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| [33m1: [WARN] The recommended file /README is missing. See Section 03 (Modality agnostic files) of the BIDS specification. (code: 101 - README_FILE_MISSING)[39m | |
| [36m Please visit https://neurostars.org/search?q=README_FILE_MISSING for existing conversations about this issue.[39m | |
| [34m[4mSummary:[24m[39m [34m[4mAvailable Tasks:[24m[39m [34m[4mAvailable Modalities:[24m[39m | |
| 15 Files, 425.93MB Stroop T1w | |
| 1 - Subject T2w | |
| 1 - Session bold | |
| events | |
| sbref | |
| fieldmap | |
| [36m If you have any questions, please post on https://neurostars.org/tags/bids.[39m | |
| Making sure the input data is BIDS compliant (warnings can be ignored in most cases). | |
| 200315-19:12:11,362 nipype.workflow IMPORTANT: | |
| Running fMRIPREP version 1.5.9: | |
| * BIDS dataset path: /data. | |
| * Participant list: ['01']. | |
| * Run identifier: 20200315-191211_4cd0c019-ae6b-4f4d-b58b-267298a496aa. | |
| 200315-19:12:11,844 nipype.utils INFO: | |
| No new version available. | |
| 200315-19:12:14,885 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. | |
| 200315-19:12:14,912 nipype.workflow IMPORTANT: | |
| Using single-band reference file sub-01_ses-01_task-Stroop_run-01_sbref.nii.gz | |
| 200315-19:12:17,500 nipype.workflow IMPORTANT: | |
| Slice-timing correction will be included. | |
| 200315-19:12:18,980 nipype.workflow IMPORTANT: | |
| Creating BOLD surface-sampling workflow. | |
| 200315-19:12:23,836 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 | |
| 200315-19:12:33,169 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/shj16108/hw5/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/func_derivatives_wf/raw_sources". | |
| 200315-19:12:33,179 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/shj16108/hw5/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". | |
| 200315-19:12:33,182 nipype.workflow INFO: | |
| [Node] Running "raw_sources" ("nipype.interfaces.utility.wrappers.Function") | |
| 200315-19:12:33,187 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". | |
| 200315-19:12:33,191 nipype.workflow INFO: | |
| [Node] Running "split" ("nipype.interfaces.utility.wrappers.Function") | |
| 200315-19:12:33,791 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". | |
| 200315-19:12:34,978 nipype.workflow INFO: | |
| [Node] Setting-up "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.brain_extraction_wf.lap_tmpl" in "/gpfs/scratchfs1/shj16108/hw5/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/brain_extraction_wf/lap_tmpl". | |
| 200315-19:12:34,981 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/shj16108/.cache/templateflow/tpl-OASIS30ANTs/tpl-OASIS30ANTs_res-01_T1w.nii.gz 1.5 1 | |
| 200315-19:12:34,990 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/shj16108/hw5/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/bold_reference_wf/validate". | |
| 200315-19:12:34,993 nipype.workflow INFO: | |
| [Node] Running "validate" ("niworkflows.interfaces.images.ValidateImage") | |
| 200315-19:12:35,37 nipype.workflow INFO: | |
| [Node] Setting-up "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.brain_extraction_wf.res_tmpl" in "/gpfs/scratchfs1/shj16108/hw5/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/brain_extraction_wf/res_tmpl". | |
| 200315-19:12:35,41 nipype.workflow INFO: | |
| [Node] Running "res_tmpl" ("niworkflows.interfaces.ants.ResampleImageBySpacing"), a CommandLine Interface with command: | |
| ResampleImageBySpacing 3 /home/shj16108/.cache/templateflow/tpl-OASIS30ANTs/tpl-OASIS30ANTs_res-01_T1w.nii.gz tpl-OASIS30ANTs_res-01_T1w_resampled.nii.gz 4 4 4 1 | |
| 200315-19:12:35,77 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/shj16108/hw5/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/val_sbref". | |
| 200315-19:12:35,79 nipype.workflow INFO: | |
| [Node] Running "val_sbref" ("niworkflows.interfaces.images.ValidateImage") | |
| 200315-19:12:35,227 nipype.workflow INFO: | |
| [Node] Setting-up "fmriprep_wf.single_subject_01_wf.bidssrc" in "/gpfs/scratchfs1/shj16108/hw5/hw5/work/fmriprep_wf/single_subject_01_wf/bidssrc". | |
| 200315-19:12:35,230 nipype.workflow INFO: | |
| [Node] Running "bidssrc" ("niworkflows.interfaces.bids.BIDSDataGrabber") | |
| 200315-19:12:35,281 nipype.interface WARNING: | |
| No "flair" images found for sub-<undefined> | |
| 200315-19:12:35,281 nipype.interface WARNING: | |
| No "roi" images found for sub-<undefined> | |
| 200315-19:12:35,285 nipype.workflow INFO: | |
| [Node] Finished "fmriprep_wf.single_subject_01_wf.bidssrc". | |
| 200315-19:12:35,586 nipype.workflow INFO: | |
| [Node] Finished "fmriprep_wf.single_subject_01_wf.func_preproc_ses_01_task_Stroop_run_01_wf.val_sbref". | |
| 200315-19:12:35,586 nipype.workflow INFO: | |
| [Node] Finished "fmriprep_wf.single_subject_01_wf.func_preproc_ses_01_task_Stroop_run_01_wf.bold_reference_wf.validate". | |
| 200315-19:12:37,296 nipype.workflow INFO: | |
| [Node] Finished "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.brain_extraction_wf.res_tmpl". | |
| 200315-19:12:39,96 nipype.workflow INFO: | |
| [Node] Setting-up "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.anat_template_wf.t1w_ref_dimensions" in "/gpfs/scratchfs1/shj16108/hw5/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/anat_template_wf/t1w_ref_dimensions". | |
| 200315-19:12:39,99 nipype.workflow INFO: | |
| [Node] Running "t1w_ref_dimensions" ("niworkflows.interfaces.images.TemplateDimensions") | |
| 200315-19:12:39,241 nipype.workflow INFO: | |
| [Node] Finished "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.anat_template_wf.t1w_ref_dimensions". | |
| 200315-19:12:39,370 nipype.workflow INFO: | |
| [Node] Setting-up "fmriprep_wf.single_subject_01_wf.bids_info" in "/gpfs/scratchfs1/shj16108/hw5/hw5/work/fmriprep_wf/single_subject_01_wf/bids_info". | |
| 200315-19:12:39,373 nipype.workflow INFO: | |
| [Node] Running "bids_info" ("niworkflows.interfaces.bids.BIDSInfo") | |
| 200315-19:12:39,540 nipype.workflow INFO: | |
| [Node] Finished "fmriprep_wf.single_subject_01_wf.bids_info". | |
| 200315-19:12:40,86 nipype.workflow INFO: | |
| [Node] Setting-up "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.anat_derivatives_wf.raw_sources" in "/gpfs/scratchfs1/shj16108/hw5/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/anat_derivatives_wf/raw_sources". | |
| 200315-19:12:40,86 nipype.workflow INFO: | |
| [Node] Setting-up "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.anat_derivatives_wf.t1w_name" in "/gpfs/scratchfs1/shj16108/hw5/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/anat_derivatives_wf/t1w_name". | |
| 200315-19:12:40,89 nipype.workflow INFO: | |
| [Node] Running "raw_sources" ("nipype.interfaces.utility.wrappers.Function") | |
| 200315-19:12:40,92 nipype.workflow INFO: | |
| [Node] Finished "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.anat_derivatives_wf.raw_sources". | |
| 200315-19:12:40,95 nipype.workflow INFO: | |
| [Node] Running "t1w_name" ("nipype.interfaces.utility.wrappers.Function") | |
