Node] Setting-up "fmriprep_wf.single_subject_01_wf.func_preproc_ses_01_task_Stroop_run_01_wf.bold_bold_trans_wf.bold_transform" in "/gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/bold_bold_trans_wf/bold_transform".
200322-12:25:17,669 nipype.workflow INFO:
[Node] Running "bold_transform" ("niworkflows.interfaces.itk.MultiApplyTransforms")
200322-12:33:00,122 nipype.workflow INFO:
[Node] Finished "fmriprep_wf.single_subject_01_wf.func_preproc_ses_01_task_Stroop_run_01_wf.bold_bold_trans_wf.bold_transform".
200322-12:33:01,592 nipype.workflow INFO:
[Node] Setting-up "fmriprep_wf.single_subject_01_wf.func_preproc_ses_01_task_Stroop_run_01_wf.sdc_estimate_wf.pepolar_unwarp_wf.enhance_and_skullstrip_bold_wf.n4_correct" in "/gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/sdc_estimate_wf/pepolar_unwarp_wf/enhance_and_skullstrip_bold_wf/n4_correct".
200322-12:33:01,604 nipype.workflow INFO:
[Node] Setting-up "fmriprep_wf.single_subject_01_wf.func_preproc_ses_01_task_Stroop_run_01_wf.bold_bold_trans_wf.merge" in "/gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/bold_bold_trans_wf/merge".
200322-12:33:01,771 nipype.workflow INFO:
[Node] Running "n4_correct" ("niworkflows.interfaces.fixes.FixN4BiasFieldCorrection"), a CommandLine Interface with command:
N4BiasFieldCorrection --bspline-fitting [ 200 ] -d 3 --input-image /gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/sdc_estimate_wf/pepolar_unwarp_wf/enhance_and_skullstrip_bold_wf/n4_correct/ref_sbref_corrected_trans_scaled.nii.gz --mask-image /gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/sdc_estimate_wf/pepolar_unwarp_wf/enhance_and_skullstrip_bold_wf/check_hdr/tpl-MNI152NLin2009cAsym_res-02_desc-brain_mask_trans_dil_hdr.nii.gz --output ref_sbref_corrected_trans_corrected.nii.gz -r
200322-12:33:02,316 nipype.workflow INFO:
[Node] Running "merge" ("niworkflows.interfaces.nilearn.Merge")
200322-12:33:07,451 nipype.workflow INFO:
[Node] Finished "fmriprep_wf.single_subject_01_wf.func_preproc_ses_01_task_Stroop_run_01_wf.sdc_estimate_wf.pepolar_unwarp_wf.enhance_and_skullstrip_bold_wf.n4_correct".
200322-12:33:07,591 nipype.workflow INFO:
[Node] Setting-up "fmriprep_wf.single_subject_01_wf.func_preproc_ses_01_task_Stroop_run_01_wf.sdc_estimate_wf.pepolar_unwarp_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_pass" in "/gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/sdc_estimate_wf/pepolar_unwarp_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_pass".
200322-12:33:07,596 nipype.workflow INFO:
[Node] Running "skullstrip_first_pass" ("nipype.interfaces.fsl.preprocess.BET"), a CommandLine Interface with command:
bet /gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/sdc_estimate_wf/pepolar_unwarp_wf/enhance_and_skullstrip_bold_wf/n4_correct/ref_sbref_corrected_trans_corrected.nii.gz /gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/sdc_estimate_wf/pepolar_unwarp_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_pass/ref_sbref_corrected_trans_corrected_brain.nii.gz -f 0.20 -m
200322-12:33:09,107 nipype.workflow INFO:
[Node] Finished "fmriprep_wf.single_subject_01_wf.func_preproc_ses_01_task_Stroop_run_01_wf.sdc_estimate_wf.pepolar_unwarp_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_pass".
200322-12:33:09,595 nipype.workflow INFO:
[Node] Setting-up "fmriprep_wf.single_subject_01_wf.func_preproc_ses_01_task_Stroop_run_01_wf.sdc_estimate_wf.pepolar_unwarp_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_dilate" in "/gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/sdc_estimate_wf/pepolar_unwarp_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_dilate".
200322-12:33:09,601 nipype.workflow INFO:
[Node] Running "skullstrip_first_dilate" ("nipype.interfaces.fsl.maths.DilateImage"), a CommandLine Interface with command:
fslmaths -dt char /gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/sdc_estimate_wf/pepolar_unwarp_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_pass/ref_sbref_corrected_trans_corrected_brain_mask.nii.gz -kernel sphere 6.0000 -dilF /gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/sdc_estimate_wf/pepolar_unwarp_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_dilate/ref_sbref_corrected_trans_corrected_brain_mask_dil.nii.gz
200322-12:33:11,707 nipype.workflow INFO:
[Node] Finished "fmriprep_wf.single_subject_01_wf.func_preproc_ses_01_task_Stroop_run_01_wf.sdc_estimate_wf.pepolar_unwarp_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_dilate".
200322-12:33:13,600 nipype.workflow INFO:
[Node] Setting-up "fmriprep_wf.single_subject_01_wf.func_preproc_ses_01_task_Stroop_run_01_wf.sdc_estimate_wf.pepolar_unwarp_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_mask" in "/gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/sdc_estimate_wf/pepolar_unwarp_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_mask".
200322-12:33:13,608 nipype.workflow INFO:
[Node] Running "skullstrip_first_mask" ("nipype.interfaces.fsl.maths.ApplyMask"), a CommandLine Interface with command:
fslmaths /gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/sdc_estimate_wf/pepolar_unwarp_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_pass/ref_sbref_corrected_trans_corrected_brain.nii.gz -mas /gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/sdc_estimate_wf/pepolar_unwarp_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_dilate/ref_sbref_corrected_trans_corrected_brain_mask_dil.nii.gz /gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/sdc_estimate_wf/pepolar_unwarp_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_mask/ref_sbref_corrected_trans_corrected_brain_masked.nii.gz
200322-12:33:13,772 nipype.workflow INFO:
[Node] Finished "fmriprep_wf.single_subject_01_wf.func_preproc_ses_01_task_Stroop_run_01_wf.sdc_estimate_wf.pepolar_unwarp_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_mask".
200322-12:33:15,596 nipype.workflow INFO:
[Node] Setting-up "fmriprep_wf.single_subject_01_wf.func_preproc_ses_01_task_Stroop_run_01_wf.sdc_estimate_wf.pepolar_unwarp_wf.enhance_and_skullstrip_bold_wf.unifize" in "/gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/sdc_estimate_wf/pepolar_unwarp_wf/enhance_and_skullstrip_bold_wf/unifize".
200322-12:33:15,603 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 /gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/sdc_estimate_wf/pepolar_unwarp_wf/enhance_and_skullstrip_bold_wf/unifize/ref_sbref_corrected_trans_corrected_brain_masked.nii.gz
200322-12:33:18,745 nipype.workflow INFO:
[Node] Finished "fmriprep_wf.single_subject_01_wf.func_preproc_ses_01_task_Stroop_run_01_wf.sdc_estimate_wf.pepolar_unwarp_wf.enhance_and_skullstrip_bold_wf.unifize".
200322-12:33:19,605 nipype.workflow INFO:
[Node] Setting-up "fmriprep_wf.single_subject_01_wf.func_preproc_ses_01_task_Stroop_run_01_wf.sdc_estimate_wf.pepolar_unwarp_wf.enhance_and_skullstrip_bold_wf.fixhdr_unifize" in "/gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/sdc_estimate_wf/pepolar_unwarp_wf/enhance_and_skullstrip_bold_wf/fixhdr_unifize".
200322-12:33:19,612 nipype.workflow INFO:
[Node] Running "fixhdr_unifize" ("niworkflows.interfaces.utils.CopyXForm")
200322-12:33:19,715 nipype.workflow INFO:
[Node] Finished "fmriprep_wf.single_subject_01_wf.func_preproc_ses_01_task_Stroop_run_01_wf.sdc_estimate_wf.pepolar_unwarp_wf.enhance_and_skullstrip_bold_wf.fixhdr_unifize".
200322-12:33:21,604 nipype.workflow INFO:
[Node] Setting-up "fmriprep_wf.single_subject_01_wf.func_preproc_ses_01_task_Stroop_run_01_wf.sdc_estimate_wf.pepolar_unwarp_wf.enhance_and_skullstrip_bold_wf.skullstrip_second_pass" in "/gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/sdc_estimate_wf/pepolar_unwarp_wf/enhance_and_skullstrip_bold_wf/skullstrip_second_pass".
200322-12:33:21,611 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 /gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/sdc_estimate_wf/pepolar_unwarp_wf/enhance_and_skullstrip_bold_wf/skullstrip_second_pass/uni_xform.nii.gz
200322-12:33:21,849 nipype.workflow INFO:
[Node] Finished "fmriprep_wf.single_subject_01_wf.func_preproc_ses_01_task_Stroop_run_01_wf.sdc_estimate_wf.pepolar_unwarp_wf.enhance_and_skullstrip_bold_wf.skullstrip_second_pass".
200322-12:33:23,602 nipype.workflow INFO:
[Node] Setting-up "fmriprep_wf.single_subject_01_wf.func_preproc_ses_01_task_Stroop_run_01_wf.sdc_estimate_wf.pepolar_unwarp_wf.enhance_and_skullstrip_bold_wf.fixhdr_skullstrip2" in "/gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/sdc_estimate_wf/pepolar_unwarp_wf/enhance_and_skullstrip_bold_wf/fixhdr_skullstrip2".
200322-12:33:23,611 nipype.workflow INFO:
[Node] Running "fixhdr_skullstrip2" ("niworkflows.interfaces.utils.CopyXForm")
200322-12:33:23,666 nipype.workflow INFO:
[Node] Finished "fmriprep_wf.single_subject_01_wf.func_preproc_ses_01_task_Stroop_run_01_wf.sdc_estimate_wf.pepolar_unwarp_wf.enhance_and_skullstrip_bold_wf.fixhdr_skullstrip2".
200322-12:33:25,610 nipype.workflow INFO:
[Node] Setting-up "fmriprep_wf.single_subject_01_wf.func_preproc_ses_01_task_Stroop_run_01_wf.sdc_estimate_wf.pepolar_unwarp_wf.enhance_and_skullstrip_bold_wf.combine_masks" in "/gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/sdc_estimate_wf/pepolar_unwarp_wf/enhance_and_skullstrip_bold_wf/combine_masks".
200322-12:33:25,618 nipype.workflow INFO:
[Node] Running "combine_masks" ("nipype.interfaces.fsl.maths.BinaryMaths"), a CommandLine Interface with command:
fslmaths /gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/sdc_estimate_wf/pepolar_unwarp_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_pass/ref_sbref_corrected_trans_corrected_brain_mask.nii.gz -mul /gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/sdc_estimate_wf/pepolar_unwarp_wf/enhance_and_skullstrip_bold_wf/fixhdr_skullstrip2/uni_xform_mask_xform.nii.gz /gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/sdc_estimate_wf/pepolar_unwarp_wf/enhance_and_skullstrip_bold_wf/combine_masks/ref_sbref_corrected_trans_corrected_brain_mask_maths.nii.gz
200322-12:33:25,731 nipype.workflow INFO:
[Node] Finished "fmriprep_wf.single_subject_01_wf.func_preproc_ses_01_task_Stroop_run_01_wf.sdc_estimate_wf.pepolar_unwarp_wf.enhance_and_skullstrip_bold_wf.combine_masks".
200322-12:33:27,606 nipype.workflow INFO:
[Node] Setting-up "fmriprep_wf.single_subject_01_wf.func_preproc_ses_01_task_Stroop_run_01_wf.sdc_estimate_wf.pepolar_unwarp_wf.enhance_and_skullstrip_bold_wf.apply_mask" in "/gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/sdc_estimate_wf/pepolar_unwarp_wf/enhance_and_skullstrip_bold_wf/apply_mask".
200322-12:33:27,615 nipype.workflow INFO:
[Node] Running "apply_mask" ("nipype.interfaces.fsl.maths.ApplyMask"), a CommandLine Interface with command:
fslmaths /gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/sdc_estimate_wf/pepolar_unwarp_wf/enhance_and_skullstrip_bold_wf/fixhdr_unifize/uni_xform.nii.gz -mas /gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/sdc_estimate_wf/pepolar_unwarp_wf/enhance_and_skullstrip_bold_wf/combine_masks/ref_sbref_corrected_trans_corrected_brain_mask_maths.nii.gz /gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/sdc_estimate_wf/pepolar_unwarp_wf/enhance_and_skullstrip_bold_wf/apply_mask/uni_xform_masked.nii.gz
200322-12:33:27,762 nipype.workflow INFO:
[Node] Finished "fmriprep_wf.single_subject_01_wf.func_preproc_ses_01_task_Stroop_run_01_wf.sdc_estimate_wf.pepolar_unwarp_wf.enhance_and_skullstrip_bold_wf.apply_mask".
200322-12:34:46,937 nipype.workflow INFO:
[Node] Finished "fmriprep_wf.single_subject_01_wf.func_preproc_ses_01_task_Stroop_run_01_wf.bold_bold_trans_wf.merge".
200322-12:34:47,683 nipype.workflow INFO:
[Node] Setting-up "fmriprep_wf.single_subject_01_wf.func_preproc_ses_01_task_Stroop_run_01_wf.bold_bold_trans_wf.bold_reference_wf.validate" in "/gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/bold_bold_trans_wf/bold_reference_wf/validate".
200322-12:34:47,690 nipype.workflow INFO:
[Node] Running "validate" ("niworkflows.interfaces.images.ValidateImage")
200322-12:34:47,753 nipype.workflow INFO:
[Node] Finished "fmriprep_wf.single_subject_01_wf.func_preproc_ses_01_task_Stroop_run_01_wf.bold_bold_trans_wf.bold_reference_wf.validate".
200322-12:34:49,681 nipype.workflow INFO:
[Node] Setting-up "fmriprep_wf.single_subject_01_wf.func_preproc_ses_01_task_Stroop_run_01_wf.bold_bold_trans_wf.bold_reference_wf.gen_ref" in "/gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/bold_bold_trans_wf/bold_reference_wf/gen_ref".
200322-12:34:49,687 nipype.workflow INFO:
[Node] Running "gen_ref" ("niworkflows.interfaces.registration.EstimateReferenceImage")
200322-12:34:50,814 nipype.workflow INFO:
[Node] Finished "fmriprep_wf.single_subject_01_wf.func_preproc_ses_01_task_Stroop_run_01_wf.bold_bold_trans_wf.bold_reference_wf.gen_ref".
200322-12:34:51,681 nipype.workflow INFO:
[Node] Setting-up "fmriprep_wf.single_subject_01_wf.func_preproc_ses_01_task_Stroop_run_01_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.init_aff" in "/gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/init_aff".
200322-12:34:51,687 nipype.workflow INFO:
[Node] Running "init_aff" ("niworkflows.interfaces.ants.AI"), a CommandLine Interface with command:
antsAI -c [10,0.000001,10] -d 3 -x /home/jac18015/.cache/templateflow/tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_res-02_desc-brain_mask.nii.gz -m Mattes[/home/jac18015/.cache/templateflow/tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_res-02_desc-fMRIPrep_boldref.nii.gz,/gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/bold_bold_trans_wf/bold_reference_wf/gen_ref/ref_bold.nii.gz,32,Regular,0.200000] -o initialization.mat -p 0 -s [20.000000,0.120000] -t Affine[0.100000] -v 1
200322-12:34:55,566 nipype.workflow INFO:
[Node] Finished "fmriprep_wf.single_subject_01_wf.func_preproc_ses_01_task_Stroop_run_01_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.init_aff".
200322-12:34:55,689 nipype.workflow INFO:
[Node] Setting-up "fmriprep_wf.single_subject_01_wf.func_preproc_ses_01_task_Stroop_run_01_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.norm" in "/gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/norm".
200322-12:34:55,701 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 [ /gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/init_aff/initialization.mat, 0 ] --initialize-transforms-per-stage 0 --interpolation Linear --output transform --transform Affine[ 0.1 ] --metric Mattes[ /home/jac18015/.cache/templateflow/tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_res-02_desc-fMRIPrep_boldref.nii.gz, /gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/bold_bold_trans_wf/bold_reference_wf/gen_ref/ref_bold.nii.gz, 1, 64, Random, 0.2 ] --convergence [ 200, 1e-09, 10 ] --smoothing-sigmas 2.0mm --shrink-factors 2 --use-estimate-learning-rate-once 1 --use-histogram-matching 1 --winsorize-image-intensities [ 0.05, 0.98 ] --write-composite-transform 0
200322-12:34:56,765 nipype.workflow INFO:
[Node] Finished "fmriprep_wf.single_subject_01_wf.func_preproc_ses_01_task_Stroop_run_01_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.norm".
200322-12:34:57,684 nipype.workflow INFO:
[Node] Setting-up "fmriprep_wf.single_subject_01_wf.func_preproc_ses_01_task_Stroop_run_01_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.map_brainmask" in "/gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/map_brainmask".
200322-12:34:57,692 nipype.workflow INFO:
[Node] Running "map_brainmask" ("niworkflows.interfaces.fixes.FixHeaderApplyTransforms"), a CommandLine Interface with command:
antsApplyTransforms --default-value 0 --float 1 --input /home/jac18015/.cache/templateflow/tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_res-02_desc-brain_mask.nii.gz --interpolation MultiLabel --output tpl-MNI152NLin2009cAsym_res-02_desc-brain_mask_trans.nii.gz --reference-image /gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/bold_bold_trans_wf/bold_reference_wf/gen_ref/ref_bold.nii.gz --transform [ /gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/norm/transform0GenericAffine.mat, 1 ]
200322-12:35:02,614 nipype.workflow INFO:
[Node] Finished "fmriprep_wf.single_subject_01_wf.func_preproc_ses_01_task_Stroop_run_01_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.map_brainmask".
200322-12:35:03,690 nipype.workflow INFO:
[Node] Setting-up "fmriprep_wf.single_subject_01_wf.func_preproc_ses_01_task_Stroop_run_01_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.pre_mask_dilate" in "/gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/pre_mask_dilate".
200322-12:35:03,696 nipype.workflow INFO:
[Node] Running "pre_mask_dilate" ("nipype.interfaces.fsl.maths.DilateImage"), a CommandLine Interface with command:
fslmaths -dt char /gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/map_brainmask/tpl-MNI152NLin2009cAsym_res-02_desc-brain_mask_trans.nii.gz -kernel sphere 3.0000 -dilF /gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/pre_mask_dilate/tpl-MNI152NLin2009cAsym_res-02_desc-brain_mask_trans_dil.nii.gz
200322-12:35:04,36 nipype.workflow INFO:
[Node] Finished "fmriprep_wf.single_subject_01_wf.func_preproc_ses_01_task_Stroop_run_01_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.pre_mask_dilate".
200322-12:35:05,873 nipype.workflow INFO:
[Node] Setting-up "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.brain_extraction_wf.init_aff" in "/gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/brain_extraction_wf/init_aff".
200322-12:35:05,882 nipype.workflow INFO:
[Node] Running "init_aff" ("niworkflows.interfaces.ants.AI"), a CommandLine Interface with command:
antsAI -c [10,0.000001,10] -d 3 -x /home/jac18015/.cache/templateflow/tpl-OASIS30ANTs/tpl-OASIS30ANTs_res-01_desc-BrainCerebellumExtraction_mask.nii.gz -m Mattes[/gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/brain_extraction_wf/res_tmpl/tpl-OASIS30ANTs_res-01_T1w_resampled.nii.gz,/gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/brain_extraction_wf/res_target/sub-01_ses-01_T1w_maths_corrected_resampled.nii.gz,32,Regular,0.250000] -o initialization.mat -p 0 -s [15.000000,0.100000] -t Affine[0.100000] -v 1
200322-12:35:07,918 nipype.workflow INFO:
[Node] Finished "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.brain_extraction_wf.init_aff".
200322-12:35:09,703 nipype.workflow INFO:
[Node] Setting-up "fmriprep_wf.single_subject_01_wf.func_preproc_ses_01_task_Stroop_run_01_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.n4_correct" in "/gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/n4_correct".
200322-12:35:09,813 nipype.workflow INFO:
[Node] Running "n4_correct" ("niworkflows.interfaces.fixes.FixN4BiasFieldCorrection"), a CommandLine Interface with command:
N4BiasFieldCorrection --bspline-fitting [ 200 ] -d 3 --input-image /gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/n4_correct/ref_bold_scaled.nii.gz --mask-image /gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/check_hdr/tpl-MNI152NLin2009cAsym_res-02_desc-brain_mask_trans_dil_hdr.nii.gz --output ref_bold_corrected.nii.gz -r
200322-12:35:15,447 nipype.workflow INFO:
[Node] Finished "fmriprep_wf.single_subject_01_wf.func_preproc_ses_01_task_Stroop_run_01_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.n4_correct".
200322-12:35:15,702 nipype.workflow INFO:
[Node] Setting-up "fmriprep_wf.single_subject_01_wf.func_preproc_ses_01_task_Stroop_run_01_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_pass" in "/gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_pass".
200322-12:35:15,707 nipype.workflow INFO:
[Node] Running "skullstrip_first_pass" ("nipype.interfaces.fsl.preprocess.BET"), a CommandLine Interface with command:
bet /gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/n4_correct/ref_bold_corrected.nii.gz /gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_pass/ref_bold_corrected_brain.nii.gz -f 0.20 -m
200322-12:35:17,139 nipype.workflow INFO:
[Node] Finished "fmriprep_wf.single_subject_01_wf.func_preproc_ses_01_task_Stroop_run_01_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_pass".
200322-12:35:17,707 nipype.workflow INFO:
[Node] Setting-up "fmriprep_wf.single_subject_01_wf.func_preproc_ses_01_task_Stroop_run_01_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_dilate" in "/gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_dilate".