| 200315-19:12:40,98 nipype.workflow INFO: | |
| [Node] Finished "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.anat_derivatives_wf.t1w_name". | |
| 200315-19:12:40,193 nipype.workflow INFO: | |
| [Node] Setting-up "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.anat_template_wf.t1w_conform" in "/gpfs/scratchfs1/shj16108/hw5/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/anat_template_wf/t1w_conform". | |
| 200315-19:12:40,197 nipype.workflow INFO: | |
| [Node] Setting-up "_t1w_conform0" in "/gpfs/scratchfs1/shj16108/hw5/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/anat_template_wf/t1w_conform/mapflow/_t1w_conform0". | |
| 200315-19:12:40,200 nipype.workflow INFO: | |
| [Node] Running "_t1w_conform0" ("niworkflows.interfaces.images.Conform") | |
| 200315-19:12:40,220 nipype.workflow INFO: | |
| [Node] Finished "_t1w_conform0". | |
| 200315-19:12:40,221 nipype.workflow INFO: | |
| [Node] Finished "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.anat_template_wf.t1w_conform". | |
| 200315-19:12:40,716 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/shj16108/hw5/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/bold_reference_wf/gen_ref". | |
| 200315-19:12:40,726 nipype.workflow INFO: | |
| [Node] Running "gen_ref" ("niworkflows.interfaces.registration.EstimateReferenceImage") | |
| 200315-19:12:40,728 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/shj16108/hw5/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". | |
| 200315-19:12:40,733 nipype.workflow INFO: | |
| [Node] Running "merge_op" ("niworkflows.interfaces.freesurfer.StructuralReference"), a CommandLine Interface with command: | |
| mri_robust_template --satit --fixtp --mov /gpfs/scratchfs1/shj16108/hw5/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/shj16108/hw5/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/shj16108/hw5/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 | |
| 200315-19:12:40,803 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/shj16108/hw5/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". | |
| 200315-19:12:40,808 nipype.workflow INFO: | |
| [Node] Running "merge_ma" ("niworkflows.interfaces.freesurfer.StructuralReference"), a CommandLine Interface with command: | |
| mri_robust_template --satit --fixtp --mov /gpfs/scratchfs1/shj16108/hw5/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/shj16108/hw5/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/shj16108/hw5/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 | |
| 200315-19:12:41,474 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". | |
| 200315-19:12:42,95 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/shj16108/hw5/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/bold_hmc_wf/mcflirt". | |
| 200315-19:12:42,100 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/shj16108/hw5/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/shj16108/hw5/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 | |
| 200315-19:12:42,210 nipype.workflow INFO: | |
| [Node] Setting-up "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.anat_template_wf.get1st" in "/gpfs/scratchfs1/shj16108/hw5/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/anat_template_wf/get1st". | |
| 200315-19:12:42,213 nipype.workflow INFO: | |
| [Node] Running "get1st" ("nipype.interfaces.utility.base.Select") | |
| 200315-19:12:42,215 nipype.workflow INFO: | |
| [Node] Finished "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.anat_template_wf.get1st". | |
| 200315-19:12:44,95 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/shj16108/hw5/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/bold_stc_wf/slice_timing_correction". | |
| 200315-19:12:44,103 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/shj16108/hw5/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 | |
| 200315-19:12:45,159 nipype.workflow INFO: | |
| [Node] Finished "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.brain_extraction_wf.lap_tmpl". | |
| 200315-19:12:46,98 nipype.workflow INFO: | |
| [Node] Setting-up "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.brain_extraction_wf.mrg_tmpl" in "/gpfs/scratchfs1/shj16108/hw5/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/brain_extraction_wf/mrg_tmpl". | |
| 200315-19:12:46,99 nipype.workflow INFO: | |
| [Node] Setting-up "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.surface_recon_wf.fov_check" in "/gpfs/scratchfs1/shj16108/hw5/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/surface_recon_wf/fov_check". | |
| 200315-19:12:46,101 nipype.workflow INFO: | |
| [Node] Setting-up "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.brain_extraction_wf.truncate_images" in "/gpfs/scratchfs1/shj16108/hw5/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/brain_extraction_wf/truncate_images". | |
| 200315-19:12:46,102 nipype.workflow INFO: | |
| [Node] Running "fov_check" ("nipype.interfaces.utility.wrappers.Function") | |
| 200315-19:12:46,106 nipype.workflow INFO: | |
| [Node] Setting-up "_truncate_images0" in "/gpfs/scratchfs1/shj16108/hw5/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/brain_extraction_wf/truncate_images/mapflow/_truncate_images0". | |
| 200315-19:12:46,108 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 | |
| 200315-19:12:46,109 nipype.workflow INFO: | |
| [Node] Running "mrg_tmpl" ("nipype.interfaces.utility.base.Merge") | |
| 200315-19:12:46,118 nipype.workflow INFO: | |
| [Node] Finished "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.brain_extraction_wf.mrg_tmpl". | |
| 200315-19:12:46,141 nipype.workflow INFO: | |
| [Node] Setting-up "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.surface_recon_wf.recon_config" in "/gpfs/scratchfs1/shj16108/hw5/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/surface_recon_wf/recon_config". | |
| 200315-19:12:46,303 nipype.workflow INFO: | |
| [Node] Running "recon_config" ("niworkflows.interfaces.freesurfer.FSDetectInputs") | |
| 200315-19:12:46,387 nipype.workflow INFO: | |
| [Node] Finished "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.surface_recon_wf.recon_config". | |
| 200315-19:12:46,460 nipype.workflow INFO: | |
| [Node] Finished "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.surface_recon_wf.fov_check". | |
| 200315-19:12:52,114 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". | |
| 200315-19:12:53,485 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". | |
| 200315-19:13:00,573 nipype.workflow INFO: | |
| [Node] Finished "_truncate_images0". | |
| 200315-19:13:00,574 nipype.workflow INFO: | |
| [Node] Finished "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.brain_extraction_wf.truncate_images". | |
| 200315-19:13:34,905 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". | |
| 200315-19:13:36,134 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/shj16108/hw5/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/bold_stc_wf/copy_xform". | |
| 200315-19:13:36,138 nipype.workflow INFO: | |