200322-12:35:17,713 nipype.workflow INFO:
[Node] Running "skullstrip_first_dilate" ("nipype.interfaces.fsl.maths.DilateImage"), a CommandLine Interface with command:
fslmaths -dt char /gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_pass/ref_bold_corrected_brain_mask.nii.gz -kernel sphere 6.0000 -dilF /gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_dilate/ref_bold_corrected_brain_mask_dil.nii.gz
200322-12:35:19,702 nipype.workflow INFO:
[Node] Finished "fmriprep_wf.single_subject_01_wf.func_preproc_ses_01_task_Stroop_run_01_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_dilate".
200322-12:35:21,713 nipype.workflow INFO:
[Node] Setting-up "fmriprep_wf.single_subject_01_wf.func_preproc_ses_01_task_Stroop_run_01_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_mask" in "/gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_mask".
200322-12:35:21,727 nipype.workflow INFO:
[Node] Running "skullstrip_first_mask" ("nipype.interfaces.fsl.maths.ApplyMask"), a CommandLine Interface with command:
fslmaths /gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_pass/ref_bold_corrected_brain.nii.gz -mas /gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_dilate/ref_bold_corrected_brain_mask_dil.nii.gz /gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_mask/ref_bold_corrected_brain_masked.nii.gz
200322-12:35:21,891 nipype.workflow INFO:
[Node] Finished "fmriprep_wf.single_subject_01_wf.func_preproc_ses_01_task_Stroop_run_01_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.skullstrip_first_mask".
200322-12:35:23,716 nipype.workflow INFO:
[Node] Setting-up "fmriprep_wf.single_subject_01_wf.func_preproc_ses_01_task_Stroop_run_01_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.unifize" in "/gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/unifize".
200322-12:35:23,726 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 /gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/unifize/ref_bold_corrected_brain_masked.nii.gz
200322-12:35:26,775 nipype.workflow INFO:
[Node] Finished "fmriprep_wf.single_subject_01_wf.func_preproc_ses_01_task_Stroop_run_01_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.unifize".
200322-12:35:27,713 nipype.workflow INFO:
[Node] Setting-up "fmriprep_wf.single_subject_01_wf.func_preproc_ses_01_task_Stroop_run_01_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.fixhdr_unifize" in "/gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/fixhdr_unifize".
200322-12:35:27,722 nipype.workflow INFO:
[Node] Running "fixhdr_unifize" ("niworkflows.interfaces.utils.CopyXForm")
200322-12:35:27,838 nipype.workflow INFO:
[Node] Finished "fmriprep_wf.single_subject_01_wf.func_preproc_ses_01_task_Stroop_run_01_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.fixhdr_unifize".
200322-12:35:29,724 nipype.workflow INFO:
[Node] Setting-up "fmriprep_wf.single_subject_01_wf.func_preproc_ses_01_task_Stroop_run_01_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.skullstrip_second_pass" in "/gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_second_pass".
200322-12:35:29,731 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 /gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_second_pass/uni_xform.nii.gz
200322-12:35:29,960 nipype.workflow INFO:
[Node] Finished "fmriprep_wf.single_subject_01_wf.func_preproc_ses_01_task_Stroop_run_01_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.skullstrip_second_pass".
200322-12:35:31,725 nipype.workflow INFO:
[Node] Setting-up "fmriprep_wf.single_subject_01_wf.func_preproc_ses_01_task_Stroop_run_01_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.fixhdr_skullstrip2" in "/gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/fixhdr_skullstrip2".
200322-12:35:31,733 nipype.workflow INFO:
[Node] Running "fixhdr_skullstrip2" ("niworkflows.interfaces.utils.CopyXForm")
200322-12:35:31,817 nipype.workflow INFO:
[Node] Finished "fmriprep_wf.single_subject_01_wf.func_preproc_ses_01_task_Stroop_run_01_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.fixhdr_skullstrip2".
200322-12:35:33,723 nipype.workflow INFO:
[Node] Setting-up "fmriprep_wf.single_subject_01_wf.func_preproc_ses_01_task_Stroop_run_01_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.combine_masks" in "/gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/combine_masks".
200322-12:35:33,733 nipype.workflow INFO:
[Node] Running "combine_masks" ("nipype.interfaces.fsl.maths.BinaryMaths"), a CommandLine Interface with command:
fslmaths /gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/skullstrip_first_pass/ref_bold_corrected_brain_mask.nii.gz -mul /gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/fixhdr_skullstrip2/uni_xform_mask_xform.nii.gz /gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/combine_masks/ref_bold_corrected_brain_mask_maths.nii.gz
200322-12:35:33,844 nipype.workflow INFO:
[Node] Finished "fmriprep_wf.single_subject_01_wf.func_preproc_ses_01_task_Stroop_run_01_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.combine_masks".
200322-12:35:35,726 nipype.workflow INFO:
[Node] Setting-up "fmriprep_wf.single_subject_01_wf.func_preproc_ses_01_task_Stroop_run_01_wf.bold_confounds_wf.dvars" in "/gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/bold_confounds_wf/dvars".
200322-12:35:35,729 nipype.workflow INFO:
[Node] Setting-up "fmriprep_wf.single_subject_01_wf.func_preproc_ses_01_task_Stroop_run_01_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.apply_mask" in "/gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/apply_mask".
200322-12:35:35,738 nipype.workflow INFO:
[Node] Running "apply_mask" ("nipype.interfaces.fsl.maths.ApplyMask"), a CommandLine Interface with command:
fslmaths /gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/fixhdr_unifize/uni_xform.nii.gz -mas /gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/combine_masks/ref_bold_corrected_brain_mask_maths.nii.gz /gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/apply_mask/uni_xform_masked.nii.gz
200322-12:35:35,762 nipype.workflow INFO:
[Node] Running "dvars" ("nipype.algorithms.confounds.ComputeDVARS")
200322-12:35:35,880 nipype.workflow INFO:
[Node] Finished "fmriprep_wf.single_subject_01_wf.func_preproc_ses_01_task_Stroop_run_01_wf.bold_bold_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.apply_mask".
200322-12:36:14,842 nipype.workflow INFO:
[Node] Finished "fmriprep_wf.single_subject_01_wf.func_preproc_ses_01_task_Stroop_run_01_wf.bold_confounds_wf.dvars".
200322-12:36:15,961 nipype.workflow INFO:
[Node] Setting-up "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.brain_extraction_wf.norm" in "/gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/brain_extraction_wf/norm".
200322-12:36:15,979 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 [ /gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/brain_extraction_wf/init_aff/initialization.mat, 0 ] --initialize-transforms-per-stage 0 --interpolation LanczosWindowedSinc --output [ anat_to_template, anat_to_template_Warped.nii.gz ] --transform Rigid[ 0.1 ] --metric MI[ /home/jac18015/.cache/templateflow/tpl-OASIS30ANTs/tpl-OASIS30ANTs_res-01_T1w.nii.gz, /gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/brain_extraction_wf/inu_n4/mapflow/_inu_n40/sub-01_ses-01_T1w_maths_corrected.nii.gz, 1, 32, Regular, 0.25 ] --convergence [ 1000x500x250x100, 1e-08, 10 ] --smoothing-sigmas 4.0x2.0x1.0x0.0vox --shrink-factors 8x4x2x1 --use-histogram-matching 1 --masks [ /home/jac18015/.cache/templateflow/tpl-OASIS30ANTs/tpl-OASIS30ANTs_res-01_desc-BrainCerebellumExtraction_mask.nii.gz, NULL ] --transform Affine[ 0.1 ] --metric MI[ /home/jac18015/.cache/templateflow/tpl-OASIS30ANTs/tpl-OASIS30ANTs_res-01_T1w.nii.gz, /gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/brain_extraction_wf/inu_n4/mapflow/_inu_n40/sub-01_ses-01_T1w_maths_corrected.nii.gz, 1, 32, Regular, 0.25 ] --convergence [ 1000x500x250x100, 1e-08, 10 ] --smoothing-sigmas 4.0x2.0x1.0x0.0vox --shrink-factors 8x4x2x1 --use-histogram-matching 1 --masks [ /home/jac18015/.cache/templateflow/tpl-OASIS30ANTs/tpl-OASIS30ANTs_res-01_desc-BrainCerebellumExtraction_mask.nii.gz, NULL ] --transform SyN[ 0.1, 3.0, 0.0 ] --metric CC[ /home/jac18015/.cache/templateflow/tpl-OASIS30ANTs/tpl-OASIS30ANTs_res-01_T1w.nii.gz, /gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/brain_extraction_wf/inu_n4/mapflow/_inu_n40/sub-01_ses-01_T1w_maths_corrected.nii.gz, 0.5, 4, None, 1 ] --metric CC[ /gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/brain_extraction_wf/lap_tmpl/tpl-OASIS30ANTs_res-01_T1w_maths.nii.gz, /gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/brain_extraction_wf/lap_target/sub-01_ses-01_T1w_maths_corrected_maths.nii.gz, 0.5, 4, None, 1 ] --convergence [ 50x10x0, 1e-09, 15 ] --smoothing-sigmas 2.0x1.0x0.0vox --shrink-factors 4x2x1 --use-histogram-matching 1 --masks [ /home/jac18015/.cache/templateflow/tpl-OASIS30ANTs/tpl-OASIS30ANTs_res-01_desc-BrainCerebellumExtraction_mask.nii.gz, NULL ] -v --winsorize-image-intensities [ 0.025, 0.975 ] --write-composite-transform 0
200322-13:00:49,512 nipype.workflow INFO:
[Node] Finished "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.brain_extraction_wf.norm".
200322-13:00:51,250 nipype.workflow INFO:
[Node] Setting-up "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.brain_extraction_wf.map_brainmask" in "/gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/brain_extraction_wf/map_brainmask".
200322-13:00:51,276 nipype.workflow INFO:
[Node] Running "map_brainmask" ("niworkflows.interfaces.fixes.FixHeaderApplyTransforms"), a CommandLine Interface with command:
antsApplyTransforms --default-value 0 --float 1 --input /home/jac18015/.cache/templateflow/tpl-OASIS30ANTs/tpl-OASIS30ANTs_res-01_label-brain_probseg.nii.gz --interpolation Gaussian --output tpl-OASIS30ANTs_res-01_label-brain_probseg_trans.nii.gz --reference-image /data/sub-01/ses-01/anat/sub-01_ses-01_T1w.nii.gz --transform [ /gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/brain_extraction_wf/norm/anat_to_template0GenericAffine.mat, 1 ] --transform [ /gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/brain_extraction_wf/norm/anat_to_template1InverseWarp.nii.gz, 0 ]
200322-13:01:49,556 nipype.workflow INFO:
[Node] Finished "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.brain_extraction_wf.map_brainmask".
200322-13:01:51,308 nipype.workflow INFO:
[Node] Setting-up "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.brain_extraction_wf.thr_brainmask" in "/gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/brain_extraction_wf/thr_brainmask".
200322-13:01:51,315 nipype.workflow INFO:
[Node] Running "thr_brainmask" ("niworkflows.interfaces.ants.ThresholdImage"), a CommandLine Interface with command:
ThresholdImage 3 /gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/brain_extraction_wf/map_brainmask/tpl-OASIS30ANTs_res-01_label-brain_probseg_trans.nii.gz tpl-OASIS30ANTs_res-01_label-brain_probseg_trans_resampled.nii.gz 0.500000 1.000000 1.000000 0.000000
200322-13:01:52,882 nipype.workflow INFO:
[Node] Finished "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.brain_extraction_wf.thr_brainmask".
200322-13:01:53,308 nipype.workflow INFO:
[Node] Setting-up "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.03_pad_mask" in "/gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/03_pad_mask".
200322-13:01:53,309 nipype.workflow INFO:
[Node] Setting-up "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.brain_extraction_wf.dil_brainmask" in "/gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/brain_extraction_wf/dil_brainmask".
200322-13:01:53,314 nipype.workflow INFO:
[Node] Running "dil_brainmask" ("niworkflows.interfaces.ants.ImageMath"), a CommandLine Interface with command:
ImageMath 3 tpl-OASIS30ANTs_res-01_label-brain_probseg_trans_resampled_maths.nii.gz MD /gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/brain_extraction_wf/thr_brainmask/tpl-OASIS30ANTs_res-01_label-brain_probseg_trans_resampled.nii.gz 2
200322-13:01:53,314 nipype.workflow INFO:
[Node] Running "03_pad_mask" ("niworkflows.interfaces.ants.ImageMath"), a CommandLine Interface with command:
ImageMath 3 tpl-OASIS30ANTs_res-01_label-brain_probseg_trans_resampled_maths.nii.gz PadImage /gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/brain_extraction_wf/thr_brainmask/tpl-OASIS30ANTs_res-01_label-brain_probseg_trans_resampled.nii.gz 10
200322-13:01:54,918 nipype.workflow INFO:
[Node] Finished "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.03_pad_mask".
200322-13:01:55,630 nipype.workflow INFO:
[Node] Finished "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.brain_extraction_wf.dil_brainmask".
200322-13:01:57,309 nipype.workflow INFO:
[Node] Setting-up "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.brain_extraction_wf.get_brainmask" in "/gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/brain_extraction_wf/get_brainmask".
200322-13:01:57,318 nipype.workflow INFO:
[Node] Running "get_brainmask" ("niworkflows.interfaces.ants.ImageMath"), a CommandLine Interface with command:
ImageMath 3 tpl-OASIS30ANTs_res-01_label-brain_probseg_trans_resampled_maths_maths.nii.gz GetLargestComponent /gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/brain_extraction_wf/dil_brainmask/tpl-OASIS30ANTs_res-01_label-brain_probseg_trans_resampled_maths.nii.gz
200322-13:01:59,350 nipype.workflow INFO:
[Node] Finished "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.brain_extraction_wf.get_brainmask".
200322-13:02:01,311 nipype.workflow INFO:
[Node] Setting-up "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.01_atropos" in "/gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/01_atropos".
200322-13:02:01,322 nipype.workflow INFO:
[Node] Running "01_atropos" ("nipype.interfaces.ants.segmentation.Atropos"), a CommandLine Interface with command:
Atropos --image-dimensionality 3 --initialization KMeans[3] --intensity-image /gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/brain_extraction_wf/inu_n4/mapflow/_inu_n40/sub-01_ses-01_T1w_maths_corrected.nii.gz --likelihood-model Gaussian --mask-image /gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/brain_extraction_wf/get_brainmask/tpl-OASIS30ANTs_res-01_label-brain_probseg_trans_resampled_maths_maths.nii.gz --mrf [0.1,1x1x1] --convergence [3,0] --output [sub-01_ses-01_T1w_maths_corrected_labeled.nii.gz] --use-random-seed 1
200322-13:03:40,871 nipype.workflow INFO:
[Node] Finished "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.01_atropos".
200322-13:03:41,418 nipype.workflow INFO:
[Node] Setting-up "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.02_pad_segm" in "/gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/02_pad_segm".
200322-13:03:41,429 nipype.workflow INFO:
[Node] Running "02_pad_segm" ("niworkflows.interfaces.ants.ImageMath"), a CommandLine Interface with command:
ImageMath 3 sub-01_ses-01_T1w_maths_corrected_labeled_maths.nii.gz PadImage /gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/01_atropos/sub-01_ses-01_T1w_maths_corrected_labeled.nii.gz 10
200322-13:03:43,397 nipype.workflow INFO:
[Node] Finished "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.02_pad_segm".
200322-13:03:45,422 nipype.workflow INFO:
[Node] Setting-up "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.04_sel_labels" in "/gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/04_sel_labels".
200322-13:03:45,429 nipype.workflow INFO:
[Node] Running "04_sel_labels" ("nipype.interfaces.utility.wrappers.Function")
200322-13:03:45,901 nipype.workflow INFO:
[Node] Finished "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.04_sel_labels".
200322-13:03:47,428 nipype.workflow INFO:
[Node] Setting-up "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.27_depad_csf" in "/gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/27_depad_csf".
200322-13:03:47,428 nipype.workflow INFO:
[Node] Setting-up "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.10_me_csf" in "/gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/10_me_csf".
200322-13:03:47,429 nipype.workflow INFO:
[Node] Setting-up "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.06_get_gm" in "/gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/06_get_gm".
200322-13:03:47,429 nipype.workflow INFO:
[Node] Setting-up "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.05_get_wm" in "/gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/05_get_wm".
200322-13:03:47,438 nipype.workflow INFO:
[Node] Running "05_get_wm" ("niworkflows.interfaces.ants.ImageMath"), a CommandLine Interface with command:
ImageMath 3 sub-01_ses-01_T1w_maths_corrected_labeled_maths_class-03_maths.nii.gz GetLargestComponent /gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/04_sel_labels/sub-01_ses-01_T1w_maths_corrected_labeled_maths_class-03.nii.gz
200322-13:03:47,438 nipype.workflow INFO:
[Node] Running "10_me_csf" ("niworkflows.interfaces.ants.ImageMath"), a CommandLine Interface with command:
ImageMath 3 sub-01_ses-01_T1w_maths_corrected_labeled_maths_class-01_maths.nii.gz ME /gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/04_sel_labels/sub-01_ses-01_T1w_maths_corrected_labeled_maths_class-01.nii.gz 10
200322-13:03:47,438 nipype.workflow INFO:
[Node] Running "06_get_gm" ("niworkflows.interfaces.ants.ImageMath"), a CommandLine Interface with command:
ImageMath 3 sub-01_ses-01_T1w_maths_corrected_labeled_maths_class-02_maths.nii.gz GetLargestComponent /gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/04_sel_labels/sub-01_ses-01_T1w_maths_corrected_labeled_maths_class-02.nii.gz
200322-13:03:47,444 nipype.workflow INFO:
[Node] Running "27_depad_csf" ("niworkflows.interfaces.ants.ImageMath"), a CommandLine Interface with command:
ImageMath 3 sub-01_ses-01_T1w_maths_corrected_labeled_maths_class-01_maths.nii.gz PadImage /gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/04_sel_labels/sub-01_ses-01_T1w_maths_corrected_labeled_maths_class-01.nii.gz -10
200322-13:03:48,815 nipype.workflow INFO:
[Node] Finished "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.27_depad_csf".
200322-13:03:49,884 nipype.workflow INFO:
[Node] Finished "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.05_get_wm".
200322-13:03:49,968 nipype.workflow INFO:
[Node] Finished "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.06_get_gm".
200322-13:03:51,425 nipype.workflow INFO:
[Node] Setting-up "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.07_fill_gm" in "/gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/07_fill_gm".
200322-13:03:51,425 nipype.workflow INFO:
[Node] Setting-up "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.09_relabel_wm" in "/gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/09_relabel_wm".
200322-13:03:51,432 nipype.workflow INFO:
[Node] Running "07_fill_gm" ("niworkflows.interfaces.ants.ImageMath"), a CommandLine Interface with command:
ImageMath 3 sub-01_ses-01_T1w_maths_corrected_labeled_maths_class-02_maths_maths.nii.gz FillHoles /gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/06_get_gm/sub-01_ses-01_T1w_maths_corrected_labeled_maths_class-02_maths.nii.gz 2
200322-13:03:51,432 nipype.workflow INFO:
[Node] Running "09_relabel_wm" ("nipype.interfaces.ants.utils.MultiplyImages"), a CommandLine Interface with command:
MultiplyImages 3 /gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/05_get_wm/sub-01_ses-01_T1w_maths_corrected_labeled_maths_class-03_maths.nii.gz 3.0 09_relabel_wm.nii.gz
200322-13:03:52,768 nipype.workflow INFO:
[Node] Finished "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.09_relabel_wm".
200322-13:03:53,431 nipype.workflow INFO:
[Node] Setting-up "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.26_depad_wm" in "/gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/26_depad_wm".
200322-13:03:53,440 nipype.workflow INFO:
[Node] Running "26_depad_wm" ("niworkflows.interfaces.ants.ImageMath"), a CommandLine Interface with command:
ImageMath 3 09_relabel_wm_maths.nii.gz PadImage /gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/09_relabel_wm/09_relabel_wm.nii.gz -10
200322-13:03:54,484 nipype.workflow INFO:
[Node] Finished "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.10_me_csf".
200322-13:03:55,108 nipype.workflow INFO:
[Node] Finished "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.26_depad_wm".
200322-13:04:05,195 nipype.workflow INFO:
[Node] Finished "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.07_fill_gm".
200322-13:04:05,441 nipype.workflow INFO:
[Node] Setting-up "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.08_mult_gm" in "/gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/08_mult_gm".
200322-13:04:05,448 nipype.workflow INFO:
[Node] Running "08_mult_gm" ("nipype.interfaces.ants.utils.MultiplyImages"), a CommandLine Interface with command:
MultiplyImages 3 /gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/06_get_gm/sub-01_ses-01_T1w_maths_corrected_labeled_maths_class-02_maths.nii.gz /gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/07_fill_gm/sub-01_ses-01_T1w_maths_corrected_labeled_maths_class-02_maths_maths.nii.gz 08_mult_gm.nii.gz
200322-13:04:06,982 nipype.workflow INFO:
[Node] Finished "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.08_mult_gm".
200322-13:04:07,442 nipype.workflow INFO:
[Node] Setting-up "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.11_add_gm" in "/gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/11_add_gm".
200322-13:04:07,452 nipype.workflow INFO:
[Node] Running "11_add_gm" ("niworkflows.interfaces.ants.ImageMath"), a CommandLine Interface with command:
ImageMath 3 08_mult_gm_maths.nii.gz addtozero /gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/08_mult_gm/08_mult_gm.nii.gz /gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/10_me_csf/sub-01_ses-01_T1w_maths_corrected_labeled_maths_class-01_maths.nii.gz
200322-13:04:13,614 nipype.workflow INFO:
[Node] Finished "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.11_add_gm".
200322-13:04:15,455 nipype.workflow INFO:
[Node] Setting-up "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.12_relabel_gm" in "/gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/12_relabel_gm".
200322-13:04:15,463 nipype.workflow INFO:
[Node] Running "12_relabel_gm" ("nipype.interfaces.ants.utils.MultiplyImages"), a CommandLine Interface with command:
MultiplyImages 3 /gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/11_add_gm/08_mult_gm_maths.nii.gz 2.0 12_relabel_gm.nii.gz
200322-13:04:16,618 nipype.workflow INFO:
[Node] Finished "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.12_relabel_gm".