| [Node] Running "copy_xform" ("niworkflows.interfaces.utils.CopyXForm") | |
| 200315-19:13:53,942 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". | |
| 200315-19:13:54,153 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/shj16108/hw5/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/bold_split". | |
| 200315-19:13:54,158 nipype.workflow INFO: | |
| [Node] Running "bold_split" ("nipype.interfaces.fsl.utils.Split"), a CommandLine Interface with command: | |
| fslsplit /gpfs/scratchfs1/shj16108/hw5/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 | |
| 200315-19:14:31,872 nipype.workflow INFO: | |
| [Node] Finished "fmriprep_wf.single_subject_01_wf.func_preproc_ses_01_task_Stroop_run_01_wf.bold_split". | |
| 200315-19:15:00,246 nipype.workflow INFO: | |
| [Node] Finished "fmriprep_wf.single_subject_01_wf.func_preproc_ses_01_task_Stroop_run_01_wf.bold_hmc_wf.mcflirt". | |
| 200315-19:15:02,221 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/shj16108/hw5/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". | |
| 200315-19:15:02,264 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/shj16108/.cache/templateflow/tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_res-02_desc-brain_mask.nii.gz -m Mattes[/home/shj16108/.cache/templateflow/tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_res-02_desc-fMRIPrep_boldref.nii.gz,/gpfs/scratchfs1/shj16108/hw5/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 | |
| 200315-19:15:04,927 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". | |
| 200315-19:15:06,224 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/shj16108/hw5/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". | |
| 200315-19:15:06,235 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/shj16108/hw5/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/shj16108/.cache/templateflow/tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_res-02_desc-fMRIPrep_boldref.nii.gz, /gpfs/scratchfs1/shj16108/hw5/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 | |
| 200315-19:15:07,143 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". | |
| 200315-19:15:08,224 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/shj16108/hw5/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/bold_hmc_wf/normalize_motion". | |
| 200315-19:15:08,224 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/shj16108/hw5/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". | |
| 200315-19:15:08,229 nipype.workflow INFO: | |
| [Node] Running "map_brainmask" ("niworkflows.interfaces.fixes.FixHeaderApplyTransforms"), a CommandLine Interface with command: | |
| antsApplyTransforms --default-value 0 --float 1 --input /home/shj16108/.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/shj16108/hw5/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/shj16108/hw5/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 ] | |
| 200315-19:15:08,262 nipype.workflow INFO: | |
| [Node] Running "normalize_motion" ("niworkflows.interfaces.utils.NormalizeMotionParams") | |
| 200315-19:15:08,274 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". | |
| 200315-19:15:10,332 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/shj16108/hw5/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/bold_confounds_wf/fdisp". | |
| 200315-19:15:10,335 nipype.workflow INFO: | |
| [Node] Running "fdisp" ("nipype.algorithms.confounds.FramewiseDisplacement") | |
| 200315-19:15:10,346 nipype.workflow INFO: | |
| [Node] Finished "fmriprep_wf.single_subject_01_wf.func_preproc_ses_01_task_Stroop_run_01_wf.bold_confounds_wf.fdisp". | |
| 200315-19:15:13,348 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". | |
| 200315-19:15:14,229 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/shj16108/hw5/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". | |
| 200315-19:15:14,233 nipype.workflow INFO: | |
| [Node] Running "pre_mask_dilate" ("nipype.interfaces.fsl.maths.DilateImage"), a CommandLine Interface with command: | |
| fslmaths -dt char /gpfs/scratchfs1/shj16108/hw5/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/shj16108/hw5/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 | |
| 200315-19:15:14,585 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". | |
| 200315-19:15:16,254 nipype.interface WARNING: | |
| q-forms of reference and mask are substantially different | |
| 200315-19:15:16,372 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/shj16108/hw5/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". | |
| 200315-19:15:16,377 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/shj16108/.cache/templateflow/tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_res-02_desc-brain_mask.nii.gz -m Mattes[/home/shj16108/.cache/templateflow/tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_res-02_desc-fMRIPrep_boldref.nii.gz,/gpfs/scratchfs1/shj16108/hw5/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 | |
| 200315-19:15:18,616 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". | |
| 200315-19:15:20,236 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/shj16108/hw5/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". | |
| 200315-19:15:20,322 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/shj16108/hw5/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/shj16108/hw5/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 | |
| 200315-19:15:25,862 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". | |
| 200315-19:15:26,241 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/shj16108/hw5/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". | |
| 200315-19:15:26,246 nipype.workflow INFO: | |
| [Node] Running "skullstrip_first_pass" ("nipype.interfaces.fsl.preprocess.BET"), a CommandLine Interface with command: | |
| bet /gpfs/scratchfs1/shj16108/hw5/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/shj16108/hw5/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 | |
| 200315-19:15:27,707 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.prepare_epi_wf.ref_ma_wf.skullstrip_first_pass". | |
| 200315-19:15:28,243 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/shj16108/hw5/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". | |
| 200315-19:15:28,248 nipype.workflow INFO: | |
| [Node] Running "skullstrip_first_dilate" ("nipype.interfaces.fsl.maths.DilateImage"), a CommandLine Interface with command: | |
| fslmaths -dt char /gpfs/scratchfs1/shj16108/hw5/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/shj16108/hw5/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 | |
| 200315-19:15:30,182 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". | |
| 200315-19:15:32,244 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/shj16108/hw5/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". | |
| 200315-19:15:32,249 nipype.workflow INFO: | |
| [Node] Running "skullstrip_first_mask" ("nipype.interfaces.fsl.maths.ApplyMask"), a CommandLine Interface with command: | |