200322-13:04:17,456 nipype.workflow INFO:
[Node] Setting-up "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.25_depad_gm" in "/gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/25_depad_gm".
200322-13:04:17,456 nipype.workflow INFO:
[Node] Setting-up "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.13_add_gm_wm" in "/gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/13_add_gm_wm".
200322-13:04:17,463 nipype.workflow INFO:
[Node] Running "25_depad_gm" ("niworkflows.interfaces.ants.ImageMath"), a CommandLine Interface with command:
ImageMath 3 12_relabel_gm_maths.nii.gz PadImage /gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/12_relabel_gm/12_relabel_gm.nii.gz -10
200322-13:04:17,463 nipype.workflow INFO:
[Node] Running "13_add_gm_wm" ("niworkflows.interfaces.ants.ImageMath"), a CommandLine Interface with command:
ImageMath 3 09_relabel_wm_maths.nii.gz addtozero /gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/09_relabel_wm/09_relabel_wm.nii.gz /gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/12_relabel_gm/12_relabel_gm.nii.gz
200322-13:04:19,171 nipype.workflow INFO:
[Node] Finished "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.25_depad_gm".
200322-13:04:19,455 nipype.workflow INFO:
[Node] Setting-up "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.merge_tpms" in "/gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/merge_tpms".
200322-13:04:19,479 nipype.workflow INFO:
[Node] Running "merge_tpms" ("nipype.interfaces.utility.base.Merge")
200322-13:04:19,483 nipype.workflow INFO:
[Node] Finished "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.merge_tpms".
200322-13:04:23,803 nipype.workflow INFO:
[Node] Finished "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.13_add_gm_wm".
200322-13:04:25,461 nipype.workflow INFO:
[Node] Setting-up "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.24_depad_segm" in "/gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/24_depad_segm".
200322-13:04:25,461 nipype.workflow INFO:
[Node] Setting-up "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.14_sel_labels2" in "/gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/14_sel_labels2".
200322-13:04:25,466 nipype.workflow INFO:
[Node] Running "14_sel_labels2" ("nipype.interfaces.utility.wrappers.Function")
200322-13:04:25,467 nipype.workflow INFO:
[Node] Running "24_depad_segm" ("niworkflows.interfaces.ants.ImageMath"), a CommandLine Interface with command:
ImageMath 3 09_relabel_wm_maths_maths.nii.gz PadImage /gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/13_add_gm_wm/09_relabel_wm_maths.nii.gz -10
200322-13:04:25,789 nipype.workflow INFO:
[Node] Finished "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.14_sel_labels2".
200322-13:04:27,159 nipype.workflow INFO:
[Node] Finished "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.24_depad_segm".
200322-13:04:27,462 nipype.workflow INFO:
[Node] Setting-up "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.15_add_7" in "/gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/15_add_7".
200322-13:04:27,470 nipype.workflow INFO:
[Node] Running "15_add_7" ("niworkflows.interfaces.ants.ImageMath"), a CommandLine Interface with command:
ImageMath 3 09_relabel_wm_maths_class-03_maths.nii.gz addtozero /gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/14_sel_labels2/09_relabel_wm_maths_class-03.nii.gz /gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/14_sel_labels2/09_relabel_wm_maths_class-02.nii.gz
200322-13:04:33,165 nipype.workflow INFO:
[Node] Finished "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.15_add_7".
200322-13:04:33,466 nipype.workflow INFO:
[Node] Setting-up "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.16_me_7" in "/gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/16_me_7".
200322-13:04:33,472 nipype.workflow INFO:
[Node] Running "16_me_7" ("niworkflows.interfaces.ants.ImageMath"), a CommandLine Interface with command:
ImageMath 3 09_relabel_wm_maths_class-03_maths_maths.nii.gz ME /gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/15_add_7/09_relabel_wm_maths_class-03_maths.nii.gz 2
200322-13:04:38,50 nipype.workflow INFO:
[Node] Finished "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.16_me_7".
200322-13:04:39,478 nipype.workflow INFO:
[Node] Setting-up "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.17_comp_7" in "/gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/17_comp_7".
200322-13:04:39,485 nipype.workflow INFO:
[Node] Running "17_comp_7" ("niworkflows.interfaces.ants.ImageMath"), a CommandLine Interface with command:
ImageMath 3 09_relabel_wm_maths_class-03_maths_maths_maths.nii.gz GetLargestComponent /gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/16_me_7/09_relabel_wm_maths_class-03_maths_maths.nii.gz
200322-13:04:41,931 nipype.workflow INFO:
[Node] Finished "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.17_comp_7".
200322-13:04:43,479 nipype.workflow INFO:
[Node] Setting-up "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.18_md_7" in "/gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/18_md_7".
200322-13:04:43,485 nipype.workflow INFO:
[Node] Running "18_md_7" ("niworkflows.interfaces.ants.ImageMath"), a CommandLine Interface with command:
ImageMath 3 09_relabel_wm_maths_class-03_maths_maths_maths_maths.nii.gz MD /gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/17_comp_7/09_relabel_wm_maths_class-03_maths_maths_maths.nii.gz 4
200322-13:04:46,377 nipype.workflow INFO:
[Node] Finished "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.18_md_7".
200322-13:04:47,484 nipype.workflow INFO:
[Node] Setting-up "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.19_fill_7" in "/gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/19_fill_7".
200322-13:04:47,491 nipype.workflow INFO:
[Node] Running "19_fill_7" ("niworkflows.interfaces.ants.ImageMath"), a CommandLine Interface with command:
ImageMath 3 09_relabel_wm_maths_class-03_maths_maths_maths_maths_maths.nii.gz FillHoles /gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/18_md_7/09_relabel_wm_maths_class-03_maths_maths_maths_maths.nii.gz 2
200322-13:04:59,509 nipype.workflow INFO:
[Node] Finished "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.19_fill_7".
200322-13:05:01,495 nipype.workflow INFO:
[Node] Setting-up "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.20_add_7_2" in "/gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/20_add_7_2".
200322-13:05:01,503 nipype.workflow INFO:
[Node] Running "20_add_7_2" ("niworkflows.interfaces.ants.ImageMath"), a CommandLine Interface with command:
ImageMath 3 09_relabel_wm_maths_class-03_maths_maths_maths_maths_maths_maths.nii.gz addtozero /gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/19_fill_7/09_relabel_wm_maths_class-03_maths_maths_maths_maths_maths.nii.gz /gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/03_pad_mask/tpl-OASIS30ANTs_res-01_label-brain_probseg_trans_resampled_maths.nii.gz
200322-13:05:07,345 nipype.workflow INFO:
[Node] Finished "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.20_add_7_2".
200322-13:05:07,503 nipype.workflow INFO:
[Node] Setting-up "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.21_md_7_2" in "/gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/21_md_7_2".
200322-13:05:07,510 nipype.workflow INFO:
[Node] Running "21_md_7_2" ("niworkflows.interfaces.ants.ImageMath"), a CommandLine Interface with command:
ImageMath 3 09_relabel_wm_maths_class-03_maths_maths_maths_maths_maths_maths_maths.nii.gz MD /gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/20_add_7_2/09_relabel_wm_maths_class-03_maths_maths_maths_maths_maths_maths.nii.gz 5
200322-13:05:10,318 nipype.workflow INFO:
[Node] Finished "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.21_md_7_2".
200322-13:05:11,519 nipype.workflow INFO:
[Node] Setting-up "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.22_me_7_2" in "/gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/22_me_7_2".
200322-13:05:11,541 nipype.workflow INFO:
[Node] Running "22_me_7_2" ("niworkflows.interfaces.ants.ImageMath"), a CommandLine Interface with command:
ImageMath 3 09_relabel_wm_maths_class-03_maths_maths_maths_maths_maths_maths_maths_maths.nii.gz ME /gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/21_md_7_2/09_relabel_wm_maths_class-03_maths_maths_maths_maths_maths_maths_maths.nii.gz 5
200322-13:05:16,256 nipype.workflow INFO:
[Node] Finished "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.22_me_7_2".
200322-13:05:17,513 nipype.workflow INFO:
[Node] Setting-up "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.23_depad_mask" in "/gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/23_depad_mask".
200322-13:05:17,521 nipype.workflow INFO:
[Node] Running "23_depad_mask" ("niworkflows.interfaces.ants.ImageMath"), a CommandLine Interface with command:
ImageMath 3 09_relabel_wm_maths_class-03_maths_maths_maths_maths_maths_maths_maths_maths_maths.nii.gz PadImage /gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/22_me_7_2/09_relabel_wm_maths_class-03_maths_maths_maths_maths_maths_maths_maths_maths.nii.gz -10
200322-13:05:18,836 nipype.workflow INFO:
[Node] Finished "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.23_depad_mask".
200322-13:05:19,515 nipype.workflow INFO:
[Node] Setting-up "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.msk_conform" in "/gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/msk_conform".
200322-13:05:19,530 nipype.workflow INFO:
[Node] Running "msk_conform" ("nipype.interfaces.utility.wrappers.Function")
200322-13:05:19,933 nipype.workflow INFO:
[Node] Finished "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.msk_conform".
200322-13:05:23,325 nipype.workflow INFO:
[Node] Setting-up "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.surface_recon_wf.autorecon1" in "/gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/surface_recon_wf/autorecon1".
200322-13:05:23,344 nipype.workflow INFO:
[Node] Running "autorecon1" ("smriprep.interfaces.freesurfer.ReconAll"), a CommandLine Interface with command:
recon-all -autorecon1 -i /data/sub-01/ses-01/anat/sub-01_ses-01_T1w.nii.gz -T2 /data/sub-01/ses-01/anat/sub-01_ses-01_T2w.nii.gz -noskullstrip -cw256 -hires -openmp 4 -subjid sub-01 -sd /out/freesurfer -expert /gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/surface_recon_wf/autorecon1/expert.opts
200322-13:19:43,929 nipype.workflow INFO:
[Node] Finished "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.surface_recon_wf.autorecon1".
200322-13:19:44,507 nipype.workflow INFO:
[Node] Setting-up "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.surface_recon_wf.fsnative2t1w_xfm" in "/gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/surface_recon_wf/fsnative2t1w_xfm".
200322-13:19:44,664 nipype.workflow INFO:
[Node] Running "fsnative2t1w_xfm" ("niworkflows.interfaces.freesurfer.PatchedRobustRegister"), a CommandLine Interface with command:
mri_robust_register --satit --iscale --lta /gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/surface_recon_wf/fsnative2t1w_xfm/T1_robustreg.lta --mov /out/freesurfer/sub-01/mri/T1.mgz --dst /data/sub-01/ses-01/anat/sub-01_ses-01_T1w.nii.gz
200322-13:21:16,788 nipype.workflow INFO:
[Node] Finished "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.surface_recon_wf.fsnative2t1w_xfm".
200322-13:21:18,486 nipype.workflow INFO:
[Node] Setting-up "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.brain_extraction_wf.inu_n4_final" in "/gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/brain_extraction_wf/inu_n4_final".
200322-13:21:18,497 nipype.workflow INFO:
[Node] Setting-up "_inu_n4_final0" in "/gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/brain_extraction_wf/inu_n4_final/mapflow/_inu_n4_final0".
200322-13:21:18,503 nipype.workflow INFO:
[Node] Running "_inu_n4_final0" ("nipype.interfaces.ants.segmentation.N4BiasFieldCorrection"), a CommandLine Interface with command:
N4BiasFieldCorrection --bspline-fitting [ 200 ] -d 3 --input-image /data/sub-01/ses-01/anat/sub-01_ses-01_T1w.nii.gz --convergence [ 50x50x50x50x50, 1e-07 ] --output [ sub-01_ses-01_T1w_corrected.nii.gz, sub-01_ses-01_T1w_bias.nii.gz ] -r --shrink-factor 4 --weight-image /gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/copy_xform/09_relabel_wm_maths_xform.nii.gz
200322-13:22:26,635 nipype.workflow INFO:
[Node] Finished "_inu_n4_final0".
200322-13:22:26,638 nipype.workflow INFO:
[Node] Finished "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.brain_extraction_wf.inu_n4_final".
200322-13:22:28,561 nipype.workflow INFO:
[Node] Setting-up "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.brain_extraction_wf.apply_mask" in "/gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/brain_extraction_wf/apply_mask".
200322-13:22:28,561 nipype.workflow INFO:
[Node] Setting-up "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.anat_derivatives_wf.lta2itk_inv" in "/gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/anat_derivatives_wf/lta2itk_inv".
200322-13:22:28,562 nipype.workflow INFO:
[Node] Setting-up "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.surface_recon_wf.t1w2fsnative_xfm" in "/gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/surface_recon_wf/t1w2fsnative_xfm".
200322-13:22:28,567 nipype.workflow INFO:
[Node] Setting-up "_apply_mask0" in "/gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/brain_extraction_wf/apply_mask/mapflow/_apply_mask0".
200322-13:22:28,570 nipype.workflow INFO:
[Node] Running "_apply_mask0" ("nipype.interfaces.fsl.maths.ApplyMask"), a CommandLine Interface with command:
fslmaths /gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/brain_extraction_wf/inu_n4_final/mapflow/_inu_n4_final0/sub-01_ses-01_T1w_corrected.nii.gz -mas /gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/copy_xform/09_relabel_wm_mask_xform.nii.gz /gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/brain_extraction_wf/apply_mask/mapflow/_apply_mask0/sub-01_ses-01_T1w_corrected_masked.nii.gz
200322-13:22:28,586 nipype.workflow INFO:
[Node] Running "lta2itk_inv" ("niworkflows.interfaces.freesurfer.PatchedLTAConvert"), a CommandLine Interface with command:
lta_convert --inlta /gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/surface_recon_wf/fsnative2t1w_xfm/T1_robustreg.lta --outitk /gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/anat_derivatives_wf/lta2itk_inv/out.txt
200322-13:22:28,587 nipype.workflow INFO:
[Node] Running "t1w2fsnative_xfm" ("niworkflows.interfaces.freesurfer.PatchedLTAConvert"), a CommandLine Interface with command:
lta_convert --inlta /gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/surface_recon_wf/fsnative2t1w_xfm/T1_robustreg.lta --invert --outlta /gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/surface_recon_wf/t1w2fsnative_xfm/out.lta
200322-13:22:28,677 nipype.workflow INFO:
[Node] Finished "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.anat_derivatives_wf.lta2itk_inv".
200322-13:22:28,678 nipype.workflow INFO:
[Node] Finished "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.surface_recon_wf.t1w2fsnative_xfm".
200322-13:22:30,677 nipype.workflow INFO:
[Node] Setting-up "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.anat_derivatives_wf.lta2itk_fwd" in "/gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/anat_derivatives_wf/lta2itk_fwd".
200322-13:22:30,684 nipype.workflow INFO:
[Node] Running "lta2itk_fwd" ("niworkflows.interfaces.freesurfer.PatchedLTAConvert"), a CommandLine Interface with command:
lta_convert --inlta /gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/surface_recon_wf/t1w2fsnative_xfm/out.lta --outitk /gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/anat_derivatives_wf/lta2itk_fwd/out.txt
200322-13:22:30,772 nipype.workflow INFO:
[Node] Finished "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.anat_derivatives_wf.lta2itk_fwd".
200322-13:22:30,920 nipype.workflow INFO:
[Node] Finished "_apply_mask0".
200322-13:22:30,923 nipype.workflow INFO:
[Node] Finished "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.brain_extraction_wf.apply_mask".
200322-13:22:50,59 nipype.workflow INFO:
[Node] Setting-up "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.anat_norm_wf.trunc_mov" in "/gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/anat_norm_wf/trunc_mov".
200322-13:22:50,60 nipype.workflow INFO:
[Node] Setting-up "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.surface_recon_wf.skull_strip_extern" in "/gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/surface_recon_wf/skull_strip_extern".
200322-13:22:50,70 nipype.workflow INFO:
[Node] Running "trunc_mov" ("niworkflows.interfaces.ants.ImageMath"), a CommandLine Interface with command:
ImageMath 3 sub-01_ses-01_T1w_corrected_xform_maths.nii.gz TruncateImageIntensity /gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/brain_extraction_wf/copy_xform/sub-01_ses-01_T1w_corrected_xform.nii.gz 0.01 0.999 256
200322-13:22:50,93 nipype.workflow INFO:
[Node] Running "skull_strip_extern" ("niworkflows.interfaces.freesurfer.FSInjectBrainExtracted")
200322-13:22:53,396 nipype.workflow INFO:
[Node] Finished "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.surface_recon_wf.skull_strip_extern".
200322-13:22:59,858 nipype.workflow INFO:
[Node] Finished "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.anat_norm_wf.trunc_mov".
200322-13:23:00,325 nipype.workflow INFO:
[Node] Setting-up "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.surface_recon_wf.autorecon_resume_wf.autorecon2_vol" in "/gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/surface_recon_wf/autorecon_resume_wf/autorecon2_vol".
200322-13:23:00,335 nipype.interface INFO:
resume recon-all : recon-all -autorecon2-volonly -openmp 4 -subjid sub-01 -sd /out/freesurfer
200322-13:23:00,335 nipype.workflow INFO:
[Node] Running "autorecon2_vol" ("smriprep.interfaces.freesurfer.ReconAll"), a CommandLine Interface with command:
recon-all -autorecon2-volonly -openmp 4 -subjid sub-01 -sd /out/freesurfer
200322-13:23:00,337 nipype.interface INFO:
resume recon-all : recon-all -autorecon2-volonly -openmp 4 -subjid sub-01 -sd /out/freesurfer
200322-16:36:30,291 nipype.workflow INFO:
[Node] Finished "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.surface_recon_wf.autorecon_resume_wf.autorecon2_vol".
200322-16:36:34,41 nipype.workflow INFO:
[Node] Setting-up "_autorecon_surfs0" in "/gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/surface_recon_wf/autorecon_resume_wf/autorecon_surfs/mapflow/_autorecon_surfs0".
200322-16:36:34,50 nipype.interface INFO:
resume recon-all : recon-all -autorecon-hemi lh -noparcstats -noparcstats2 -noparcstats3 -nohyporelabel -nobalabels -openmp 4 -subjid sub-01 -sd /out/freesurfer
200322-16:36:34,50 nipype.workflow INFO:
[Node] Running "_autorecon_surfs0" ("smriprep.interfaces.freesurfer.ReconAll"), a CommandLine Interface with command:
recon-all -autorecon-hemi lh -noparcstats -noparcstats2 -noparcstats3 -nohyporelabel -nobalabels -openmp 4 -subjid sub-01 -sd /out/freesurfer
200322-16:36:34,52 nipype.interface INFO:
resume recon-all : recon-all -autorecon-hemi lh -noparcstats -noparcstats2 -noparcstats3 -nohyporelabel -nobalabels -openmp 4 -subjid sub-01 -sd /out/freesurfer
200322-18:37:07,389 nipype.workflow INFO:
[Node] Finished "_autorecon_surfs0".
200322-18:37:09,379 nipype.workflow INFO:
[Node] Setting-up "_autorecon_surfs1" in "/gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/surface_recon_wf/autorecon_resume_wf/autorecon_surfs/mapflow/_autorecon_surfs1".
200322-18:37:09,394 nipype.interface INFO:
resume recon-all : recon-all -autorecon-hemi rh -noparcstats -noparcstats2 -noparcstats3 -nohyporelabel -nobalabels -openmp 4 -subjid sub-01 -sd /out/freesurfer
200322-18:37:09,396 nipype.workflow INFO:
[Node] Running "_autorecon_surfs1" ("smriprep.interfaces.freesurfer.ReconAll"), a CommandLine Interface with command:
recon-all -autorecon-hemi rh -noparcstats -noparcstats2 -noparcstats3 -nohyporelabel -nobalabels -openmp 4 -subjid sub-01 -sd /out/freesurfer
200322-18:37:09,397 nipype.interface INFO:
resume recon-all : recon-all -autorecon-hemi rh -noparcstats -noparcstats2 -noparcstats3 -nohyporelabel -nobalabels -openmp 4 -subjid sub-01 -sd /out/freesurfer
200322-20:49:01,261 nipype.workflow INFO:
[Node] Finished "_autorecon_surfs1".
200322-20:49:01,362 nipype.workflow INFO:
[Node] Setting-up "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.surface_recon_wf.autorecon_resume_wf.autorecon_surfs" in "/gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/surface_recon_wf/autorecon_resume_wf/autorecon_surfs".
200322-20:49:01,372 nipype.workflow INFO:
[Node] Setting-up "_autorecon_surfs0" in "/gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/surface_recon_wf/autorecon_resume_wf/autorecon_surfs/mapflow/_autorecon_surfs0".
200322-20:49:01,393 nipype.interface INFO:
recon-all complete : Not running
200322-20:49:01,393 nipype.workflow INFO:
[Node] Running "_autorecon_surfs0" ("smriprep.interfaces.freesurfer.ReconAll"), a CommandLine Interface with command:
echo recon-all: nothing to do
200322-20:49:01,394 nipype.interface INFO:
recon-all complete : Not running
200322-20:49:01,465 nipype.workflow INFO:
[Node] Finished "_autorecon_surfs0".
200322-20:49:01,467 nipype.workflow INFO:
[Node] Setting-up "_autorecon_surfs1" in "/gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/surface_recon_wf/autorecon_resume_wf/autorecon_surfs/mapflow/_autorecon_surfs1".
200322-20:49:01,478 nipype.interface INFO:
recon-all complete : Not running
200322-20:49:01,479 nipype.workflow INFO:
[Node] Running "_autorecon_surfs1" ("smriprep.interfaces.freesurfer.ReconAll"), a CommandLine Interface with command:
echo recon-all: nothing to do
200322-20:49:01,480 nipype.interface INFO:
recon-all complete : Not running
200322-20:49:01,547 nipype.workflow INFO:
[Node] Finished "_autorecon_surfs1".
200322-20:49:01,550 nipype.workflow INFO:
[Node] Finished "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.surface_recon_wf.autorecon_resume_wf.autorecon_surfs".