| fslmaths /gpfs/scratchfs1/shj16108/hw5/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/shj16108/hw5/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/shj16108/hw5/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 | |
| 200315-19:15:32,357 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". | |
| 200315-19:15:34,249 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/shj16108/hw5/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". | |
| 200315-19:15:34,254 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/shj16108/hw5/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 | |
| 200315-19:15:37,42 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". | |
| 200315-19:15:38,253 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/shj16108/hw5/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". | |
| 200315-19:15:38,258 nipype.workflow INFO: | |
| [Node] Running "fixhdr_unifize" ("niworkflows.interfaces.utils.CopyXForm") | |
| 200315-19:15:38,316 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.prepare_epi_wf.ref_ma_wf.fixhdr_unifize". | |
| 200315-19:15:40,256 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/shj16108/hw5/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". | |
| 200315-19:15:40,260 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/shj16108/hw5/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 | |
| 200315-19:15:40,464 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". | |
| 200315-19:15:42,257 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/shj16108/hw5/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". | |
| 200315-19:15:42,261 nipype.workflow INFO: | |
| [Node] Running "fixhdr_skullstrip2" ("niworkflows.interfaces.utils.CopyXForm") | |
| 200315-19:15:42,292 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". | |
| 200315-19:15:44,260 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/shj16108/hw5/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". | |
| 200315-19:15:44,266 nipype.workflow INFO: | |
| [Node] Running "combine_masks" ("nipype.interfaces.fsl.maths.BinaryMaths"), a CommandLine Interface with command: | |
| fslmaths /gpfs/scratchfs1/shj16108/hw5/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/shj16108/hw5/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/shj16108/hw5/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 | |
| 200315-19:15:44,360 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". | |
| 200315-19:15:46,262 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/shj16108/hw5/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". | |
| 200315-19:15:46,266 nipype.workflow INFO: | |
| [Node] Running "apply_mask" ("nipype.interfaces.fsl.maths.ApplyMask"), a CommandLine Interface with command: | |
| fslmaths /gpfs/scratchfs1/shj16108/hw5/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/shj16108/hw5/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/shj16108/hw5/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 | |
| 200315-19:15:46,375 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". | |
| 200315-19:15:48,264 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/shj16108/hw5/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". | |
| 200315-19:15:48,272 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/shj16108/hw5/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/shj16108/.cache/templateflow/tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_res-02_desc-fMRIPrep_boldref.nii.gz, /gpfs/scratchfs1/shj16108/hw5/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 | |
| 200315-19:15:49,26 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". | |
| 200315-19:15:50,266 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/shj16108/hw5/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". | |
| 200315-19:15:50,313 nipype.workflow INFO: | |
| [Node] Running "map_brainmask" ("niworkflows.interfaces.fixes.FixHeaderApplyTransforms"), a CommandLine Interface with command: | |
| antsApplyTransforms --default-value 0 --float 1 --input /home/shj16108/.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/shj16108/hw5/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/shj16108/hw5/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 ] | |
| 200315-19:15:55,118 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". | |
| 200315-19:15:56,272 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/shj16108/hw5/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". | |
| 200315-19:15:56,276 nipype.workflow INFO: | |
| [Node] Running "pre_mask_dilate" ("nipype.interfaces.fsl.maths.DilateImage"), a CommandLine Interface with command: | |
| fslmaths -dt char /gpfs/scratchfs1/shj16108/hw5/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/shj16108/hw5/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 | |
| 200315-19:15:56,608 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". | |
| 200315-19:15:58,295 nipype.interface WARNING: | |
| q-forms of reference and mask are substantially different | |
| 200315-19:15:58,407 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/shj16108/hw5/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/bold_hmc_wf/fsl2itk". | |
| 200315-19:15:58,520 nipype.workflow INFO: | |
| [Node] Running "fsl2itk" ("niworkflows.interfaces.itk.MCFLIRT2ITK") | |
| 200315-19:16:30,351 nipype.workflow INFO: | |
| [Node] Finished "fmriprep_wf.single_subject_01_wf.func_preproc_ses_01_task_Stroop_run_01_wf.bold_hmc_wf.fsl2itk". | |
| 200315-19:16:32,306 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/shj16108/hw5/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". | |
| 200315-19:16:32,392 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/shj16108/hw5/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/shj16108/hw5/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 | |
| 200315-19:16:37,859 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". | |
| 200315-19:16:38,308 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/shj16108/hw5/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". | |
| 200315-19:16:38,327 nipype.workflow INFO: | |
| [Node] Running "skullstrip_first_pass" ("nipype.interfaces.fsl.preprocess.BET"), a CommandLine Interface with command: | |
| bet /gpfs/scratchfs1/shj16108/hw5/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/shj16108/hw5/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 | |
| 200315-19:16:39,780 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". | |
| 200315-19:16:40,310 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/shj16108/hw5/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". | |
| 200315-19:16:40,314 nipype.workflow INFO: | |
| [Node] Running "skullstrip_first_dilate" ("nipype.interfaces.fsl.maths.DilateImage"), a CommandLine Interface with command: | |
| fslmaths -dt char /gpfs/scratchfs1/shj16108/hw5/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/shj16108/hw5/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 | |
| 200315-19:16:42,258 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". | |