200322-20:49:03,376 nipype.workflow INFO:
[Node] Setting-up "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.surface_recon_wf.autorecon_resume_wf.cortribbon" in "/gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/surface_recon_wf/autorecon_resume_wf/cortribbon".
200322-20:49:03,384 nipype.interface INFO:
resume recon-all : recon-all -parallel -subjid sub-01 -sd /out/freesurfer -T2pial -cortribbon
200322-20:49:03,384 nipype.workflow INFO:
[Node] Running "cortribbon" ("smriprep.interfaces.freesurfer.ReconAll"), a CommandLine Interface with command:
recon-all -parallel -subjid sub-01 -sd /out/freesurfer -T2pial -cortribbon
200322-20:49:03,385 nipype.interface INFO:
resume recon-all : recon-all -parallel -subjid sub-01 -sd /out/freesurfer -T2pial -cortribbon
200322-21:59:21,35 nipype.workflow INFO:
[Node] Finished "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.surface_recon_wf.autorecon_resume_wf.cortribbon".
200322-21:59:23,439 nipype.workflow INFO:
[Node] Setting-up "_parcstats0" in "/gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/surface_recon_wf/autorecon_resume_wf/parcstats/mapflow/_parcstats0".
200322-21:59:23,444 nipype.interface INFO:
resume recon-all : recon-all -autorecon-hemi lh -nohyporelabel -openmp 4 -subjid sub-01 -sd /out/freesurfer -notessellate -nosmooth1 -noinflate1 -noqsphere -nofix -nowhite -nosmooth2 -noinflate2 -nocurvHK -nocurvstats -nosphere -nosurfreg -nojacobian_white -noavgcurv -nocortparc -nopial -nocortparc2 -nocortparc3 -nopctsurfcon
200322-21:59:23,444 nipype.workflow INFO:
[Node] Running "_parcstats0" ("smriprep.interfaces.freesurfer.ReconAll"), a CommandLine Interface with command:
recon-all -autorecon-hemi lh -nohyporelabel -openmp 4 -subjid sub-01 -sd /out/freesurfer -notessellate -nosmooth1 -noinflate1 -noqsphere -nofix -nowhite -nosmooth2 -noinflate2 -nocurvHK -nocurvstats -nosphere -nosurfreg -nojacobian_white -noavgcurv -nocortparc -nopial -nocortparc2 -nocortparc3 -nopctsurfcon
200322-21:59:23,446 nipype.interface INFO:
resume recon-all : recon-all -autorecon-hemi lh -nohyporelabel -openmp 4 -subjid sub-01 -sd /out/freesurfer -notessellate -nosmooth1 -noinflate1 -noqsphere -nofix -nowhite -nosmooth2 -noinflate2 -nocurvHK -nocurvstats -nosphere -nosurfreg -nojacobian_white -noavgcurv -nocortparc -nopial -nocortparc2 -nocortparc3 -nopctsurfcon
200322-22:07:16,321 nipype.workflow INFO:
[Node] Finished "_parcstats0".
200322-22:07:17,934 nipype.workflow INFO:
[Node] Setting-up "_parcstats1" in "/gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/surface_recon_wf/autorecon_resume_wf/parcstats/mapflow/_parcstats1".
200322-22:07:17,939 nipype.interface INFO:
resume recon-all : recon-all -autorecon-hemi rh -nohyporelabel -openmp 4 -subjid sub-01 -sd /out/freesurfer -notessellate -nosmooth1 -noinflate1 -noqsphere -nofix -nowhite -nosmooth2 -noinflate2 -nocurvHK -nocurvstats -nosphere -nosurfreg -nojacobian_white -noavgcurv -nocortparc -nopial -nocortparc2 -nocortparc3 -nopctsurfcon
200322-22:07:17,939 nipype.workflow INFO:
[Node] Running "_parcstats1" ("smriprep.interfaces.freesurfer.ReconAll"), a CommandLine Interface with command:
recon-all -autorecon-hemi rh -nohyporelabel -openmp 4 -subjid sub-01 -sd /out/freesurfer -notessellate -nosmooth1 -noinflate1 -noqsphere -nofix -nowhite -nosmooth2 -noinflate2 -nocurvHK -nocurvstats -nosphere -nosurfreg -nojacobian_white -noavgcurv -nocortparc -nopial -nocortparc2 -nocortparc3 -nopctsurfcon
200322-22:07:17,941 nipype.interface INFO:
resume recon-all : recon-all -autorecon-hemi rh -nohyporelabel -openmp 4 -subjid sub-01 -sd /out/freesurfer -notessellate -nosmooth1 -noinflate1 -noqsphere -nofix -nowhite -nosmooth2 -noinflate2 -nocurvHK -nocurvstats -nosphere -nosurfreg -nojacobian_white -noavgcurv -nocortparc -nopial -nocortparc2 -nocortparc3 -nopctsurfcon
200322-22:15:17,170 nipype.workflow INFO:
[Node] Finished "_parcstats1".
200322-22:15:18,439 nipype.workflow INFO:
[Node] Setting-up "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.surface_recon_wf.autorecon_resume_wf.parcstats" in "/gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/surface_recon_wf/autorecon_resume_wf/parcstats".
200322-22:15:18,446 nipype.workflow INFO:
[Node] Setting-up "_parcstats0" in "/gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/surface_recon_wf/autorecon_resume_wf/parcstats/mapflow/_parcstats0".
200322-22:15:18,450 nipype.interface INFO:
recon-all complete : Not running
200322-22:15:18,451 nipype.workflow INFO:
[Node] Running "_parcstats0" ("smriprep.interfaces.freesurfer.ReconAll"), a CommandLine Interface with command:
echo recon-all: nothing to do
200322-22:15:18,452 nipype.interface INFO:
recon-all complete : Not running
200322-22:15:18,521 nipype.workflow INFO:
[Node] Finished "_parcstats0".
200322-22:15:18,523 nipype.workflow INFO:
[Node] Setting-up "_parcstats1" in "/gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/surface_recon_wf/autorecon_resume_wf/parcstats/mapflow/_parcstats1".
200322-22:15:18,527 nipype.interface INFO:
recon-all complete : Not running
200322-22:15:18,528 nipype.workflow INFO:
[Node] Running "_parcstats1" ("smriprep.interfaces.freesurfer.ReconAll"), a CommandLine Interface with command:
echo recon-all: nothing to do
200322-22:15:18,529 nipype.interface INFO:
recon-all complete : Not running
200322-22:15:18,593 nipype.workflow INFO:
[Node] Finished "_parcstats1".
200322-22:15:18,596 nipype.workflow INFO:
[Node] Finished "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.surface_recon_wf.autorecon_resume_wf.parcstats".
200322-22:15:20,439 nipype.workflow INFO:
[Node] Setting-up "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.surface_recon_wf.autorecon_resume_wf.autorecon3" in "/gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/surface_recon_wf/autorecon_resume_wf/autorecon3".
200322-22:15:20,443 nipype.interface INFO:
resume recon-all : recon-all -autorecon3 -openmp 4 -subjid sub-01 -sd /out/freesurfer -nosphere -nosurfreg -nojacobian_white -noavgcurv -nocortparc -nopial -noparcstats -nocortparc2 -noparcstats2 -nocortparc3 -noparcstats3 -nopctsurfcon -nocortribbon -nobalabels
200322-22:15:20,443 nipype.workflow INFO:
[Node] Running "autorecon3" ("smriprep.interfaces.freesurfer.ReconAll"), a CommandLine Interface with command:
recon-all -autorecon3 -openmp 4 -subjid sub-01 -sd /out/freesurfer -nosphere -nosurfreg -nojacobian_white -noavgcurv -nocortparc -nopial -noparcstats -nocortparc2 -noparcstats2 -nocortparc3 -noparcstats3 -nopctsurfcon -nocortribbon -nobalabels
200322-22:15:20,445 nipype.interface INFO:
resume recon-all : recon-all -autorecon3 -openmp 4 -subjid sub-01 -sd /out/freesurfer -nosphere -nosurfreg -nojacobian_white -noavgcurv -nocortparc -nopial -noparcstats -nocortparc2 -noparcstats2 -nocortparc3 -noparcstats3 -nopctsurfcon -nocortribbon -nobalabels
200322-22:45:29,445 nipype.workflow INFO:
[Node] Finished "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.surface_recon_wf.autorecon_resume_wf.autorecon3".
200322-22:45:30,368 nipype.workflow INFO:
[Node] Setting-up "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.anat_reports_wf.recon_report" in "/gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/anat_reports_wf/recon_report".
200322-22:45:30,369 nipype.workflow INFO:
[Node] Setting-up "fmriprep_wf.single_subject_01_wf.func_preproc_ses_01_task_Stroop_run_01_wf.bold_surf_wf.targets" in "/gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/bold_surf_wf/targets".
200322-22:45:30,370 nipype.workflow INFO:
[Node] Setting-up "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.surface_recon_wf.segs_to_native_aparc_aseg.fs_datasource" in "/gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/surface_recon_wf/segs_to_native_aparc_aseg/fs_datasource".
200322-22:45:30,370 nipype.workflow INFO:
[Node] Setting-up "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.surface_recon_wf.segs_to_native_aseg.fs_datasource" in "/gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/surface_recon_wf/segs_to_native_aseg/fs_datasource".
200322-22:45:30,373 nipype.workflow INFO:
[Node] Running "recon_report" ("smriprep.interfaces.reports.FSSurfaceReport")
200322-22:45:30,374 nipype.workflow INFO:
[Node] Running "fs_datasource" ("nipype.interfaces.io.FreeSurferSource")
200322-22:45:30,374 nipype.workflow INFO:
[Node] Setting-up "_targets0" in "/gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/bold_surf_wf/targets/mapflow/_targets0".
200322-22:45:30,375 nipype.workflow INFO:
[Node] Running "fs_datasource" ("nipype.interfaces.io.FreeSurferSource")
200322-22:45:30,376 nipype.workflow INFO:
[Node] Running "_targets0" ("nipype.interfaces.utility.wrappers.Function")
200322-22:45:30,379 nipype.workflow INFO:
[Node] Finished "_targets0".
200322-22:45:30,380 nipype.workflow INFO:
[Node] Finished "fmriprep_wf.single_subject_01_wf.func_preproc_ses_01_task_Stroop_run_01_wf.bold_surf_wf.targets".
200322-22:45:30,385 nipype.workflow INFO:
[Node] Finished "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.surface_recon_wf.segs_to_native_aparc_aseg.fs_datasource".
200322-22:45:30,387 nipype.workflow INFO:
[Node] Finished "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.surface_recon_wf.segs_to_native_aseg.fs_datasource".
200322-22:45:32,385 nipype.workflow INFO:
[Node] Setting-up "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.surface_recon_wf.segs_to_native_aparc_aseg.tonative" in "/gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/surface_recon_wf/segs_to_native_aparc_aseg/tonative".
200322-22:45:32,385 nipype.workflow INFO:
[Node] Setting-up "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.surface_recon_wf.segs_to_native_aseg.tonative" in "/gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/surface_recon_wf/segs_to_native_aseg/tonative".
200322-22:45:32,385 nipype.workflow INFO:
[Node] Setting-up "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.surface_recon_wf.gifti_surface_wf.get_surfaces" in "/gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/get_surfaces".
200322-22:45:32,389 nipype.workflow INFO:
[Node] Running "get_surfaces" ("nipype.interfaces.io.FreeSurferSource")
200322-22:45:32,391 nipype.workflow INFO:
[Node] Running "tonative" ("nipype.interfaces.freesurfer.model.Label2Vol"), a CommandLine Interface with command:
mri_label2vol --regheader /out/freesurfer/sub-01/mri/aseg.mgz --seg /gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/surface_recon_wf/segs_to_native_aparc_aseg/tonative/aparc+aseg.mgz --temp /out/freesurfer/sub-01/mri/rawavg.mgz --o /gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/surface_recon_wf/segs_to_native_aparc_aseg/tonative/aparc+aseg_vol.nii.gz
200322-22:45:32,391 nipype.workflow INFO:
[Node] Running "tonative" ("nipype.interfaces.freesurfer.model.Label2Vol"), a CommandLine Interface with command:
mri_label2vol --regheader /out/freesurfer/sub-01/mri/aseg.mgz --seg /gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/surface_recon_wf/segs_to_native_aseg/tonative/aseg.mgz --temp /out/freesurfer/sub-01/mri/rawavg.mgz --o /gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/surface_recon_wf/segs_to_native_aseg/tonative/aseg_vol.nii.gz
200322-22:45:32,411 nipype.workflow INFO:
[Node] Finished "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.surface_recon_wf.gifti_surface_wf.get_surfaces".
200322-22:45:36,393 nipype.workflow INFO:
[Node] Setting-up "_midthickness0" in "/gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/midthickness/mapflow/_midthickness0".
200322-22:45:36,398 nipype.workflow INFO:
[Node] Running "_midthickness0" ("niworkflows.interfaces.freesurfer.MakeMidthickness"), a CommandLine Interface with command:
mris_expand -pial /gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/midthickness/mapflow/_midthickness0/rh.pial -thickness -thickness_name /gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/midthickness/mapflow/_midthickness0/rh.thickness /gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/midthickness/mapflow/_midthickness0/rh.smoothwm 0.5 midthickness
200322-22:45:41,694 nipype.workflow INFO:
[Node] Finished "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.anat_reports_wf.recon_report".
200322-22:45:42,509 nipype.workflow INFO:
[Node] Setting-up "_midthickness1" in "/gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/midthickness/mapflow/_midthickness1".
200322-22:45:42,514 nipype.workflow INFO:
[Node] Running "_midthickness1" ("niworkflows.interfaces.freesurfer.MakeMidthickness"), a CommandLine Interface with command:
mris_expand -pial /gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/midthickness/mapflow/_midthickness1/lh.pial -thickness -thickness_name /gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/midthickness/mapflow/_midthickness1/lh.thickness /gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/midthickness/mapflow/_midthickness1/lh.smoothwm 0.5 midthickness
200322-22:45:43,581 nipype.workflow INFO:
[Node] Finished "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.surface_recon_wf.segs_to_native_aseg.tonative".
200322-22:45:43,624 nipype.workflow INFO:
[Node] Finished "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.surface_recon_wf.segs_to_native_aparc_aseg.tonative".
200322-22:45:44,394 nipype.workflow INFO:
[Node] Setting-up "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.surface_recon_wf.segs_to_native_aparc_aseg.tonii" in "/gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/surface_recon_wf/segs_to_native_aparc_aseg/tonii".
200322-22:45:44,395 nipype.workflow INFO:
[Node] Setting-up "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.surface_recon_wf.segs_to_native_aseg.tonii" in "/gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/surface_recon_wf/segs_to_native_aseg/tonii".
200322-22:45:44,403 nipype.workflow INFO:
[Node] Running "tonii" ("nipype.interfaces.freesurfer.preprocess.MRIConvert"), a CommandLine Interface with command:
mri_convert --out_type nii --resample_type nearest --reslice_like /gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/brain_extraction_wf/copy_xform/sub-01_ses-01_T1w_corrected_xform.nii.gz --input_volume /gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/surface_recon_wf/segs_to_native_aseg/tonative/aseg_vol.nii.gz --output_volume /gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/surface_recon_wf/segs_to_native_aseg/tonii/aseg_vol_out.nii.gz
200322-22:45:44,403 nipype.workflow INFO:
[Node] Running "tonii" ("nipype.interfaces.freesurfer.preprocess.MRIConvert"), a CommandLine Interface with command:
mri_convert --out_type nii --resample_type nearest --reslice_like /gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/brain_extraction_wf/copy_xform/sub-01_ses-01_T1w_corrected_xform.nii.gz --input_volume /gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/surface_recon_wf/segs_to_native_aparc_aseg/tonative/aparc+aseg_vol.nii.gz --output_volume /gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/surface_recon_wf/segs_to_native_aparc_aseg/tonii/aparc+aseg_vol_out.nii.gz
200322-22:45:46,81 nipype.workflow INFO:
[Node] Finished "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.surface_recon_wf.segs_to_native_aseg.tonii".
200322-22:45:46,88 nipype.workflow INFO:
[Node] Finished "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.surface_recon_wf.segs_to_native_aparc_aseg.tonii".
200322-22:45:52,386 nipype.workflow INFO:
[Node] Setting-up "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.surface_recon_wf.refine" in "/gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/surface_recon_wf/refine".
200322-22:45:52,393 nipype.workflow INFO:
[Node] Running "refine" ("niworkflows.interfaces.freesurfer.RefineBrainMask")
200322-22:46:58,616 nipype.workflow INFO:
[Node] Finished "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.surface_recon_wf.refine".
200322-22:47:01,385 nipype.workflow INFO:
[Node] Setting-up "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.applyrefined" in "/gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/applyrefined".
200322-22:47:01,390 nipype.workflow INFO:
[Node] Running "applyrefined" ("nipype.interfaces.fsl.maths.ApplyMask"), a CommandLine Interface with command:
fslmaths /gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/brain_extraction_wf/copy_xform/sub-01_ses-01_T1w_corrected_xform.nii.gz -mas /gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/surface_recon_wf/refine/sub-01_ses-01_T1w_corrected_xform_rbrainmask.nii.gz /gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/applyrefined/sub-01_ses-01_T1w_corrected_xform_masked.nii.gz
200322-22:47:03,645 nipype.workflow INFO:
[Node] Finished "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.applyrefined".
200322-22:47:04,556 nipype.workflow INFO:
[Node] Setting-up "fmriprep_wf.single_subject_01_wf.func_preproc_ses_01_task_Stroop_run_01_wf.bold_t1_trans_wf.gen_ref" in "/gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/bold_t1_trans_wf/gen_ref".
200322-22:47:04,557 nipype.workflow INFO:
[Node] Setting-up "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.t1w_dseg" in "/gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/t1w_dseg".
200322-22:47:04,562 nipype.workflow INFO:
[Node] Running "t1w_dseg" ("nipype.interfaces.fsl.preprocess.FAST"), a CommandLine Interface with command:
fast -N -p -g -S 1 /gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/t1w_dseg/sub-01_ses-01_T1w_corrected_xform_masked.nii.gz
200322-22:47:04,564 nipype.workflow INFO:
[Node] Running "gen_ref" ("niworkflows.interfaces.utils.GenerateSamplingReference")
200322-22:47:05,546 nipype.workflow INFO:
[Node] Finished "fmriprep_wf.single_subject_01_wf.func_preproc_ses_01_task_Stroop_run_01_wf.bold_t1_trans_wf.gen_ref".
200322-22:47:06,559 nipype.workflow INFO:
[Node] Setting-up "fmriprep_wf.single_subject_01_wf.func_preproc_ses_01_task_Stroop_run_01_wf.bold_t1_trans_wf.aparc_t1w_tfm" in "/gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/bold_t1_trans_wf/aparc_t1w_tfm".
200322-22:47:06,564 nipype.workflow INFO:
[Node] Running "aparc_t1w_tfm" ("niworkflows.interfaces.fixes.FixHeaderApplyTransforms"), a CommandLine Interface with command:
antsApplyTransforms --default-value 0 --float 1 --input /gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/surface_recon_wf/segs_to_native_aparc_aseg/tonii/aparc+aseg_vol_out.nii.gz --interpolation MultiLabel --output aparc+aseg_vol_out_trans.nii.gz --reference-image /gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/bold_t1_trans_wf/gen_ref/sub-01_ses-01_T1w_corrected_xform_masked_reference.nii.gz -t identity
200322-22:47:10,358 nipype.workflow INFO:
[Node] Finished "fmriprep_wf.single_subject_01_wf.func_preproc_ses_01_task_Stroop_run_01_wf.bold_t1_trans_wf.aparc_t1w_tfm".
200322-22:47:10,572 nipype.workflow INFO:
[Node] Setting-up "fmriprep_wf.single_subject_01_wf.func_preproc_ses_01_task_Stroop_run_01_wf.bold_t1_trans_wf.aseg_t1w_tfm" in "/gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/bold_t1_trans_wf/aseg_t1w_tfm".
200322-22:47:10,577 nipype.workflow INFO:
[Node] Running "aseg_t1w_tfm" ("niworkflows.interfaces.fixes.FixHeaderApplyTransforms"), a CommandLine Interface with command:
antsApplyTransforms --default-value 0 --float 1 --input /gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/surface_recon_wf/segs_to_native_aseg/tonii/aseg_vol_out.nii.gz --interpolation MultiLabel --output aseg_vol_out_trans.nii.gz --reference-image /gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/bold_t1_trans_wf/gen_ref/sub-01_ses-01_T1w_corrected_xform_masked_reference.nii.gz -t identity
200322-22:47:14,341 nipype.workflow INFO:
[Node] Finished "fmriprep_wf.single_subject_01_wf.func_preproc_ses_01_task_Stroop_run_01_wf.bold_t1_trans_wf.aseg_t1w_tfm".
200322-22:50:15,162 nipype.workflow INFO:
[Node] Finished "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.t1w_dseg".
200322-22:50:23,871 nipype.workflow INFO:
[Node] Setting-up "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.anat_derivatives_wf.lut_t1w_dseg" in "/gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/anat_derivatives_wf/lut_t1w_dseg".
200322-22:50:23,873 nipype.workflow INFO:
[Node] Setting-up "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.anat_reports_wf.seg_rpt" in "/gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/anat_reports_wf/seg_rpt".
200322-22:50:23,875 nipype.workflow INFO:
[Node] Running "lut_t1w_dseg" ("nipype.interfaces.utility.wrappers.Function")
200322-22:50:23,900 nipype.workflow INFO:
[Node] Running "seg_rpt" ("niworkflows.interfaces.masks.ROIsPlot")
200322-22:50:24,487 nipype.workflow INFO:
[Node] Finished "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.anat_derivatives_wf.lut_t1w_dseg".
200322-22:50:29,274 nipype.workflow INFO:
[Node] Setting-up "fmriprep_wf.single_subject_01_wf.func_preproc_ses_01_task_Stroop_run_01_wf.bold_confounds_wf.wm_roi" in "/gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/bold_confounds_wf/wm_roi".