| 200315-19:16:44,312 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/shj16108/hw5/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". | |
| 200315-19:16:44,317 nipype.workflow INFO: | |
| [Node] Running "skullstrip_first_mask" ("nipype.interfaces.fsl.maths.ApplyMask"), a CommandLine Interface with command: | |
| fslmaths /gpfs/scratchfs1/shj16108/hw5/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/shj16108/hw5/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/shj16108/hw5/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 | |
| 200315-19:16:44,430 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". | |
| 200315-19:16:46,318 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/shj16108/hw5/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". | |
| 200315-19:16:46,322 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/shj16108/hw5/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 | |
| 200315-19:16:49,93 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". | |
| 200315-19:16:50,320 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/shj16108/hw5/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". | |
| 200315-19:16:50,324 nipype.workflow INFO: | |
| [Node] Running "fixhdr_unifize" ("niworkflows.interfaces.utils.CopyXForm") | |
| 200315-19:16:50,382 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". | |
| 200315-19:16:52,322 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/shj16108/hw5/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". | |
| 200315-19:16:52,326 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/shj16108/hw5/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 | |
| 200315-19:16:52,509 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". | |
| 200315-19:16:54,324 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/shj16108/hw5/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". | |
| 200315-19:16:54,328 nipype.workflow INFO: | |
| [Node] Running "fixhdr_skullstrip2" ("niworkflows.interfaces.utils.CopyXForm") | |
| 200315-19:16:54,359 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". | |
| 200315-19:16:56,327 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/shj16108/hw5/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". | |
| 200315-19:16:56,331 nipype.workflow INFO: | |
| [Node] Running "combine_masks" ("nipype.interfaces.fsl.maths.BinaryMaths"), a CommandLine Interface with command: | |
| fslmaths /gpfs/scratchfs1/shj16108/hw5/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/shj16108/hw5/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/shj16108/hw5/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 | |
| 200315-19:16:56,418 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". | |
| 200315-19:16:58,328 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/shj16108/hw5/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". | |
| 200315-19:16:58,332 nipype.workflow INFO: | |
| [Node] Running "apply_mask" ("nipype.interfaces.fsl.maths.ApplyMask"), a CommandLine Interface with command: | |
| fslmaths /gpfs/scratchfs1/shj16108/hw5/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/shj16108/hw5/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/shj16108/hw5/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 | |
| 200315-19:16:58,441 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". | |
| 200315-19:17:00,337 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/shj16108/hw5/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". | |
| 200315-19:17:00,342 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/shj16108/.cache/templateflow/tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_res-02_desc-brain_mask.nii.gz -m Mattes[/home/shj16108/.cache/templateflow/tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_res-02_desc-fMRIPrep_boldref.nii.gz,/gpfs/scratchfs1/shj16108/hw5/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 | |
| 200315-19:17:02,524 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". | |
| 200315-19:17:04,336 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/shj16108/hw5/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". | |
| 200315-19:17:04,343 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/shj16108/hw5/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/shj16108/.cache/templateflow/tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_res-02_desc-fMRIPrep_boldref.nii.gz, /gpfs/scratchfs1/shj16108/hw5/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 | |
| 200315-19:17:05,22 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". | |
| 200315-19:17:06,336 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/shj16108/hw5/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". | |
| 200315-19:17:06,341 nipype.workflow INFO: | |
| [Node] Running "map_brainmask" ("niworkflows.interfaces.fixes.FixHeaderApplyTransforms"), a CommandLine Interface with command: | |
| antsApplyTransforms --default-value 0 --float 1 --input /home/shj16108/.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/shj16108/hw5/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/shj16108/hw5/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 ] | |
| 200315-19:17:10,901 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". | |
| 200315-19:17:12,342 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/shj16108/hw5/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". | |
| 200315-19:17:12,346 nipype.workflow INFO: | |
| [Node] Running "pre_mask_dilate" ("nipype.interfaces.fsl.maths.DilateImage"), a CommandLine Interface with command: | |
| fslmaths -dt char /gpfs/scratchfs1/shj16108/hw5/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/shj16108/hw5/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 | |
| 200315-19:17:12,680 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". | |
| 200315-19:17:14,478 nipype.workflow INFO: | |
| [Node] Setting-up "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.brain_extraction_wf.inu_n4" in "/gpfs/scratchfs1/shj16108/hw5/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/brain_extraction_wf/inu_n4". | |
| 200315-19:17:14,483 nipype.workflow INFO: | |
| [Node] Setting-up "_inu_n40" in "/gpfs/scratchfs1/shj16108/hw5/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/brain_extraction_wf/inu_n4/mapflow/_inu_n40". | |
| 200315-19:17:14,486 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/shj16108/hw5/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 | |
| 200315-19:18:52,162 nipype.workflow INFO: | |
| [Node] Finished "_inu_n40". | |
| 200315-19:18:52,163 nipype.workflow INFO: | |
| [Node] Finished "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.brain_extraction_wf.inu_n4". | |
| 200315-19:18:52,445 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/shj16108/hw5/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". | |
| 200315-19:18:52,445 nipype.workflow INFO: | |
| [Node] Setting-up "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.brain_extraction_wf.lap_target" in "/gpfs/scratchfs1/shj16108/hw5/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/brain_extraction_wf/lap_target". | |