200322-22:50:29,279 nipype.workflow INFO:
[Node] Running "wm_roi" ("niworkflows.interfaces.utils.TPM2ROI")
200322-22:50:35,769 nipype.workflow INFO:
[Node] Finished "fmriprep_wf.single_subject_01_wf.func_preproc_ses_01_task_Stroop_run_01_wf.bold_confounds_wf.wm_roi".
200322-22:50:37,387 nipype.workflow INFO:
[Node] Setting-up "fmriprep_wf.single_subject_01_wf.func_preproc_ses_01_task_Stroop_run_01_wf.bold_confounds_wf.csf_roi" in "/gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/bold_confounds_wf/csf_roi".
200322-22:50:37,392 nipype.workflow INFO:
[Node] Running "csf_roi" ("niworkflows.interfaces.utils.TPM2ROI")
200322-22:50:38,466 nipype.workflow INFO:
[Node] Finished "fmriprep_wf.single_subject_01_wf.func_preproc_ses_01_task_Stroop_run_01_wf.bold_confounds_wf.csf_roi".
200322-22:50:39,390 nipype.workflow INFO:
[Node] Setting-up "fmriprep_wf.single_subject_01_wf.func_preproc_ses_01_task_Stroop_run_01_wf.bold_confounds_wf.tpms_add_csf_wm" in "/gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/bold_confounds_wf/tpms_add_csf_wm".
200322-22:50:39,394 nipype.workflow INFO:
[Node] Running "tpms_add_csf_wm" ("niworkflows.interfaces.utils.AddTPMs")
200322-22:50:40,941 nipype.workflow INFO:
[Node] Finished "fmriprep_wf.single_subject_01_wf.func_preproc_ses_01_task_Stroop_run_01_wf.bold_confounds_wf.tpms_add_csf_wm".
200322-22:50:41,389 nipype.workflow INFO:
[Node] Setting-up "fmriprep_wf.single_subject_01_wf.func_preproc_ses_01_task_Stroop_run_01_wf.bold_confounds_wf.acc_roi" in "/gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/bold_confounds_wf/acc_roi".
200322-22:50:41,393 nipype.workflow INFO:
[Node] Running "acc_roi" ("niworkflows.interfaces.utils.TPM2ROI")
200322-22:50:47,720 nipype.workflow INFO:
[Node] Finished "fmriprep_wf.single_subject_01_wf.func_preproc_ses_01_task_Stroop_run_01_wf.bold_confounds_wf.acc_roi".
200322-22:51:38,732 nipype.workflow INFO:
[Node] Finished "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.anat_reports_wf.seg_rpt".
200322-23:05:56,974 nipype.workflow INFO:
[Node] Finished "_midthickness1".
200322-23:06:03,72 nipype.workflow INFO:
[Node] Finished "_midthickness0".
200322-23:06:04,331 nipype.workflow INFO:
[Node] Setting-up "fmriprep_wf.single_subject_01_wf.func_preproc_ses_01_task_Stroop_run_01_wf.bold_reg_wf.bbreg_wf.mri_coreg" in "/gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/bold_reg_wf/bbreg_wf/mri_coreg".
200322-23:06:04,339 nipype.workflow INFO:
[Node] Running "mri_coreg" ("niworkflows.interfaces.freesurfer.PatchedMRICoregRPT"), a CommandLine Interface with command:
mri_coreg --s sub-01 --dof 6 --ftol 1.000000e-04 --linmintol 1.000000e-02 --threads 4 --lta /gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/bold_reg_wf/bbreg_wf/mri_coreg/registration.lta --sep 4 --mov /gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/bold_reg_wf/bbreg_wf/mri_coreg/uni_xform_masked.nii.gz --sd /out/freesurfer
200322-23:06:50,433 nipype.interface INFO:
stdout 2020-03-22T23:06:50.433869:
200322-23:06:50,434 nipype.interface INFO:
stdout 2020-03-22T23:06:50.433869:Matrix from LTA:
200322-23:06:50,434 nipype.interface INFO:
stdout 2020-03-22T23:06:50.433869: 0.99863 -0.04660 -0.02361 0.68169;
200322-23:06:50,434 nipype.interface INFO:
stdout 2020-03-22T23:06:50.433869: 0.00513 -0.36237 0.93202 -6.48920;
200322-23:06:50,434 nipype.interface INFO:
stdout 2020-03-22T23:06:50.433869:-0.05199 -0.93087 -0.36164 -0.34785;
200322-23:06:50,434 nipype.interface INFO:
stdout 2020-03-22T23:06:50.433869: 0.00000 0.00000 0.00000 1.00000;
200322-23:06:50,665 nipype.interface INFO:
stdout 2020-03-22T23:06:50.665915:
200322-23:06:50,666 nipype.interface INFO:
stdout 2020-03-22T23:06:50.665915:/gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/bold_reg_wf/bbreg_wf/mri_coreg/uni_xform_masked.nii.gz /out/freesurfer/sub-01/mri/brainmask.mgz
200322-23:06:50,666 nipype.interface INFO:
stdout 2020-03-22T23:06:50.665915:movvol /gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/bold_reg_wf/bbreg_wf/mri_coreg/uni_xform_masked.nii.gz
200322-23:06:50,666 nipype.interface INFO:
stdout 2020-03-22T23:06:50.665915:targvol /out/freesurfer/sub-01/mri/brainmask.mgz
200322-23:06:50,666 nipype.interface INFO:
stdout 2020-03-22T23:06:50.665915:outvol /gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/bold_reg_wf/bbreg_wf/mri_coreg/uni_xform_masked_warped.nii.gz
200322-23:06:50,666 nipype.interface INFO:
stdout 2020-03-22T23:06:50.665915:regfile /gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/bold_reg_wf/bbreg_wf/mri_coreg/registration.lta
200322-23:06:50,666 nipype.interface INFO:
stdout 2020-03-22T23:06:50.665915:invert 0
200322-23:06:50,666 nipype.interface INFO:
stdout 2020-03-22T23:06:50.665915:tal 0
200322-23:06:50,666 nipype.interface INFO:
stdout 2020-03-22T23:06:50.665915:talres 2
200322-23:06:50,666 nipype.interface INFO:
stdout 2020-03-22T23:06:50.665915:regheader 0
200322-23:06:50,666 nipype.interface INFO:
stdout 2020-03-22T23:06:50.665915:noresample 0
200322-23:06:50,666 nipype.interface INFO:
stdout 2020-03-22T23:06:50.665915:interp nearest (0)
200322-23:06:50,666 nipype.interface INFO:
stdout 2020-03-22T23:06:50.665915:precision float (3)
200322-23:06:50,666 nipype.interface INFO:
stdout 2020-03-22T23:06:50.665915:Gdiag_no -1
200322-23:06:50,666 nipype.interface INFO:
stdout 2020-03-22T23:06:50.665915:Synth 0
200322-23:06:50,666 nipype.interface INFO:
stdout 2020-03-22T23:06:50.665915:SynthSeed 1585477769
200322-23:06:50,666 nipype.interface INFO:
stdout 2020-03-22T23:06:50.665915:
200322-23:06:50,666 nipype.interface INFO:
stdout 2020-03-22T23:06:50.665915:Final tkRAS-to-tkRAS Matrix is:
200322-23:06:50,666 nipype.interface INFO:
stdout 2020-03-22T23:06:50.665915: 0.99863 -0.04660 -0.02361 0.68169;
200322-23:06:50,666 nipype.interface INFO:
stdout 2020-03-22T23:06:50.665915: 0.00513 -0.36237 0.93202 -6.48920;
200322-23:06:50,666 nipype.interface INFO:
stdout 2020-03-22T23:06:50.665915:-0.05199 -0.93087 -0.36164 -0.34785;
200322-23:06:50,666 nipype.interface INFO:
stdout 2020-03-22T23:06:50.665915: 0.00000 0.00000 0.00000 1.00000;
200322-23:06:50,666 nipype.interface INFO:
stdout 2020-03-22T23:06:50.665915:
200322-23:06:50,666 nipype.interface INFO:
stdout 2020-03-22T23:06:50.665915:
200322-23:06:50,667 nipype.interface INFO:
stdout 2020-03-22T23:06:50.665915:Vox2Vox Matrix is:
200322-23:06:50,667 nipype.interface INFO:
stdout 2020-03-22T23:06:50.665915: 0.33288 -0.00787 0.01553 -9.77064;
200322-23:06:50,667 nipype.interface INFO:
stdout 2020-03-22T23:06:50.665915:-0.01733 -0.12055 0.31029 17.55879;
200322-23:06:50,667 nipype.interface INFO:
stdout 2020-03-22T23:06:50.665915:-0.00171 -0.31067 -0.12079 96.60382;
200322-23:06:50,667 nipype.interface INFO:
stdout 2020-03-22T23:06:50.665915: 0.00000 0.00000 0.00000 1.00000;
200322-23:06:52,29 nipype.interface INFO:
stdout 2020-03-22T23:06:52.029843:
200322-23:06:52,30 nipype.interface INFO:
stdout 2020-03-22T23:06:52.029843:Resampling
200322-23:06:52,30 nipype.interface INFO:
stdout 2020-03-22T23:06:52.029843:Output registration matrix is identity
200322-23:06:52,30 nipype.interface INFO:
stdout 2020-03-22T23:06:52.029843:
200322-23:06:52,30 nipype.interface INFO:
stdout 2020-03-22T23:06:52.029843:mri_vol2vol done
200322-23:07:12,84 nipype.workflow INFO:
[Node] Finished "fmriprep_wf.single_subject_01_wf.func_preproc_ses_01_task_Stroop_run_01_wf.bold_reg_wf.bbreg_wf.mri_coreg".
200322-23:07:12,404 nipype.workflow INFO:
[Node] Setting-up "fmriprep_wf.single_subject_01_wf.func_preproc_ses_01_task_Stroop_run_01_wf.bold_reg_wf.bbreg_wf.bbregister" in "/gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/bold_reg_wf/bbreg_wf/bbregister".
200322-23:07:12,409 nipype.workflow INFO:
[Node] Setting-up "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.surface_recon_wf.gifti_surface_wf.midthickness" in "/gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/midthickness".
200322-23:07:12,411 nipype.workflow INFO:
[Node] Running "bbregister" ("niworkflows.interfaces.freesurfer.PatchedBBRegisterRPT"), a CommandLine Interface with command:
bbregister --t2 --6 --init-reg /gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/bold_reg_wf/bbreg_wf/mri_coreg/registration.lta --lta /gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/bold_reg_wf/bbreg_wf/bbregister/uni_xform_masked_bbreg_sub-01.lta --reg /gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/bold_reg_wf/bbreg_wf/bbregister/uni_xform_masked_bbreg_sub-01.dat --o /gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/bold_reg_wf/bbreg_wf/bbregister/uni_xform_masked_bbreg.nii.gz --mov /gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/bold_reg_wf/bbreg_wf/bbregister/uni_xform_masked.nii.gz --s sub-01
200322-23:07:12,414 nipype.workflow INFO:
[Node] Setting-up "_midthickness0" in "/gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/midthickness/mapflow/_midthickness0".
200322-23:07:12,415 nipype.workflow INFO:
[Node] Cached "_midthickness0" - collecting precomputed outputs
200322-23:07:12,415 nipype.workflow INFO:
[Node] "_midthickness0" found cached.
200322-23:07:12,416 nipype.workflow INFO:
[Node] Setting-up "_midthickness1" in "/gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/midthickness/mapflow/_midthickness1".
200322-23:07:12,416 nipype.workflow INFO:
[Node] Cached "_midthickness1" - collecting precomputed outputs
200322-23:07:12,416 nipype.workflow INFO:
[Node] "_midthickness1" found cached.
200322-23:07:12,418 nipype.workflow INFO:
[Node] Finished "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.surface_recon_wf.gifti_surface_wf.midthickness".
200322-23:07:14,411 nipype.workflow INFO:
[Node] Setting-up "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.surface_recon_wf.gifti_surface_wf.save_midthickness" in "/gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/save_midthickness".
200322-23:07:14,416 nipype.workflow INFO:
[Node] Running "save_midthickness" ("nipype.interfaces.io.DataSink")
200322-23:07:14,718 nipype.workflow INFO:
[Node] Finished "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.surface_recon_wf.gifti_surface_wf.save_midthickness".
200322-23:07:20,415 nipype.workflow INFO:
[Node] Setting-up "_fs2gii0" in "/gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/fs2gii/mapflow/_fs2gii0".
200322-23:07:20,416 nipype.workflow INFO:
[Node] Setting-up "_fs2gii1" in "/gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/fs2gii/mapflow/_fs2gii1".
200322-23:07:20,417 nipype.workflow INFO:
[Node] Setting-up "_fs2gii2" in "/gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/fs2gii/mapflow/_fs2gii2".
200322-23:07:20,420 nipype.workflow INFO:
[Node] Running "_fs2gii0" ("nipype.interfaces.freesurfer.utils.MRIsConvert"), a CommandLine Interface with command:
mris_convert /out/freesurfer/sub-01/surf/rh.smoothwm /gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/fs2gii/mapflow/_fs2gii0/rh.smoothwm_converted.gii
200322-23:07:20,421 nipype.workflow INFO:
[Node] Running "_fs2gii2" ("nipype.interfaces.freesurfer.utils.MRIsConvert"), a CommandLine Interface with command:
mris_convert /out/freesurfer/sub-01/surf/rh.pial /gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/fs2gii/mapflow/_fs2gii2/rh.pial_converted.gii
200322-23:07:20,422 nipype.workflow INFO:
[Node] Running "_fs2gii1" ("nipype.interfaces.freesurfer.utils.MRIsConvert"), a CommandLine Interface with command:
mris_convert /out/freesurfer/sub-01/surf/lh.smoothwm /gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/fs2gii/mapflow/_fs2gii1/lh.smoothwm_converted.gii
200322-23:07:22,667 nipype.workflow INFO:
[Node] Finished "_fs2gii1".
200322-23:07:22,688 nipype.workflow INFO:
[Node] Finished "_fs2gii2".
200322-23:07:22,722 nipype.workflow INFO:
[Node] Finished "_fs2gii0".
200322-23:07:24,431 nipype.workflow INFO:
[Node] Setting-up "_fs2gii3" in "/gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/fs2gii/mapflow/_fs2gii3".
200322-23:07:24,433 nipype.workflow INFO:
[Node] Setting-up "_fs2gii4" in "/gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/fs2gii/mapflow/_fs2gii4".
200322-23:07:24,434 nipype.workflow INFO:
[Node] Setting-up "_fs2gii5" in "/gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/fs2gii/mapflow/_fs2gii5".
200322-23:07:24,435 nipype.workflow INFO:
[Node] Running "_fs2gii3" ("nipype.interfaces.freesurfer.utils.MRIsConvert"), a CommandLine Interface with command:
mris_convert /out/freesurfer/sub-01/surf/lh.pial /gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/fs2gii/mapflow/_fs2gii3/lh.pial_converted.gii
200322-23:07:24,436 nipype.workflow INFO:
[Node] Running "_fs2gii4" ("nipype.interfaces.freesurfer.utils.MRIsConvert"), a CommandLine Interface with command:
mris_convert /out/freesurfer/sub-01/surf/rh.inflated /gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/fs2gii/mapflow/_fs2gii4/rh.inflated_converted.gii
200322-23:07:24,437 nipype.workflow INFO:
[Node] Running "_fs2gii5" ("nipype.interfaces.freesurfer.utils.MRIsConvert"), a CommandLine Interface with command:
mris_convert /out/freesurfer/sub-01/surf/lh.inflated /gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/fs2gii/mapflow/_fs2gii5/lh.inflated_converted.gii
200322-23:07:26,718 nipype.workflow INFO:
[Node] Finished "_fs2gii5".
200322-23:07:26,723 nipype.workflow INFO:
[Node] Finished "_fs2gii4".
200322-23:07:26,736 nipype.workflow INFO:
[Node] Finished "_fs2gii3".
200322-23:07:28,430 nipype.workflow INFO:
[Node] Setting-up "_fs2gii6" in "/gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/fs2gii/mapflow/_fs2gii6".
200322-23:07:28,431 nipype.workflow INFO:
[Node] Setting-up "_fs2gii7" in "/gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/fs2gii/mapflow/_fs2gii7".
200322-23:07:28,434 nipype.workflow INFO:
[Node] Running "_fs2gii6" ("nipype.interfaces.freesurfer.utils.MRIsConvert"), a CommandLine Interface with command:
mris_convert /out/freesurfer/sub-01/surf/rh.midthickness /gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/fs2gii/mapflow/_fs2gii6/rh.midthickness_converted.gii
200322-23:07:28,434 nipype.workflow INFO:
[Node] Running "_fs2gii7" ("nipype.interfaces.freesurfer.utils.MRIsConvert"), a CommandLine Interface with command:
mris_convert /out/freesurfer/sub-01/surf/lh.midthickness /gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/fs2gii/mapflow/_fs2gii7/lh.midthickness_converted.gii
200322-23:07:30,595 nipype.workflow INFO:
[Node] Finished "_fs2gii7".
200322-23:07:30,678 nipype.workflow INFO:
[Node] Finished "_fs2gii6".
200322-23:07:32,438 nipype.workflow INFO:
[Node] Setting-up "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.surface_recon_wf.gifti_surface_wf.fs2gii" in "/gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/fs2gii".
200322-23:07:32,443 nipype.workflow INFO:
[Node] Setting-up "_fs2gii0" in "/gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/fs2gii/mapflow/_fs2gii0".
200322-23:07:32,443 nipype.workflow INFO:
[Node] Cached "_fs2gii0" - collecting precomputed outputs
200322-23:07:32,444 nipype.workflow INFO:
[Node] "_fs2gii0" found cached.
200322-23:07:32,444 nipype.workflow INFO:
[Node] Setting-up "_fs2gii1" in "/gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/fs2gii/mapflow/_fs2gii1".
200322-23:07:32,445 nipype.workflow INFO:
[Node] Cached "_fs2gii1" - collecting precomputed outputs
200322-23:07:32,445 nipype.workflow INFO:
[Node] "_fs2gii1" found cached.
200322-23:07:32,446 nipype.workflow INFO:
[Node] Setting-up "_fs2gii2" in "/gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/fs2gii/mapflow/_fs2gii2".
200322-23:07:32,447 nipype.workflow INFO:
[Node] Cached "_fs2gii2" - collecting precomputed outputs
200322-23:07:32,447 nipype.workflow INFO:
[Node] "_fs2gii2" found cached.
200322-23:07:32,448 nipype.workflow INFO:
[Node] Setting-up "_fs2gii3" in "/gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/fs2gii/mapflow/_fs2gii3".
200322-23:07:32,448 nipype.workflow INFO:
[Node] Cached "_fs2gii3" - collecting precomputed outputs
200322-23:07:32,448 nipype.workflow INFO:
[Node] "_fs2gii3" found cached.
200322-23:07:32,449 nipype.workflow INFO:
[Node] Setting-up "_fs2gii4" in "/gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/fs2gii/mapflow/_fs2gii4".
200322-23:07:32,450 nipype.workflow INFO:
[Node] Cached "_fs2gii4" - collecting precomputed outputs
200322-23:07:32,450 nipype.workflow INFO:
[Node] "_fs2gii4" found cached.
200322-23:07:32,451 nipype.workflow INFO:
[Node] Setting-up "_fs2gii5" in "/gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/fs2gii/mapflow/_fs2gii5".
200322-23:07:32,452 nipype.workflow INFO:
[Node] Cached "_fs2gii5" - collecting precomputed outputs
200322-23:07:32,452 nipype.workflow INFO:
[Node] "_fs2gii5" found cached.
200322-23:07:32,452 nipype.workflow INFO:
[Node] Setting-up "_fs2gii6" in "/gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/fs2gii/mapflow/_fs2gii6".
200322-23:07:32,453 nipype.workflow INFO:
[Node] Cached "_fs2gii6" - collecting precomputed outputs
200322-23:07:32,453 nipype.workflow INFO:
[Node] "_fs2gii6" found cached.
200322-23:07:32,454 nipype.workflow INFO:
[Node] Setting-up "_fs2gii7" in "/gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/fs2gii/mapflow/_fs2gii7".
200322-23:07:32,455 nipype.workflow INFO:
[Node] Cached "_fs2gii7" - collecting precomputed outputs
200322-23:07:32,455 nipype.workflow INFO:
[Node] "_fs2gii7" found cached.
200322-23:07:32,458 nipype.workflow INFO:
[Node] Finished "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.surface_recon_wf.gifti_surface_wf.fs2gii".
200322-23:07:36,439 nipype.workflow INFO:
[Node] Setting-up "_fix_surfs0" in "/gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/fix_surfs/mapflow/_fix_surfs0".
200322-23:07:36,440 nipype.workflow INFO:
[Node] Setting-up "_fix_surfs1" in "/gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/fix_surfs/mapflow/_fix_surfs1".
200322-23:07:36,441 nipype.workflow INFO:
[Node] Setting-up "_fix_surfs2" in "/gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/fix_surfs/mapflow/_fix_surfs2".
200322-23:07:36,442 nipype.workflow INFO:
[Node] Running "_fix_surfs0" ("niworkflows.interfaces.surf.NormalizeSurf")
200322-23:07:36,442 nipype.workflow INFO:
[Node] Running "_fix_surfs1" ("niworkflows.interfaces.surf.NormalizeSurf")
200322-23:07:36,445 nipype.workflow INFO:
[Node] Running "_fix_surfs2" ("niworkflows.interfaces.surf.NormalizeSurf")
200322-23:07:37,31 nipype.workflow INFO:
[Node] Finished "_fix_surfs1".
200322-23:07:37,66 nipype.workflow INFO:
[Node] Finished "_fix_surfs0".
200322-23:07:37,68 nipype.workflow INFO:
[Node] Finished "_fix_surfs2".
200322-23:07:38,438 nipype.workflow INFO:
[Node] Setting-up "_fix_surfs3" in "/gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/fix_surfs/mapflow/_fix_surfs3".
200322-23:07:38,439 nipype.workflow INFO:
[Node] Setting-up "_fix_surfs4" in "/gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/fix_surfs/mapflow/_fix_surfs4".