| 200315-19:18:52,445 nipype.workflow INFO: | |
| [Node] Setting-up "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.brain_extraction_wf.res_target" in "/gpfs/scratchfs1/shj16108/hw5/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/brain_extraction_wf/res_target". | |
| 200315-19:18:52,449 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/shj16108/hw5/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 | |
| 200315-19:18:52,449 nipype.workflow INFO: | |
| [Node] Running "res_target" ("niworkflows.interfaces.ants.ResampleImageBySpacing"), a CommandLine Interface with command: | |
| ResampleImageBySpacing 3 /gpfs/scratchfs1/shj16108/hw5/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 | |
| 200315-19:18:52,484 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/shj16108/hw5/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/shj16108/hw5/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 | |
| 200315-19:18:54,600 nipype.workflow INFO: | |
| [Node] Finished "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.brain_extraction_wf.res_target". | |
| 200315-19:18:57,887 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". | |
| 200315-19:18:58,451 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/shj16108/hw5/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". | |
| 200315-19:18:58,455 nipype.workflow INFO: | |
| [Node] Running "skullstrip_first_pass" ("nipype.interfaces.fsl.preprocess.BET"), a CommandLine Interface with command: | |
| bet /gpfs/scratchfs1/shj16108/hw5/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/shj16108/hw5/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 | |
| 200315-19:18:59,845 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". | |
| 200315-19:19:00,452 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/shj16108/hw5/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". | |
| 200315-19:19:00,456 nipype.workflow INFO: | |
| [Node] Running "skullstrip_first_dilate" ("nipype.interfaces.fsl.maths.DilateImage"), a CommandLine Interface with command: | |
| fslmaths -dt char /gpfs/scratchfs1/shj16108/hw5/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/shj16108/hw5/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 | |
| 200315-19:19:02,394 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". | |
| 200315-19:19:04,461 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/shj16108/hw5/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". | |
| 200315-19:19:04,466 nipype.workflow INFO: | |
| [Node] Running "skullstrip_first_mask" ("nipype.interfaces.fsl.maths.ApplyMask"), a CommandLine Interface with command: | |
| fslmaths /gpfs/scratchfs1/shj16108/hw5/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/shj16108/hw5/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/shj16108/hw5/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 | |
| 200315-19:19:04,582 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". | |
| 200315-19:19:06,459 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/shj16108/hw5/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". | |
| 200315-19:19:06,464 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/shj16108/hw5/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 | |
| 200315-19:19:06,889 nipype.workflow INFO: | |
| [Node] Finished "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.brain_extraction_wf.lap_target". | |
| 200315-19:19:08,461 nipype.workflow INFO: | |
| [Node] Setting-up "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.brain_extraction_wf.mrg_target" in "/gpfs/scratchfs1/shj16108/hw5/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/brain_extraction_wf/mrg_target". | |
| 200315-19:19:08,465 nipype.workflow INFO: | |
| [Node] Running "mrg_target" ("nipype.interfaces.utility.base.Merge") | |
| 200315-19:19:08,468 nipype.workflow INFO: | |
| [Node] Finished "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.brain_extraction_wf.mrg_target". | |
| 200315-19:19:09,197 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". | |
| 200315-19:19:10,463 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/shj16108/hw5/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". | |
| 200315-19:19:10,467 nipype.workflow INFO: | |
| [Node] Running "fixhdr_unifize" ("niworkflows.interfaces.utils.CopyXForm") | |
| 200315-19:19:10,524 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". | |
| 200315-19:19:12,464 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/shj16108/hw5/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". | |
| 200315-19:19:12,469 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/shj16108/hw5/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 | |
| 200315-19:19:12,674 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". | |
| 200315-19:19:14,466 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/shj16108/hw5/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". | |
| 200315-19:19:14,470 nipype.workflow INFO: | |
| [Node] Running "fixhdr_skullstrip2" ("niworkflows.interfaces.utils.CopyXForm") | |
| 200315-19:19:14,498 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". | |
| 200315-19:19:16,468 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/shj16108/hw5/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". | |
| 200315-19:19:16,473 nipype.workflow INFO: | |
| [Node] Running "combine_masks" ("nipype.interfaces.fsl.maths.BinaryMaths"), a CommandLine Interface with command: | |
| fslmaths /gpfs/scratchfs1/shj16108/hw5/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/shj16108/hw5/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/shj16108/hw5/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 | |
| 200315-19:19:16,562 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". | |
| 200315-19:19:18,470 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/shj16108/hw5/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". | |
| 200315-19:19:18,475 nipype.workflow INFO: | |
| [Node] Running "apply_mask" ("nipype.interfaces.fsl.maths.ApplyMask"), a CommandLine Interface with command: | |
| fslmaths /gpfs/scratchfs1/shj16108/hw5/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/shj16108/hw5/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/shj16108/hw5/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 | |
| 200315-19:19:18,583 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". | |
| 200315-19:19:20,473 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/shj16108/hw5/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". | |
| 200315-19:19:20,481 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/shj16108/hw5/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/shj16108/hw5/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/shj16108/hw5/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/shj16108/hw5/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 | |
| 200315-19:19:44,149 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". | |
| 200315-19:19:44,496 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/shj16108/hw5/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". | |
| 200315-19:19:44,503 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/shj16108/hw5/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/shj16108/hw5/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/shj16108/hw5/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/shj16108/hw5/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 | |
| 200315-19:20:19,898 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". | |
| 200315-19:20:20,531 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/shj16108/hw5/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/sdc_estimate_wf/pepolar_unwarp_wf/qwarp". | |
| 200315-19:20:20,538 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/shj16108/hw5/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/shj16108/hw5/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 | |
| 200315-19:22:26,942 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". | |
| 200315-19:22:28,658 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/shj16108/hw5/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". | |
| 200315-19:22:28,662 nipype.workflow INFO: | |
| [Node] Running "cphdr_warp" ("niworkflows.interfaces.utils.CopyHeader") | |
| 200315-19:22:28,805 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". | |
| 200315-19:22:30,660 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/shj16108/hw5/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". | |
| 200315-19:22:30,868 nipype.workflow INFO: | |
| [Node] Running "to_ants" ("nipype.interfaces.utility.wrappers.Function") | |
| 200315-19:22:30,987 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". | |
| 200315-19:22:32,757 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/shj16108/hw5/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". | |
| 200315-19:22:32,762 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/shj16108/hw5/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/shj16108/hw5/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/shj16108/hw5/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 | |
| 200315-19:22:35,602 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". | |
| 200315-19:22:36,667 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/shj16108/hw5/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". | |
| 200315-19:22:36,672 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/shj16108/.cache/templateflow/tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_res-02_desc-brain_mask.nii.gz -m Mattes[/home/shj16108/.cache/templateflow/tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_res-02_desc-fMRIPrep_boldref.nii.gz,/gpfs/scratchfs1/shj16108/hw5/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 | |
| 200315-19:22:38,849 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.init_aff". | |
| 200315-19:22:40,671 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/shj16108/hw5/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". | |
| 200315-19:22:40,679 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/shj16108/hw5/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/shj16108/.cache/templateflow/tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_res-02_desc-fMRIPrep_boldref.nii.gz, /gpfs/scratchfs1/shj16108/hw5/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 | |
| 200315-19:22:41,683 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". | |
| 200315-19:22:42,673 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/shj16108/hw5/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". | |
| 200315-19:22:42,678 nipype.workflow INFO: | |
| [Node] Running "map_brainmask" ("niworkflows.interfaces.fixes.FixHeaderApplyTransforms"), a CommandLine Interface with command: | |
| antsApplyTransforms --default-value 0 --float 1 --input /home/shj16108/.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/shj16108/hw5/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/shj16108/hw5/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 ] | |
| 200315-19:22:47,197 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". | |
| 200315-19:22:48,679 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/shj16108/hw5/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". | |
| 200315-19:22:48,683 nipype.workflow INFO: | |
| [Node] Running "pre_mask_dilate" ("nipype.interfaces.fsl.maths.DilateImage"), a CommandLine Interface with command: | |
| fslmaths -dt char /gpfs/scratchfs1/shj16108/hw5/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/shj16108/hw5/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 | |
| 200315-19:22:49,16 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". | |
| 200315-19:22:50,813 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/shj16108/hw5/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/bold_bold_trans_wf/bold_transform". | |
| 200315-19:22:50,947 nipype.workflow INFO: | |
| [Node] Running "bold_transform" ("niworkflows.interfaces.itk.MultiApplyTransforms") | |
| 200315-19:26:53,994 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". | |
| 200315-19:26:54,923 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/shj16108/hw5/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". | |
| 200315-19:26:54,928 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/shj16108/hw5/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/bold_bold_trans_wf/merge". | |
| 200315-19:26:55,21 nipype.workflow INFO: | |
| [Node] Running "merge" ("niworkflows.interfaces.nilearn.Merge") | |
| 200315-19:26:55,80 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/shj16108/hw5/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/shj16108/hw5/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 | |
| 200315-19:27:00,406 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". | |
| 200315-19:27:00,939 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/shj16108/hw5/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". | |
| 200315-19:27:00,942 nipype.workflow INFO: | |
| [Node] Running "skullstrip_first_pass" ("nipype.interfaces.fsl.preprocess.BET"), a CommandLine Interface with command: | |
| bet /gpfs/scratchfs1/shj16108/hw5/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/shj16108/hw5/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 | |
| 200315-19:27:02,458 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". | |
| 200315-19:27:02,935 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/shj16108/hw5/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". | |
| 200315-19:27:02,939 nipype.workflow INFO: | |
| [Node] Running "skullstrip_first_dilate" ("nipype.interfaces.fsl.maths.DilateImage"), a CommandLine Interface with command: | |
| fslmaths -dt char /gpfs/scratchfs1/shj16108/hw5/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/shj16108/hw5/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 | |
| 200315-19:27:04,896 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". | |