200322-23:07:38,440 nipype.workflow INFO:
[Node] Setting-up "_fix_surfs5" in "/gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/fix_surfs/mapflow/_fix_surfs5".
200322-23:07:38,441 nipype.workflow INFO:
[Node] Running "_fix_surfs3" ("niworkflows.interfaces.surf.NormalizeSurf")
200322-23:07:38,441 nipype.workflow INFO:
[Node] Running "_fix_surfs4" ("niworkflows.interfaces.surf.NormalizeSurf")
200322-23:07:38,443 nipype.workflow INFO:
[Node] Running "_fix_surfs5" ("niworkflows.interfaces.surf.NormalizeSurf")
200322-23:07:39,93 nipype.workflow INFO:
[Node] Finished "_fix_surfs3".
200322-23:07:39,124 nipype.workflow INFO:
[Node] Finished "_fix_surfs5".
200322-23:07:39,267 nipype.workflow INFO:
[Node] Finished "_fix_surfs4".
200322-23:07:40,438 nipype.workflow INFO:
[Node] Setting-up "_fix_surfs6" in "/gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/fix_surfs/mapflow/_fix_surfs6".
200322-23:07:40,439 nipype.workflow INFO:
[Node] Setting-up "_fix_surfs7" in "/gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/fix_surfs/mapflow/_fix_surfs7".
200322-23:07:40,441 nipype.workflow INFO:
[Node] Running "_fix_surfs6" ("niworkflows.interfaces.surf.NormalizeSurf")
200322-23:07:40,441 nipype.workflow INFO:
[Node] Running "_fix_surfs7" ("niworkflows.interfaces.surf.NormalizeSurf")
200322-23:07:41,7 nipype.workflow INFO:
[Node] Finished "_fix_surfs7".
200322-23:07:41,12 nipype.workflow INFO:
[Node] Finished "_fix_surfs6".
200322-23:07:42,447 nipype.workflow INFO:
[Node] Setting-up "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.surface_recon_wf.gifti_surface_wf.fix_surfs" in "/gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/fix_surfs".
200322-23:07:42,451 nipype.workflow INFO:
[Node] Setting-up "_fix_surfs0" in "/gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/fix_surfs/mapflow/_fix_surfs0".
200322-23:07:42,452 nipype.workflow INFO:
[Node] Cached "_fix_surfs0" - collecting precomputed outputs
200322-23:07:42,452 nipype.workflow INFO:
[Node] "_fix_surfs0" found cached.
200322-23:07:42,453 nipype.workflow INFO:
[Node] Setting-up "_fix_surfs1" in "/gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/fix_surfs/mapflow/_fix_surfs1".
200322-23:07:42,453 nipype.workflow INFO:
[Node] Cached "_fix_surfs1" - collecting precomputed outputs
200322-23:07:42,454 nipype.workflow INFO:
[Node] "_fix_surfs1" found cached.
200322-23:07:42,454 nipype.workflow INFO:
[Node] Setting-up "_fix_surfs2" in "/gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/fix_surfs/mapflow/_fix_surfs2".
200322-23:07:42,455 nipype.workflow INFO:
[Node] Cached "_fix_surfs2" - collecting precomputed outputs
200322-23:07:42,455 nipype.workflow INFO:
[Node] "_fix_surfs2" found cached.
200322-23:07:42,456 nipype.workflow INFO:
[Node] Setting-up "_fix_surfs3" in "/gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/fix_surfs/mapflow/_fix_surfs3".
200322-23:07:42,456 nipype.workflow INFO:
[Node] Cached "_fix_surfs3" - collecting precomputed outputs
200322-23:07:42,456 nipype.workflow INFO:
[Node] "_fix_surfs3" found cached.
200322-23:07:42,457 nipype.workflow INFO:
[Node] Setting-up "_fix_surfs4" in "/gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/fix_surfs/mapflow/_fix_surfs4".
200322-23:07:42,458 nipype.workflow INFO:
[Node] Cached "_fix_surfs4" - collecting precomputed outputs
200322-23:07:42,458 nipype.workflow INFO:
[Node] "_fix_surfs4" found cached.
200322-23:07:42,458 nipype.workflow INFO:
[Node] Setting-up "_fix_surfs5" in "/gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/fix_surfs/mapflow/_fix_surfs5".
200322-23:07:42,459 nipype.workflow INFO:
[Node] Cached "_fix_surfs5" - collecting precomputed outputs
200322-23:07:42,459 nipype.workflow INFO:
[Node] "_fix_surfs5" found cached.
200322-23:07:42,460 nipype.workflow INFO:
[Node] Setting-up "_fix_surfs6" in "/gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/fix_surfs/mapflow/_fix_surfs6".
200322-23:07:42,460 nipype.workflow INFO:
[Node] Cached "_fix_surfs6" - collecting precomputed outputs
200322-23:07:42,461 nipype.workflow INFO:
[Node] "_fix_surfs6" found cached.
200322-23:07:42,461 nipype.workflow INFO:
[Node] Setting-up "_fix_surfs7" in "/gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/fix_surfs/mapflow/_fix_surfs7".
200322-23:07:42,462 nipype.workflow INFO:
[Node] Cached "_fix_surfs7" - collecting precomputed outputs
200322-23:07:42,462 nipype.workflow INFO:
[Node] "_fix_surfs7" found cached.
200322-23:07:42,465 nipype.workflow INFO:
[Node] Finished "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.surface_recon_wf.gifti_surface_wf.fix_surfs".
200322-23:08:20,520 nipype.interface INFO:
stdout 2020-03-22T23:08:20.520251:
200322-23:08:20,520 nipype.interface INFO:
stdout 2020-03-22T23:08:20.520251:Matrix from LTA:
200322-23:08:20,520 nipype.interface INFO:
stdout 2020-03-22T23:08:20.520251: 0.99861 -0.04752 -0.02266 0.88396;
200322-23:08:20,520 nipype.interface INFO:
stdout 2020-03-22T23:08:20.520251: 0.00318 -0.37521 0.92694 -6.70175;
200322-23:08:20,520 nipype.interface INFO:
stdout 2020-03-22T23:08:20.520251:-0.05255 -0.92572 -0.37454 0.12832;
200322-23:08:20,520 nipype.interface INFO:
stdout 2020-03-22T23:08:20.520251: 0.00000 0.00000 0.00000 1.00000;
200322-23:08:20,750 nipype.interface INFO:
stdout 2020-03-22T23:08:20.750556:
200322-23:08:20,750 nipype.interface INFO:
stdout 2020-03-22T23:08:20.750556:/gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/bold_reg_wf/bbreg_wf/bbregister/uni_xform_masked.nii.gz /out/freesurfer/sub-01/mri/brainmask.mgz
200322-23:08:20,750 nipype.interface INFO:
stdout 2020-03-22T23:08:20.750556:movvol /gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/bold_reg_wf/bbreg_wf/bbregister/uni_xform_masked.nii.gz
200322-23:08:20,750 nipype.interface INFO:
stdout 2020-03-22T23:08:20.750556:targvol /out/freesurfer/sub-01/mri/brainmask.mgz
200322-23:08:20,750 nipype.interface INFO:
stdout 2020-03-22T23:08:20.750556:outvol /gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/bold_reg_wf/bbreg_wf/bbregister/uni_xform_masked_warped.nii.gz
200322-23:08:20,750 nipype.interface INFO:
stdout 2020-03-22T23:08:20.750556:regfile /gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/bold_reg_wf/bbreg_wf/bbregister/uni_xform_masked_bbreg_sub-01.lta
200322-23:08:20,750 nipype.interface INFO:
stdout 2020-03-22T23:08:20.750556:invert 0
200322-23:08:20,750 nipype.interface INFO:
stdout 2020-03-22T23:08:20.750556:tal 0
200322-23:08:20,750 nipype.interface INFO:
stdout 2020-03-22T23:08:20.750556:talres 2
200322-23:08:20,751 nipype.interface INFO:
stdout 2020-03-22T23:08:20.750556:regheader 0
200322-23:08:20,751 nipype.interface INFO:
stdout 2020-03-22T23:08:20.750556:noresample 0
200322-23:08:20,751 nipype.interface INFO:
stdout 2020-03-22T23:08:20.750556:interp nearest (0)
200322-23:08:20,751 nipype.interface INFO:
stdout 2020-03-22T23:08:20.750556:precision float (3)
200322-23:08:20,751 nipype.interface INFO:
stdout 2020-03-22T23:08:20.750556:Gdiag_no -1
200322-23:08:20,751 nipype.interface INFO:
stdout 2020-03-22T23:08:20.750556:Synth 0
200322-23:08:20,751 nipype.interface INFO:
stdout 2020-03-22T23:08:20.750556:SynthSeed 1585562894
200322-23:08:20,751 nipype.interface INFO:
stdout 2020-03-22T23:08:20.750556:
200322-23:08:20,751 nipype.interface INFO:
stdout 2020-03-22T23:08:20.750556:Final tkRAS-to-tkRAS Matrix is:
200322-23:08:20,751 nipype.interface INFO:
stdout 2020-03-22T23:08:20.750556: 0.99861 -0.04752 -0.02266 0.88394;
200322-23:08:20,751 nipype.interface INFO:
stdout 2020-03-22T23:08:20.750556: 0.00318 -0.37521 0.92694 -6.70174;
200322-23:08:20,751 nipype.interface INFO:
stdout 2020-03-22T23:08:20.750556:-0.05255 -0.92572 -0.37454 0.12831;
200322-23:08:20,751 nipype.interface INFO:
stdout 2020-03-22T23:08:20.750556: 0.00000 0.00000 0.00000 1.00000;
200322-23:08:20,751 nipype.interface INFO:
stdout 2020-03-22T23:08:20.750556:
200322-23:08:20,751 nipype.interface INFO:
stdout 2020-03-22T23:08:20.750556:
200322-23:08:20,751 nipype.interface INFO:
stdout 2020-03-22T23:08:20.750556:Vox2Vox Matrix is:
200322-23:08:20,751 nipype.interface INFO:
stdout 2020-03-22T23:08:20.750556: 0.33287 -0.00755 0.01584 -9.95331;
200322-23:08:20,751 nipype.interface INFO:
stdout 2020-03-22T23:08:20.750556:-0.01752 -0.12485 0.30857 18.35262;
200322-23:08:20,751 nipype.interface INFO:
stdout 2020-03-22T23:08:20.750556:-0.00106 -0.30898 -0.12507 96.82498;
200322-23:08:20,751 nipype.interface INFO:
stdout 2020-03-22T23:08:20.750556: 0.00000 0.00000 0.00000 1.00000;
200322-23:08:22,115 nipype.interface INFO:
stdout 2020-03-22T23:08:22.115938:
200322-23:08:22,116 nipype.interface INFO:
stdout 2020-03-22T23:08:22.115938:Resampling
200322-23:08:22,116 nipype.interface INFO:
stdout 2020-03-22T23:08:22.115938:Output registration matrix is identity
200322-23:08:22,116 nipype.interface INFO:
stdout 2020-03-22T23:08:22.115938:
200322-23:08:22,116 nipype.interface INFO:
stdout 2020-03-22T23:08:22.115938:mri_vol2vol done
200322-23:08:42,214 nipype.workflow INFO:
[Node] Finished "fmriprep_wf.single_subject_01_wf.func_preproc_ses_01_task_Stroop_run_01_wf.bold_reg_wf.bbreg_wf.bbregister".
200322-23:08:42,681 nipype.workflow INFO:
[Node] Setting-up "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.anat_norm_wf.registration" in "/gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/anat_norm_wf/_template_MNI152NLin2009cAsym./registration".
200322-23:08:42,690 nipype.workflow INFO:
[Node] Running "registration" ("niworkflows.interfaces.mni.RobustMNINormalization")
200323-00:04:19,922 nipype.workflow INFO:
[Node] Finished "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.anat_norm_wf.registration".
200323-00:04:22,741 nipype.workflow INFO:
[Node] Setting-up "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.anat_norm_wf.std_mask" in "/gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/anat_norm_wf/_template_MNI152NLin2009cAsym./std_mask".
200323-00:04:22,741 nipype.workflow INFO:
[Node] Setting-up "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.anat_norm_wf.tpl_moving" in "/gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/anat_norm_wf/_template_MNI152NLin2009cAsym./tpl_moving".
200323-00:04:22,748 nipype.workflow INFO:
[Node] Running "std_mask" ("niworkflows.interfaces.fixes.FixHeaderApplyTransforms"), a CommandLine Interface with command:
antsApplyTransforms --default-value 0 --dimensionality 3 --float 1 --input /gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/surface_recon_wf/refine/sub-01_ses-01_T1w_corrected_xform_rbrainmask.nii.gz --interpolation MultiLabel --output sub-01_ses-01_T1w_corrected_xform_rbrainmask_trans.nii.gz --reference-image /home/jac18015/.cache/templateflow/tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_res-01_T1w.nii.gz --transform /gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/anat_norm_wf/_template_MNI152NLin2009cAsym./registration/ants_t1_to_mniComposite.h5
200323-00:04:22,748 nipype.workflow INFO:
[Node] Running "tpl_moving" ("niworkflows.interfaces.fixes.FixHeaderApplyTransforms"), a CommandLine Interface with command:
antsApplyTransforms --default-value 0 --dimensionality 3 --float 1 --input /gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/brain_extraction_wf/copy_xform/sub-01_ses-01_T1w_corrected_xform.nii.gz --interpolation LanczosWindowedSinc --output sub-01_ses-01_T1w_corrected_xform_trans.nii.gz --reference-image /home/jac18015/.cache/templateflow/tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_res-01_T1w.nii.gz --transform /gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/anat_norm_wf/_template_MNI152NLin2009cAsym./registration/ants_t1_to_mniComposite.h5
200323-00:04:22,752 nipype.workflow INFO:
[Node] Setting-up "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.anat_norm_wf.std_dseg" in "/gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/anat_norm_wf/_template_MNI152NLin2009cAsym./std_dseg".
200323-00:04:22,759 nipype.workflow INFO:
[Node] Running "std_dseg" ("niworkflows.interfaces.fixes.FixHeaderApplyTransforms"), a CommandLine Interface with command:
antsApplyTransforms --default-value 0 --dimensionality 3 --float 1 --input /gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/t1w_dseg/sub-01_ses-01_T1w_corrected_xform_masked_seg.nii.gz --interpolation MultiLabel --output sub-01_ses-01_T1w_corrected_xform_masked_seg_trans.nii.gz --reference-image /home/jac18015/.cache/templateflow/tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_res-01_T1w.nii.gz --transform /gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/anat_norm_wf/_template_MNI152NLin2009cAsym./registration/ants_t1_to_mniComposite.h5
200323-00:04:23,834 nipype.workflow INFO:
[Node] Setting-up "_lta_ras2ras0" in "/gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/bold_reg_wf/bbreg_wf/lta_ras2ras/mapflow/_lta_ras2ras0".
200323-00:04:23,837 nipype.workflow INFO:
[Node] Running "_lta_ras2ras0" ("niworkflows.interfaces.freesurfer.PatchedLTAConvert"), a CommandLine Interface with command:
lta_convert --inlta /gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/bold_reg_wf/bbreg_wf/bbregister/uni_xform_masked_bbreg_sub-01.lta --outlta /gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/bold_reg_wf/bbreg_wf/lta_ras2ras/mapflow/_lta_ras2ras0/out.lta
200323-00:04:23,914 nipype.workflow INFO:
[Node] Finished "_lta_ras2ras0".
200323-00:04:25,835 nipype.workflow INFO:
[Node] Setting-up "_lta_ras2ras1" in "/gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/bold_reg_wf/bbreg_wf/lta_ras2ras/mapflow/_lta_ras2ras1".
200323-00:04:25,838 nipype.workflow INFO:
[Node] Running "_lta_ras2ras1" ("niworkflows.interfaces.freesurfer.PatchedLTAConvert"), a CommandLine Interface with command:
lta_convert --inlta /gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/bold_reg_wf/bbreg_wf/mri_coreg/registration.lta --outlta /gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/bold_reg_wf/bbreg_wf/lta_ras2ras/mapflow/_lta_ras2ras1/out.lta
200323-00:04:25,915 nipype.workflow INFO:
[Node] Finished "_lta_ras2ras1".
200323-00:04:27,837 nipype.workflow INFO:
[Node] Setting-up "fmriprep_wf.single_subject_01_wf.func_preproc_ses_01_task_Stroop_run_01_wf.bold_reg_wf.bbreg_wf.lta_ras2ras" in "/gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/bold_reg_wf/bbreg_wf/lta_ras2ras".
200323-00:04:27,842 nipype.workflow INFO:
[Node] Setting-up "_lta_ras2ras0" in "/gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/bold_reg_wf/bbreg_wf/lta_ras2ras/mapflow/_lta_ras2ras0".
200323-00:04:27,843 nipype.workflow INFO:
[Node] Cached "_lta_ras2ras0" - collecting precomputed outputs
200323-00:04:27,843 nipype.workflow INFO:
[Node] "_lta_ras2ras0" found cached.
200323-00:04:27,843 nipype.workflow INFO:
[Node] Setting-up "_lta_ras2ras1" in "/gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/bold_reg_wf/bbreg_wf/lta_ras2ras/mapflow/_lta_ras2ras1".
200323-00:04:27,844 nipype.workflow INFO:
[Node] Cached "_lta_ras2ras1" - collecting precomputed outputs
200323-00:04:27,844 nipype.workflow INFO:
[Node] "_lta_ras2ras1" found cached.
200323-00:04:27,846 nipype.workflow INFO:
[Node] Finished "fmriprep_wf.single_subject_01_wf.func_preproc_ses_01_task_Stroop_run_01_wf.bold_reg_wf.bbreg_wf.lta_ras2ras".
200323-00:04:29,838 nipype.workflow INFO:
[Node] Setting-up "fmriprep_wf.single_subject_01_wf.func_preproc_ses_01_task_Stroop_run_01_wf.bold_reg_wf.bbreg_wf.compare_transforms" in "/gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/bold_reg_wf/bbreg_wf/compare_transforms".
200323-00:04:29,842 nipype.workflow INFO:
[Node] Running "compare_transforms" ("nipype.interfaces.utility.wrappers.Function")
200323-00:04:29,894 nipype.workflow INFO:
[Node] Finished "fmriprep_wf.single_subject_01_wf.func_preproc_ses_01_task_Stroop_run_01_wf.bold_reg_wf.bbreg_wf.compare_transforms".
200323-00:04:32,32 nipype.workflow INFO:
[Node] Setting-up "_std_tpms0" in "/gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/anat_norm_wf/_template_MNI152NLin2009cAsym./std_tpms/mapflow/_std_tpms0".
200323-00:04:32,36 nipype.workflow INFO:
[Node] Running "_std_tpms0" ("niworkflows.interfaces.fixes.FixHeaderApplyTransforms"), a CommandLine Interface with command:
antsApplyTransforms --default-value 0 --dimensionality 3 --float 1 --input /gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/t1w_dseg/sub-01_ses-01_T1w_corrected_xform_masked_prob_0.nii.gz --interpolation Gaussian --output sub-01_ses-01_T1w_corrected_xform_masked_prob_0_trans.nii.gz --reference-image /home/jac18015/.cache/templateflow/tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_res-01_T1w.nii.gz --transform /gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/anat_norm_wf/_template_MNI152NLin2009cAsym./registration/ants_t1_to_mniComposite.h5
200323-00:04:57,661 nipype.workflow INFO:
[Node] Finished "_std_tpms0".
200323-00:04:57,967 nipype.workflow INFO:
[Node] Setting-up "fmriprep_wf.single_subject_01_wf.func_preproc_ses_01_task_Stroop_run_01_wf.bold_reg_wf.bbreg_wf.lta_concat" in "/gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/bold_reg_wf/bbreg_wf/lta_concat".
200323-00:04:57,972 nipype.workflow INFO:
[Node] Running "lta_concat" ("niworkflows.interfaces.freesurfer.PatchedConcatenateLTA"), a CommandLine Interface with command:
mri_concatenate_lta /gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/bold_reg_wf/bbreg_wf/bbregister/uni_xform_masked_bbreg_sub-01.lta /gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/surface_recon_wf/fsnative2t1w_xfm/T1_robustreg.lta out.lta
200323-00:04:58,51 nipype.workflow INFO:
[Node] Finished "fmriprep_wf.single_subject_01_wf.func_preproc_ses_01_task_Stroop_run_01_wf.bold_reg_wf.bbreg_wf.lta_concat".
200323-00:04:59,867 nipype.workflow INFO:
[Node] Setting-up "fmriprep_wf.single_subject_01_wf.func_preproc_ses_01_task_Stroop_run_01_wf.bold_reg_wf.bbreg_wf.lta2fsl_inv" in "/gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/bold_reg_wf/bbreg_wf/lta2fsl_inv".
200323-00:04:59,871 nipype.workflow INFO:
[Node] Running "lta2fsl_inv" ("niworkflows.interfaces.freesurfer.PatchedLTAConvert"), a CommandLine Interface with command:
lta_convert --inlta /gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/bold_reg_wf/bbreg_wf/lta_concat/out.lta --invert --outfsl /gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/bold_reg_wf/bbreg_wf/lta2fsl_inv/out.mat
200323-00:04:59,948 nipype.workflow INFO:
[Node] Finished "fmriprep_wf.single_subject_01_wf.func_preproc_ses_01_task_Stroop_run_01_wf.bold_reg_wf.bbreg_wf.lta2fsl_inv".
200323-00:05:01,870 nipype.workflow INFO:
[Node] Setting-up "fmriprep_wf.single_subject_01_wf.func_preproc_ses_01_task_Stroop_run_01_wf.bold_reg_wf.bbreg_wf.lta2fsl_fwd" in "/gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/bold_reg_wf/bbreg_wf/lta2fsl_fwd".
200323-00:05:01,874 nipype.workflow INFO:
[Node] Running "lta2fsl_fwd" ("niworkflows.interfaces.freesurfer.PatchedLTAConvert"), a CommandLine Interface with command:
lta_convert --inlta /gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/bold_reg_wf/bbreg_wf/lta_concat/out.lta --outfsl /gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/bold_reg_wf/bbreg_wf/lta2fsl_fwd/out.mat
200323-00:05:01,952 nipype.workflow INFO:
[Node] Finished "fmriprep_wf.single_subject_01_wf.func_preproc_ses_01_task_Stroop_run_01_wf.bold_reg_wf.bbreg_wf.lta2fsl_fwd".
200323-00:05:03,872 nipype.workflow INFO:
[Node] Setting-up "fmriprep_wf.single_subject_01_wf.func_preproc_ses_01_task_Stroop_run_01_wf.bold_reg_wf.bbreg_wf.fsl2itk_inv" in "/gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/bold_reg_wf/bbreg_wf/fsl2itk_inv".
200323-00:05:03,877 nipype.workflow INFO:
[Node] Running "fsl2itk_inv" ("nipype.interfaces.c3.C3dAffineTool"), a CommandLine Interface with command:
c3d_affine_tool -ref /gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/sdc_estimate_wf/pepolar_unwarp_wf/enhance_and_skullstrip_bold_wf/apply_mask/uni_xform_masked.nii.gz -src /gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/applyrefined/sub-01_ses-01_T1w_corrected_xform_masked.nii.gz /gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/bold_reg_wf/bbreg_wf/lta2fsl_inv/out.mat -fsl2ras -oitk /gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/bold_reg_wf/bbreg_wf/fsl2itk_inv/affine.txt
200323-00:05:04,138 nipype.workflow INFO:
[Node] Finished "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.anat_norm_wf.tpl_moving".
200323-00:05:04,394 nipype.workflow INFO:
[Node] Finished "fmriprep_wf.single_subject_01_wf.func_preproc_ses_01_task_Stroop_run_01_wf.bold_reg_wf.bbreg_wf.fsl2itk_inv".
200323-00:05:07,886 nipype.workflow INFO:
[Node] Setting-up "fmriprep_wf.single_subject_01_wf.func_preproc_ses_01_task_Stroop_run_01_wf.bold_reg_wf.bbreg_wf.fsl2itk_fwd" in "/gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/bold_reg_wf/bbreg_wf/fsl2itk_fwd".
200323-00:05:07,889 nipype.workflow INFO:
[Node] Setting-up "fmriprep_wf.single_subject_01_wf.func_preproc_ses_01_task_Stroop_run_01_wf.sdc_unwarp_report_wf.map_seg" in "/gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/sdc_unwarp_report_wf/map_seg".
200323-00:05:07,890 nipype.workflow INFO:
[Node] Running "fsl2itk_fwd" ("nipype.interfaces.c3.C3dAffineTool"), a CommandLine Interface with command:
c3d_affine_tool -ref /gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/applyrefined/sub-01_ses-01_T1w_corrected_xform_masked.nii.gz -src /gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/sdc_estimate_wf/pepolar_unwarp_wf/enhance_and_skullstrip_bold_wf/apply_mask/uni_xform_masked.nii.gz /gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/bold_reg_wf/bbreg_wf/lta2fsl_fwd/out.mat -fsl2ras -oitk /gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/bold_reg_wf/bbreg_wf/fsl2itk_fwd/affine.txt
200323-00:05:07,901 nipype.workflow INFO:
[Node] Running "map_seg" ("niworkflows.interfaces.fixes.FixHeaderApplyTransforms"), a CommandLine Interface with command:
antsApplyTransforms --default-value 0 --dimensionality 3 --float 1 --input /gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/t1w_dseg/sub-01_ses-01_T1w_corrected_xform_masked_seg.nii.gz --interpolation MultiLabel --output sub-01_ses-01_T1w_corrected_xform_masked_seg_trans.nii.gz --reference-image /gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/sdc_estimate_wf/pepolar_unwarp_wf/unwarp_reference/ref_sbref_corrected_trans.nii.gz --transform /gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/bold_reg_wf/bbreg_wf/fsl2itk_inv/affine.txt
200323-00:05:08,355 nipype.workflow INFO:
[Node] Finished "fmriprep_wf.single_subject_01_wf.func_preproc_ses_01_task_Stroop_run_01_wf.bold_reg_wf.bbreg_wf.fsl2itk_fwd".
200323-00:05:10,109 nipype.workflow INFO:
[Node] Setting-up "fmriprep_wf.single_subject_01_wf.func_preproc_ses_01_task_Stroop_run_01_wf.bold_t1_trans_wf.mask_t1w_tfm" in "/gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/bold_t1_trans_wf/mask_t1w_tfm".
200323-00:05:10,116 nipype.workflow INFO:
[Node] Running "mask_t1w_tfm" ("niworkflows.interfaces.fixes.FixHeaderApplyTransforms"), a CommandLine Interface with command:
antsApplyTransforms --default-value 0 --float 1 --input /gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/sdc_estimate_wf/pepolar_unwarp_wf/enhance_and_skullstrip_bold_wf/combine_masks/ref_sbref_corrected_trans_corrected_brain_mask_maths.nii.gz --interpolation MultiLabel --output ref_sbref_corrected_trans_corrected_brain_mask_maths_trans.nii.gz --reference-image /gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/bold_t1_trans_wf/gen_ref/sub-01_ses-01_T1w_corrected_xform_masked_reference.nii.gz --transform /gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/bold_reg_wf/bbreg_wf/fsl2itk_fwd/affine.txt
200323-00:05:13,148 nipype.workflow INFO:
[Node] Finished "fmriprep_wf.single_subject_01_wf.func_preproc_ses_01_task_Stroop_run_01_wf.bold_t1_trans_wf.mask_t1w_tfm".
200323-00:05:13,338 nipype.workflow INFO:
[Node] Finished "fmriprep_wf.single_subject_01_wf.func_preproc_ses_01_task_Stroop_run_01_wf.sdc_unwarp_report_wf.map_seg".
200323-00:05:13,985 nipype.workflow INFO:
[Node] Setting-up "fmriprep_wf.single_subject_01_wf.func_preproc_ses_01_task_Stroop_run_01_wf.bold_t1_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.pre_mask_dilate" in "/gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/bold_t1_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/pre_mask_dilate".
200323-00:05:13,985 nipype.workflow INFO:
[Node] Setting-up "fmriprep_wf.single_subject_01_wf.func_preproc_ses_01_task_Stroop_run_01_wf.sdc_unwarp_report_wf.sel_wm" in "/gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/sdc_unwarp_report_wf/sel_wm".
200323-00:05:13,989 nipype.workflow INFO:
[Node] Running "sel_wm" ("nipype.interfaces.utility.wrappers.Function")
200323-00:05:13,989 nipype.workflow INFO:
[Node] Running "pre_mask_dilate" ("nipype.interfaces.fsl.maths.DilateImage"), a CommandLine Interface with command:
fslmaths -dt char /gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/bold_t1_trans_wf/mask_t1w_tfm/ref_sbref_corrected_trans_corrected_brain_mask_maths_trans.nii.gz -kernel sphere 3.0000 -dilF /gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/bold_t1_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/pre_mask_dilate/ref_sbref_corrected_trans_corrected_brain_mask_maths_trans_dil.nii.gz
200323-00:05:14,15 nipype.workflow INFO:
[Node] Finished "fmriprep_wf.single_subject_01_wf.func_preproc_ses_01_task_Stroop_run_01_wf.sdc_unwarp_report_wf.sel_wm".
200323-00:05:14,219 nipype.workflow INFO:
[Node] Finished "fmriprep_wf.single_subject_01_wf.func_preproc_ses_01_task_Stroop_run_01_wf.bold_t1_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.pre_mask_dilate".
200323-00:05:15,987 nipype.workflow INFO:
[Node] Setting-up "fmriprep_wf.single_subject_01_wf.func_preproc_ses_01_task_Stroop_run_01_wf.sdc_unwarp_report_wf.bold_rpt" in "/gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/sdc_unwarp_report_wf/bold_rpt".
200323-00:05:15,988 nipype.workflow INFO:
[Node] Setting-up "fmriprep_wf.single_subject_01_wf.func_preproc_ses_01_task_Stroop_run_01_wf.bold_confounds_wf.wm_tfm" in "/gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/bold_confounds_wf/wm_tfm".
200323-00:05:15,995 nipype.workflow INFO:
[Node] Running "bold_rpt" ("niworkflows.interfaces.registration.SimpleBeforeAfterRPT")
200323-00:05:15,996 nipype.workflow INFO:
[Node] Running "wm_tfm" ("niworkflows.interfaces.fixes.FixHeaderApplyTransforms"), a CommandLine Interface with command:
antsApplyTransforms --default-value 0 --float 1 --input /gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/bold_confounds_wf/wm_roi/sub-01_ses-01_T1w_corrected_xform_masked_prob_2_roi.nii.gz --interpolation NearestNeighbor --output sub-01_ses-01_T1w_corrected_xform_masked_prob_2_roi_trans.nii.gz --reference-image /gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/combine_masks/ref_bold_corrected_brain_mask_maths.nii.gz --transform /gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/bold_reg_wf/bbreg_wf/fsl2itk_inv/affine.txt
200323-00:05:16,286 nipype.workflow INFO:
[Node] Finished "fmriprep_wf.single_subject_01_wf.func_preproc_ses_01_task_Stroop_run_01_wf.bold_confounds_wf.wm_tfm".
200323-00:05:17,989 nipype.workflow INFO:
[Node] Setting-up "fmriprep_wf.single_subject_01_wf.func_preproc_ses_01_task_Stroop_run_01_wf.bold_confounds_wf.wm_msk" in "/gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/bold_confounds_wf/wm_msk".
200323-00:05:17,992 nipype.workflow INFO:
[Node] Running "wm_msk" ("nipype.interfaces.utility.wrappers.Function")
200323-00:05:18,25 nipype.workflow INFO:
[Node] Finished "fmriprep_wf.single_subject_01_wf.func_preproc_ses_01_task_Stroop_run_01_wf.bold_confounds_wf.wm_msk".
200323-00:05:20,2 nipype.workflow INFO:
[Node] Setting-up "fmriprep_wf.single_subject_01_wf.func_preproc_ses_01_task_Stroop_run_01_wf.bold_confounds_wf.tcc_tfm" in "/gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/bold_confounds_wf/tcc_tfm".
200323-00:05:20,8 nipype.workflow INFO:
[Node] Running "tcc_tfm" ("niworkflows.interfaces.fixes.FixHeaderApplyTransforms"), a CommandLine Interface with command:
antsApplyTransforms --default-value 0 --float 1 --input /gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/bold_confounds_wf/csf_roi/sub-01_ses-01_T1w_corrected_xform_rbrainmask_eroded.nii.gz --interpolation NearestNeighbor --output sub-01_ses-01_T1w_corrected_xform_rbrainmask_eroded_trans.nii.gz --reference-image /gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/combine_masks/ref_bold_corrected_brain_mask_maths.nii.gz --transform /gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/bold_reg_wf/bbreg_wf/fsl2itk_inv/affine.txt
200323-00:05:20,236 nipype.workflow INFO:
[Node] Finished "fmriprep_wf.single_subject_01_wf.func_preproc_ses_01_task_Stroop_run_01_wf.bold_confounds_wf.tcc_tfm".
200323-00:05:21,997 nipype.workflow INFO:
[Node] Setting-up "fmriprep_wf.single_subject_01_wf.func_preproc_ses_01_task_Stroop_run_01_wf.bold_confounds_wf.tcc_msk" in "/gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/bold_confounds_wf/tcc_msk".
200323-00:05:22,1 nipype.workflow INFO:
[Node] Running "tcc_msk" ("nipype.interfaces.utility.wrappers.Function")
200323-00:05:22,34 nipype.workflow INFO:
[Node] Finished "fmriprep_wf.single_subject_01_wf.func_preproc_ses_01_task_Stroop_run_01_wf.bold_confounds_wf.tcc_msk".
200323-00:05:23,995 nipype.workflow INFO:
[Node] Setting-up "fmriprep_wf.single_subject_01_wf.func_preproc_ses_01_task_Stroop_run_01_wf.bold_confounds_wf.tcompcor" in "/gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/bold_confounds_wf/tcompcor".
200323-00:05:24,21 nipype.workflow INFO:
[Node] Running "tcompcor" ("niworkflows.interfaces.patches.RobustTCompCor")
200323-00:05:25,174 nipype.workflow INFO:
[Node] Finished "fmriprep_wf.single_subject_01_wf.func_preproc_ses_01_task_Stroop_run_01_wf.sdc_unwarp_report_wf.bold_rpt".
200323-00:05:26,110 nipype.workflow INFO:
[Node] Setting-up "fmriprep_wf.single_subject_01_wf.func_preproc_ses_01_task_Stroop_run_01_wf.bold_confounds_wf.csf_tfm" in "/gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/bold_confounds_wf/csf_tfm".
200323-00:05:26,115 nipype.workflow INFO:
[Node] Running "csf_tfm" ("niworkflows.interfaces.fixes.FixHeaderApplyTransforms"), a CommandLine Interface with command:
antsApplyTransforms --default-value 0 --float 1 --input /gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/bold_confounds_wf/csf_roi/sub-01_ses-01_T1w_corrected_xform_masked_prob_0_roi.nii.gz --interpolation NearestNeighbor --output sub-01_ses-01_T1w_corrected_xform_masked_prob_0_roi_trans.nii.gz --reference-image /gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/combine_masks/ref_bold_corrected_brain_mask_maths.nii.gz --transform /gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/bold_reg_wf/bbreg_wf/fsl2itk_inv/affine.txt
200323-00:05:26,355 nipype.workflow INFO:
[Node] Finished "fmriprep_wf.single_subject_01_wf.func_preproc_ses_01_task_Stroop_run_01_wf.bold_confounds_wf.csf_tfm".
200323-00:05:28,3 nipype.workflow INFO:
[Node] Setting-up "fmriprep_wf.single_subject_01_wf.func_preproc_ses_01_task_Stroop_run_01_wf.bold_confounds_wf.csf_msk" in "/gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/bold_confounds_wf/csf_msk".
200323-00:05:28,7 nipype.workflow INFO:
[Node] Running "csf_msk" ("nipype.interfaces.utility.wrappers.Function")
200323-00:05:28,40 nipype.workflow INFO:
[Node] Finished "fmriprep_wf.single_subject_01_wf.func_preproc_ses_01_task_Stroop_run_01_wf.bold_confounds_wf.csf_msk".
200323-00:05:30,112 nipype.workflow INFO:
[Node] Setting-up "fmriprep_wf.single_subject_01_wf.func_preproc_ses_01_task_Stroop_run_01_wf.bold_confounds_wf.acc_tfm" in "/gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/bold_confounds_wf/acc_tfm".
200323-00:05:30,117 nipype.workflow INFO:
[Node] Running "acc_tfm" ("niworkflows.interfaces.fixes.FixHeaderApplyTransforms"), a CommandLine Interface with command:
antsApplyTransforms --default-value 0 --float 1 --input /gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/bold_confounds_wf/acc_roi/sub-01_ses-01_T1w_corrected_xform_masked_prob_0_tpmsum_roi.nii.gz --interpolation NearestNeighbor --output sub-01_ses-01_T1w_corrected_xform_masked_prob_0_tpmsum_roi_trans.nii.gz --reference-image /gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/combine_masks/ref_bold_corrected_brain_mask_maths.nii.gz --transform /gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/bold_reg_wf/bbreg_wf/fsl2itk_inv/affine.txt
200323-00:05:30,355 nipype.workflow INFO:
[Node] Finished "fmriprep_wf.single_subject_01_wf.func_preproc_ses_01_task_Stroop_run_01_wf.bold_confounds_wf.acc_tfm".
200323-00:05:32,21 nipype.workflow INFO:
[Node] Setting-up "fmriprep_wf.single_subject_01_wf.func_preproc_ses_01_task_Stroop_run_01_wf.bold_confounds_wf.signals" in "/gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/bold_confounds_wf/signals".
200323-00:05:32,29 nipype.workflow INFO:
[Node] Running "signals" ("niworkflows.interfaces.images.SignalExtraction")
200323-00:05:32,802 nipype.workflow INFO:
[Node] Finished "fmriprep_wf.single_subject_01_wf.func_preproc_ses_01_task_Stroop_run_01_wf.bold_confounds_wf.tcompcor".
200323-00:05:34,9 nipype.workflow INFO:
[Node] Setting-up "fmriprep_wf.single_subject_01_wf.func_preproc_ses_01_task_Stroop_run_01_wf.bold_confounds_wf.tcc_metadata_fmt" in "/gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/bold_confounds_wf/tcc_metadata_fmt".
200323-00:05:34,13 nipype.workflow INFO:
[Node] Running "tcc_metadata_fmt" ("niworkflows.interfaces.utils.TSV2JSON")
200323-00:05:34,95 nipype.workflow INFO:
[Node] Finished "fmriprep_wf.single_subject_01_wf.func_preproc_ses_01_task_Stroop_run_01_wf.bold_confounds_wf.tcc_metadata_fmt".
200323-00:05:36,21 nipype.workflow INFO:
[Node] Setting-up "fmriprep_wf.single_subject_01_wf.func_preproc_ses_01_task_Stroop_run_01_wf.bold_confounds_wf.acc_msk" in "/gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/bold_confounds_wf/acc_msk".
200323-00:05:36,24 nipype.workflow INFO:
[Node] Running "acc_msk" ("nipype.interfaces.utility.wrappers.Function")
200323-00:05:36,58 nipype.workflow INFO:
[Node] Finished "fmriprep_wf.single_subject_01_wf.func_preproc_ses_01_task_Stroop_run_01_wf.bold_confounds_wf.acc_msk".
200323-00:05:37,236 nipype.workflow INFO:
[Node] Finished "fmriprep_wf.single_subject_01_wf.func_preproc_ses_01_task_Stroop_run_01_wf.bold_confounds_wf.signals".
200323-00:05:38,203 nipype.workflow INFO:
[Node] Setting-up "_std_tpms1" in "/gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/anat_norm_wf/_template_MNI152NLin2009cAsym./std_tpms/mapflow/_std_tpms1".
200323-00:05:38,206 nipype.workflow INFO:
[Node] Setting-up "_std_tpms2" in "/gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/anat_norm_wf/_template_MNI152NLin2009cAsym./std_tpms/mapflow/_std_tpms2".
200323-00:05:38,207 nipype.workflow INFO:
[Node] Running "_std_tpms1" ("niworkflows.interfaces.fixes.FixHeaderApplyTransforms"), a CommandLine Interface with command:
antsApplyTransforms --default-value 0 --dimensionality 3 --float 1 --input /gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/t1w_dseg/sub-01_ses-01_T1w_corrected_xform_masked_prob_1.nii.gz --interpolation Gaussian --output sub-01_ses-01_T1w_corrected_xform_masked_prob_1_trans.nii.gz --reference-image /home/jac18015/.cache/templateflow/tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_res-01_T1w.nii.gz --transform /gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/anat_norm_wf/_template_MNI152NLin2009cAsym./registration/ants_t1_to_mniComposite.h5
200323-00:05:38,217 nipype.workflow INFO:
[Node] Running "_std_tpms2" ("niworkflows.interfaces.fixes.FixHeaderApplyTransforms"), a CommandLine Interface with command:
antsApplyTransforms --default-value 0 --dimensionality 3 --float 1 --input /gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/t1w_dseg/sub-01_ses-01_T1w_corrected_xform_masked_prob_2.nii.gz --interpolation Gaussian --output sub-01_ses-01_T1w_corrected_xform_masked_prob_2_trans.nii.gz --reference-image /home/jac18015/.cache/templateflow/tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_res-01_T1w.nii.gz --transform /gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/anat_norm_wf/_template_MNI152NLin2009cAsym./registration/ants_t1_to_mniComposite.h5
200323-00:06:03,759 nipype.workflow INFO:
[Node] Finished "_std_tpms2".
200323-00:06:03,963 nipype.workflow INFO:
[Node] Finished "_std_tpms1".
200323-00:06:04,33 nipype.workflow INFO:
[Node] Setting-up "fmriprep_wf.single_subject_01_wf.func_preproc_ses_01_task_Stroop_run_01_wf.bold_confounds_wf.rois_plot" in "/gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/bold_confounds_wf/rois_plot".
200323-00:06:04,38 nipype.workflow INFO:
[Node] Running "rois_plot" ("niworkflows.interfaces.masks.ROIsPlot")
200323-00:06:06,41 nipype.workflow INFO:
[Node] Setting-up "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.anat_norm_wf.std_tpms" in "/gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/anat_norm_wf/_template_MNI152NLin2009cAsym./std_tpms".
200323-00:06:06,47 nipype.workflow INFO:
[Node] Setting-up "_std_tpms0" in "/gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/anat_norm_wf/_template_MNI152NLin2009cAsym./std_tpms/mapflow/_std_tpms0".
200323-00:06:06,48 nipype.workflow INFO:
[Node] Cached "_std_tpms0" - collecting precomputed outputs
200323-00:06:06,48 nipype.workflow INFO:
[Node] "_std_tpms0" found cached.
200323-00:06:06,49 nipype.workflow INFO:
[Node] Setting-up "_std_tpms1" in "/gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/anat_norm_wf/_template_MNI152NLin2009cAsym./std_tpms/mapflow/_std_tpms1".
200323-00:06:06,50 nipype.workflow INFO:
[Node] Cached "_std_tpms1" - collecting precomputed outputs
200323-00:06:06,50 nipype.workflow INFO:
[Node] "_std_tpms1" found cached.
200323-00:06:06,51 nipype.workflow INFO:
[Node] Setting-up "_std_tpms2" in "/gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/anat_norm_wf/_template_MNI152NLin2009cAsym./std_tpms/mapflow/_std_tpms2".
200323-00:06:06,52 nipype.workflow INFO:
[Node] Cached "_std_tpms2" - collecting precomputed outputs
200323-00:06:06,52 nipype.workflow INFO:
[Node] "_std_tpms2" found cached.
200323-00:06:06,54 nipype.workflow INFO:
[Node] Finished "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.anat_norm_wf.std_tpms".
200323-00:06:06,905 nipype.workflow INFO:
[Node] Finished "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.anat_norm_wf.std_mask".
200323-00:06:08,692 nipype.workflow INFO:
[Node] Setting-up "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.anat_reports_wf.norm_msk" in "/gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/anat_reports_wf/_template_MNI152NLin2009cAsym./norm_msk".
200323-00:06:08,697 nipype.workflow INFO:
[Node] Running "norm_msk" ("nipype.interfaces.utility.wrappers.Function")
200323-00:06:09,983 nipype.workflow INFO:
[Node] Finished "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.anat_reports_wf.norm_msk".
200323-00:06:11,719 nipype.workflow INFO:
[Node] Setting-up "fmriprep_wf.single_subject_01_wf.func_preproc_ses_01_task_Stroop_run_01_wf.bold_confounds_wf.acompcor" in "/gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/bold_confounds_wf/acompcor".
200323-00:06:11,726 nipype.workflow INFO:
[Node] Running "acompcor" ("niworkflows.interfaces.patches.RobustACompCor")
200323-00:06:11,825 nipype.workflow INFO:
[Node] Setting-up "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.anat_reports_wf.norm_rpt" in "/gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/anat_reports_wf/_template_MNI152NLin2009cAsym./norm_rpt".
200323-00:06:11,829 nipype.workflow INFO:
[Node] Running "norm_rpt" ("niworkflows.interfaces.registration.SimpleBeforeAfterRPT")
200323-00:06:13,966 nipype.workflow INFO:
[Node] Finished "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.anat_norm_wf.std_dseg".
200323-00:06:14,597 nipype.workflow INFO:
[Node] Finished "fmriprep_wf.single_subject_01_wf.func_preproc_ses_01_task_Stroop_run_01_wf.bold_confounds_wf.rois_plot".
200323-00:06:15,831 nipype.workflow INFO:
[Node] Setting-up "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.anat_derivatives_wf.lut_std_dseg" in "/gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/anat_derivatives_wf/_template_MNI152NLin2009cAsym./lut_std_dseg".
200323-00:06:15,831 nipype.workflow INFO:
[Node] Setting-up "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.anat_norm_wf.outputnode" in "/gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/anat_norm_wf/outputnode".
200323-00:06:15,835 nipype.workflow INFO:
[Node] Running "lut_std_dseg" ("nipype.interfaces.utility.wrappers.Function")
200323-00:06:15,838 nipype.workflow INFO:
[Node] Running "outputnode" ("nipype.interfaces.utility.base.IdentityInterface")
200323-00:06:15,842 nipype.workflow INFO:
[Node] Finished "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.anat_norm_wf.outputnode".
200323-00:06:16,63 nipype.workflow INFO:
[Node] Finished "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.anat_derivatives_wf.lut_std_dseg".
200323-00:06:19,414 nipype.workflow INFO:
[Node] Finished "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.anat_reports_wf.norm_rpt".
200323-00:06:20,715 nipype.workflow INFO:
[Node] Setting-up "fmriprep_wf.single_subject_01_wf.func_preproc_ses_01_task_Stroop_run_01_wf.carpetplot_wf.mrg_xfms" in "/gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/carpetplot_wf/mrg_xfms".
200323-00:06:20,722 nipype.workflow INFO:
[Node] Running "mrg_xfms" ("nipype.interfaces.utility.base.Merge")
200323-00:06:20,725 nipype.workflow INFO:
[Node] Finished "fmriprep_wf.single_subject_01_wf.func_preproc_ses_01_task_Stroop_run_01_wf.carpetplot_wf.mrg_xfms".
200323-00:06:21,370 nipype.workflow INFO:
[Node] Finished "fmriprep_wf.single_subject_01_wf.func_preproc_ses_01_task_Stroop_run_01_wf.bold_confounds_wf.acompcor".
200323-00:06:22,230 nipype.workflow INFO:
[Node] Setting-up "fmriprep_wf.single_subject_01_wf.func_preproc_ses_01_task_Stroop_run_01_wf.bold_t1_trans_wf.bold_to_t1w_transform" in "/gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/bold_t1_trans_wf/bold_to_t1w_transform".
200323-00:06:22,614 nipype.workflow INFO:
[Node] Running "bold_to_t1w_transform" ("niworkflows.interfaces.itk.MultiApplyTransforms")
200323-00:09:43,890 nipype.workflow INFO:
[Node] Finished "fmriprep_wf.single_subject_01_wf.func_preproc_ses_01_task_Stroop_run_01_wf.bold_t1_trans_wf.bold_to_t1w_transform".
200323-00:09:44,432 nipype.workflow INFO:
[Node] Setting-up "fmriprep_wf.single_subject_01_wf.func_preproc_ses_01_task_Stroop_run_01_wf.bold_std_trans_wf.gen_ref" in "/gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/bold_std_trans_wf/_key_MNI152NLin2009cAsym/gen_ref".
200323-00:09:44,432 nipype.workflow INFO:
[Node] Setting-up "fmriprep_wf.single_subject_01_wf.func_preproc_ses_01_task_Stroop_run_01_wf.bold_t1_trans_wf.merge" in "/gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/bold_t1_trans_wf/merge".
200323-00:09:44,434 nipype.workflow INFO:
[Node] Setting-up "fmriprep_wf.single_subject_01_wf.func_preproc_ses_01_task_Stroop_run_01_wf.carpetplot_wf.resample_parc" in "/gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/carpetplot_wf/resample_parc".
200323-00:09:44,441 nipype.workflow INFO:
[Node] Running "resample_parc" ("niworkflows.interfaces.fixes.FixHeaderApplyTransforms"), a CommandLine Interface with command:
antsApplyTransforms --default-value 0 --dimensionality 3 --float 1 --input /home/jac18015/.cache/templateflow/tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_res-01_desc-carpet_dseg.nii.gz --interpolation MultiLabel --output tpl-MNI152NLin2009cAsym_res-01_desc-carpet_dseg_trans.nii.gz --reference-image /gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/combine_masks/ref_bold_corrected_brain_mask_maths.nii.gz --transform /gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/bold_reg_wf/bbreg_wf/fsl2itk_inv/affine.txt --transform /gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/anat_norm_wf/_template_MNI152NLin2009cAsym./registration/ants_t1_to_mniInverseComposite.h5
200323-00:09:44,465 nipype.workflow INFO:
[Node] Running "gen_ref" ("niworkflows.interfaces.utils.GenerateSamplingReference")
200323-00:09:44,527 nipype.workflow INFO:
[Node] Running "merge" ("niworkflows.interfaces.nilearn.Merge")
200323-00:09:44,546 nipype.workflow INFO:
[Node] Setting-up "fmriprep_wf.single_subject_01_wf.func_preproc_ses_01_task_Stroop_run_01_wf.bold_confounds_wf.acc_metadata_fmt" in "/gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/bold_confounds_wf/acc_metadata_fmt".
200323-00:09:44,550 nipype.workflow INFO:
[Node] Running "acc_metadata_fmt" ("niworkflows.interfaces.utils.TSV2JSON")
200323-00:09:44,698 nipype.workflow INFO:
[Node] Finished "fmriprep_wf.single_subject_01_wf.func_preproc_ses_01_task_Stroop_run_01_wf.bold_confounds_wf.acc_metadata_fmt".
200323-00:09:44,801 nipype.workflow INFO:
[Node] Finished "fmriprep_wf.single_subject_01_wf.func_preproc_ses_01_task_Stroop_run_01_wf.bold_std_trans_wf.gen_ref".
200323-00:09:46,439 nipype.workflow INFO:
[Node] Setting-up "fmriprep_wf.single_subject_01_wf.func_preproc_ses_01_task_Stroop_run_01_wf.bold_std_trans_wf.aparc_std_tfm" in "/gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/bold_std_trans_wf/_key_MNI152NLin2009cAsym/aparc_std_tfm".
200323-00:09:46,440 nipype.workflow INFO:
[Node] Setting-up "fmriprep_wf.single_subject_01_wf.func_preproc_ses_01_task_Stroop_run_01_wf.bold_std_trans_wf.aseg_std_tfm" in "/gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/bold_std_trans_wf/_key_MNI152NLin2009cAsym/aseg_std_tfm".
200323-00:09:46,445 nipype.workflow INFO:
[Node] Running "aseg_std_tfm" ("niworkflows.interfaces.fixes.FixHeaderApplyTransforms"), a CommandLine Interface with command:
antsApplyTransforms --default-value 0 --float 1 --input /gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/surface_recon_wf/segs_to_native_aseg/tonii/aseg_vol_out.nii.gz --interpolation MultiLabel --output aseg_vol_out_trans.nii.gz --reference-image /gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/bold_std_trans_wf/_key_MNI152NLin2009cAsym/gen_ref/tpl-MNI152NLin2009cAsym_res-01_T1w_reference.nii.gz --transform /gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/anat_norm_wf/_template_MNI152NLin2009cAsym./registration/ants_t1_to_mniComposite.h5
200323-00:09:46,446 nipype.workflow INFO:
[Node] Running "aparc_std_tfm" ("niworkflows.interfaces.fixes.FixHeaderApplyTransforms"), a CommandLine Interface with command:
antsApplyTransforms --default-value 0 --float 1 --input /gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/surface_recon_wf/segs_to_native_aparc_aseg/tonii/aparc+aseg_vol_out.nii.gz --interpolation MultiLabel --output aparc+aseg_vol_out_trans.nii.gz --reference-image /gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/bold_std_trans_wf/_key_MNI152NLin2009cAsym/gen_ref/tpl-MNI152NLin2009cAsym_res-01_T1w_reference.nii.gz --transform /gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/anat_norm_wf/_template_MNI152NLin2009cAsym./registration/ants_t1_to_mniComposite.h5
200323-00:09:50,223 nipype.workflow INFO:
[Node] Finished "fmriprep_wf.single_subject_01_wf.func_preproc_ses_01_task_Stroop_run_01_wf.carpetplot_wf.resample_parc".
200323-00:09:50,441 nipype.workflow INFO:
[Node] Setting-up "fmriprep_wf.single_subject_01_wf.func_preproc_ses_01_task_Stroop_run_01_wf.bold_std_trans_wf.mask_std_tfm" in "/gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/bold_std_trans_wf/_key_MNI152NLin2009cAsym/mask_std_tfm".
200323-00:09:50,446 nipype.workflow INFO:
[Node] Running "mask_std_tfm" ("niworkflows.interfaces.fixes.FixHeaderApplyTransforms"), a CommandLine Interface with command:
antsApplyTransforms --default-value 0 --float 1 --input /gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/bold_bold_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/combine_masks/ref_bold_corrected_brain_mask_maths.nii.gz --interpolation MultiLabel --output ref_bold_corrected_brain_mask_maths_trans.nii.gz --reference-image /gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/bold_std_trans_wf/_key_MNI152NLin2009cAsym/gen_ref/tpl-MNI152NLin2009cAsym_res-01_T1w_reference.nii.gz --transform /gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/anat_norm_wf/_template_MNI152NLin2009cAsym./registration/ants_t1_to_mniComposite.h5 --transform /gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/bold_reg_wf/bbreg_wf/fsl2itk_fwd/affine.txt
200323-00:09:55,375 nipype.workflow INFO:
[Node] Finished "fmriprep_wf.single_subject_01_wf.func_preproc_ses_01_task_Stroop_run_01_wf.bold_std_trans_wf.aseg_std_tfm".
200323-00:09:55,459 nipype.workflow INFO:
[Node] Finished "fmriprep_wf.single_subject_01_wf.func_preproc_ses_01_task_Stroop_run_01_wf.bold_std_trans_wf.aparc_std_tfm".
200323-00:09:57,83 nipype.workflow INFO:
[Node] Setting-up "fmriprep_wf.single_subject_01_wf.func_preproc_ses_01_task_Stroop_run_01_wf.bold_confounds_wf.compcor_plot" in "/gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/bold_confounds_wf/compcor_plot".
200323-00:09:57,86 nipype.workflow INFO:
[Node] Running "compcor_plot" ("niworkflows.interfaces.plotting.CompCorVariancePlot")
200323-00:09:57,457 nipype.workflow INFO:
[Node] Finished "fmriprep_wf.single_subject_01_wf.func_preproc_ses_01_task_Stroop_run_01_wf.bold_confounds_wf.compcor_plot".
200323-00:09:57,655 nipype.workflow INFO:
[Node] Finished "fmriprep_wf.single_subject_01_wf.func_preproc_ses_01_task_Stroop_run_01_wf.bold_std_trans_wf.mask_std_tfm".
200323-00:09:58,825 nipype.workflow INFO:
[Node] Setting-up "fmriprep_wf.single_subject_01_wf.func_preproc_ses_01_task_Stroop_run_01_wf.bold_std_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.pre_mask_dilate" in "/gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/bold_std_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/_key_MNI152NLin2009cAsym/pre_mask_dilate".
200323-00:09:58,829 nipype.workflow INFO:
[Node] Running "pre_mask_dilate" ("nipype.interfaces.fsl.maths.DilateImage"), a CommandLine Interface with command:
fslmaths -dt char /gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/bold_std_trans_wf/_key_MNI152NLin2009cAsym/mask_std_tfm/ref_bold_corrected_brain_mask_maths_trans.nii.gz -kernel sphere 3.0000 -dilF /gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/bold_std_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/_key_MNI152NLin2009cAsym/pre_mask_dilate/ref_bold_corrected_brain_mask_maths_trans_dil.nii.gz
200323-00:09:59,308 nipype.workflow INFO:
[Node] Finished "fmriprep_wf.single_subject_01_wf.func_preproc_ses_01_task_Stroop_run_01_wf.bold_std_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.pre_mask_dilate".
200323-00:09:59,694 nipype.workflow INFO:
[Node] Setting-up "fmriprep_wf.single_subject_01_wf.func_preproc_ses_01_task_Stroop_run_01_wf.bold_confounds_wf.conf_corr_plot" in "/gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/bold_confounds_wf/conf_corr_plot".
200323-00:09:59,694 nipype.workflow INFO:
[Node] Setting-up "fmriprep_wf.single_subject_01_wf.func_preproc_ses_01_task_Stroop_run_01_wf.bold_confounds_wf.model_expansion" in "/gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/bold_confounds_wf/model_expansion".
200323-00:09:59,705 nipype.workflow INFO:
[Node] Running "conf_corr_plot" ("niworkflows.interfaces.plotting.ConfoundsCorrelationPlot")
200323-00:09:59,705 nipype.workflow INFO:
[Node] Running "model_expansion" ("niworkflows.interfaces.confounds.ExpandModel")
200323-00:10:00,161 nipype.workflow INFO:
[Node] Finished "fmriprep_wf.single_subject_01_wf.func_preproc_ses_01_task_Stroop_run_01_wf.bold_confounds_wf.model_expansion".
200323-00:10:00,634 nipype.workflow INFO:
[Node] Setting-up "fmriprep_wf.single_subject_01_wf.func_preproc_ses_01_task_Stroop_run_01_wf.bold_confounds_wf.spike_regressors" in "/gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/bold_confounds_wf/spike_regressors".
200323-00:10:00,637 nipype.workflow INFO:
[Node] Running "spike_regressors" ("niworkflows.interfaces.confounds.SpikeRegressors")
200323-00:10:00,981 nipype.workflow INFO:
[Node] Finished "fmriprep_wf.single_subject_01_wf.func_preproc_ses_01_task_Stroop_run_01_wf.bold_confounds_wf.spike_regressors".
200323-00:10:02,630 nipype.workflow INFO:
[Node] Setting-up "fmriprep_wf.single_subject_01_wf.func_preproc_ses_01_task_Stroop_run_01_wf.carpetplot_wf.conf_plot" in "/gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/carpetplot_wf/conf_plot".
200323-00:10:02,636 nipype.workflow INFO:
[Node] Running "conf_plot" ("fmriprep.interfaces.confounds.FMRISummary")
200323-00:10:03,188 nipype.workflow INFO:
[Node] Finished "fmriprep_wf.single_subject_01_wf.func_preproc_ses_01_task_Stroop_run_01_wf.bold_confounds_wf.conf_corr_plot".
200323-00:10:09,633 nipype.workflow INFO:
[Node] Finished "fmriprep_wf.single_subject_01_wf.func_preproc_ses_01_task_Stroop_run_01_wf.carpetplot_wf.conf_plot".
200323-00:10:28,849 nipype.workflow INFO:
[Node] Finished "fmriprep_wf.single_subject_01_wf.func_preproc_ses_01_task_Stroop_run_01_wf.bold_t1_trans_wf.merge".
200323-00:10:30,657 nipype.workflow INFO:
[Node] Setting-up "fmriprep_wf.single_subject_01_wf.func_preproc_ses_01_task_Stroop_run_01_wf.bold_surf_wf.resampling_xfm" in "/gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/bold_surf_wf/resampling_xfm".
200323-00:10:30,662 nipype.workflow INFO:
[Node] Running "resampling_xfm" ("niworkflows.interfaces.freesurfer.PatchedLTAConvert"), a CommandLine Interface with command:
lta_convert --inlta identity.nofile --outlta /gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/bold_surf_wf/resampling_xfm/out.lta --src /gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/bold_t1_trans_wf/merge/vol0000_xform-00000_merged.nii --trg /gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/brain_extraction_wf/copy_xform/sub-01_ses-01_T1w_corrected_xform.nii.gz
200323-00:10:30,767 nipype.workflow INFO:
[Node] Setting-up "fmriprep_wf.single_subject_01_wf.func_preproc_ses_01_task_Stroop_run_01_wf.bold_t1_trans_wf.bold_reference_wf.validate" in "/gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/bold_t1_trans_wf/bold_reference_wf/validate".
200323-00:10:30,770 nipype.workflow INFO:
[Node] Running "validate" ("niworkflows.interfaces.images.ValidateImage")
200323-00:10:30,774 nipype.workflow INFO:
[Node] Finished "fmriprep_wf.single_subject_01_wf.func_preproc_ses_01_task_Stroop_run_01_wf.bold_t1_trans_wf.bold_reference_wf.validate".
200323-00:10:30,830 nipype.workflow INFO:
[Node] Finished "fmriprep_wf.single_subject_01_wf.func_preproc_ses_01_task_Stroop_run_01_wf.bold_surf_wf.resampling_xfm".
200323-00:10:32,657 nipype.workflow INFO:
[Node] Setting-up "fmriprep_wf.single_subject_01_wf.func_preproc_ses_01_task_Stroop_run_01_wf.bold_t1_trans_wf.bold_reference_wf.gen_ref" in "/gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/bold_t1_trans_wf/bold_reference_wf/gen_ref".
200323-00:10:32,657 nipype.workflow INFO:
[Node] Setting-up "fmriprep_wf.single_subject_01_wf.func_preproc_ses_01_task_Stroop_run_01_wf.bold_surf_wf.set_xfm_source" in "/gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/bold_surf_wf/set_xfm_source".
200323-00:10:32,660 nipype.workflow INFO:
[Node] Running "gen_ref" ("niworkflows.interfaces.registration.EstimateReferenceImage")
200323-00:10:32,662 nipype.workflow INFO:
[Node] Running "set_xfm_source" ("niworkflows.interfaces.freesurfer.PatchedConcatenateLTA"), a CommandLine Interface with command:
mri_concatenate_lta -out_type 1 /gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/bold_surf_wf/resampling_xfm/out.lta /gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/surface_recon_wf/t1w2fsnative_xfm/out.lta out_concat.lta
200323-00:10:32,756 nipype.workflow INFO:
[Node] Finished "fmriprep_wf.single_subject_01_wf.func_preproc_ses_01_task_Stroop_run_01_wf.bold_surf_wf.set_xfm_source".
200323-00:10:33,102 nipype.workflow INFO:
[Node] Finished "fmriprep_wf.single_subject_01_wf.func_preproc_ses_01_task_Stroop_run_01_wf.bold_t1_trans_wf.bold_reference_wf.gen_ref".
200323-00:10:34,679 nipype.workflow INFO:
[Node] Setting-up "fmriprep_wf.single_subject_01_wf.func_preproc_ses_01_task_Stroop_run_01_wf.bold_surf_wf.sampler" in "/gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/bold_surf_wf/_hemi_rh/sampler".
200323-00:10:34,682 nipype.workflow INFO:
[Node] Setting-up "fmriprep_wf.single_subject_01_wf.func_preproc_ses_01_task_Stroop_run_01_wf.bold_surf_wf.sampler" in "/gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/bold_surf_wf/_hemi_lh/sampler".
200323-00:10:34,685 nipype.workflow INFO:
[Node] Setting-up "_sampler0" in "/gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/bold_surf_wf/_hemi_rh/sampler/mapflow/_sampler0".
200323-00:10:34,688 nipype.workflow INFO:
[Node] Setting-up "_sampler0" in "/gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/bold_surf_wf/_hemi_lh/sampler/mapflow/_sampler0".
200323-00:10:34,689 nipype.workflow INFO:
[Node] Running "_sampler0" ("nipype.interfaces.freesurfer.utils.SampleToSurface"), a CommandLine Interface with command:
mri_vol2surf --cortex --hemi rh --interp trilinear --o /gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/bold_surf_wf/_hemi_rh/sampler/mapflow/_sampler0/rh.fsaverage5.gii --srcsubject sub-01 --reg /gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/bold_surf_wf/set_xfm_source/out_concat.lta --projfrac-avg 0.000 1.000 0.200 --mov /gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/bold_surf_wf/rename_src/mapflow/_rename_src0/fsaverage5.nii --trgsubject fsaverage5
200323-00:10:34,692 nipype.workflow INFO:
[Node] Running "_sampler0" ("nipype.interfaces.freesurfer.utils.SampleToSurface"), a CommandLine Interface with command:
mri_vol2surf --cortex --hemi lh --interp trilinear --o /gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/bold_surf_wf/_hemi_lh/sampler/mapflow/_sampler0/lh.fsaverage5.gii --srcsubject sub-01 --reg /gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/bold_surf_wf/set_xfm_source/out_concat.lta --projfrac-avg 0.000 1.000 0.200 --mov /gpfs/scratchfs1/jac18015/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/bold_surf_wf/rename_src/mapflow/_rename_src0/fsaverage5.nii --trgsubject fsaverage5
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