| 200315-19:27:06,943 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/shj16108/hw5/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". | |
| 200315-19:27:06,995 nipype.workflow INFO: | |
| [Node] Running "skullstrip_first_mask" ("nipype.interfaces.fsl.maths.ApplyMask"), a CommandLine Interface with command: | |
| fslmaths /gpfs/scratchfs1/shj16108/hw5/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/shj16108/hw5/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/shj16108/hw5/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 | |
| 200315-19:27:07,150 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". | |
| 200315-19:27:08,943 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/shj16108/hw5/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". | |
| 200315-19:27:08,947 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/shj16108/hw5/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 | |
| 200315-19:27:11,911 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". | |
| 200315-19:27:12,947 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/shj16108/hw5/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". | |
| 200315-19:27:12,950 nipype.workflow INFO: | |
| [Node] Running "fixhdr_unifize" ("niworkflows.interfaces.utils.CopyXForm") | |
| 200315-19:27:13,13 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". | |
| 200315-19:27:14,952 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/shj16108/hw5/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". | |
| 200315-19:27:14,956 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/shj16108/hw5/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 | |
| 200315-19:27:15,155 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". | |
| 200315-19:27:16,949 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/shj16108/hw5/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". | |
| 200315-19:27:16,953 nipype.workflow INFO: | |
| [Node] Running "fixhdr_skullstrip2" ("niworkflows.interfaces.utils.CopyXForm") | |
| 200315-19:27:16,981 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". | |
| 200315-19:27:18,949 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/shj16108/hw5/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". | |
| 200315-19:27:18,953 nipype.workflow INFO: | |
| [Node] Running "combine_masks" ("nipype.interfaces.fsl.maths.BinaryMaths"), a CommandLine Interface with command: | |
| fslmaths /gpfs/scratchfs1/shj16108/hw5/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/shj16108/hw5/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/shj16108/hw5/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 | |
| 200315-19:27:19,106 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". | |
| 200315-19:27:20,951 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/shj16108/hw5/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". | |
| 200315-19:27:20,955 nipype.workflow INFO: | |
| [Node] Running "apply_mask" ("nipype.interfaces.fsl.maths.ApplyMask"), a CommandLine Interface with command: | |
| fslmaths /gpfs/scratchfs1/shj16108/hw5/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/shj16108/hw5/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/shj16108/hw5/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 | |
| 200315-19:27:21,74 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". | |
| 200315-19:28:33,673 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". | |
| 200315-19:28:35,27 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/shj16108/hw5/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". | |
| 200315-19:28:35,31 nipype.workflow INFO: | |
| [Node] Running "validate" ("niworkflows.interfaces.images.ValidateImage") | |
| 200315-19:28:35,154 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". | |
| 200315-19:28:37,23 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/shj16108/hw5/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". | |
| 200315-19:28:37,26 nipype.workflow INFO: | |
| [Node] Running "gen_ref" ("niworkflows.interfaces.registration.EstimateReferenceImage") | |
| 200315-19:28:38,69 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". | |
| 200315-19:28:39,28 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/shj16108/hw5/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". | |
| 200315-19:28:39,70 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/shj16108/.cache/templateflow/tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_res-02_desc-brain_mask.nii.gz -m Mattes[/home/shj16108/.cache/templateflow/tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_res-02_desc-fMRIPrep_boldref.nii.gz,/gpfs/scratchfs1/shj16108/hw5/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 | |
| 200315-19:28:41,250 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". | |
| 200315-19:28:43,30 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/shj16108/hw5/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". | |
| 200315-19:28:43,36 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/shj16108/hw5/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/shj16108/.cache/templateflow/tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_res-02_desc-fMRIPrep_boldref.nii.gz, /gpfs/scratchfs1/shj16108/hw5/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 | |
| 200315-19:28:44,746 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". | |
| 200315-19:28:45,31 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/shj16108/hw5/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". | |
| 200315-19:28:45,36 nipype.workflow INFO: | |
| [Node] Running "map_brainmask" ("niworkflows.interfaces.fixes.FixHeaderApplyTransforms"), a CommandLine Interface with command: | |
| antsApplyTransforms --default-value 0 --float 1 --input /home/shj16108/.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/shj16108/hw5/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/shj16108/hw5/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 ] | |
| 200315-19:28:49,545 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". | |
| 200315-19:28:51,38 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/shj16108/hw5/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". | |
| 200315-19:28:51,42 nipype.workflow INFO: | |
| [Node] Running "pre_mask_dilate" ("nipype.interfaces.fsl.maths.DilateImage"), a CommandLine Interface with command: | |
| fslmaths -dt char /gpfs/scratchfs1/shj16108/hw5/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/shj16108/hw5/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 | |
| 200315-19:28:51,385 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". | |
| 200315-19:28:53,198 nipype.workflow INFO: | |
| [Node] Setting-up "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.brain_extraction_wf.init_aff" in "/gpfs/scratchfs1/shj16108/hw5/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/brain_extraction_wf/init_aff". | |
| 200315-19:28:53,245 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/shj16108/.cache/templateflow/tpl-OASIS30ANTs/tpl-OASIS30ANTs_res-01_desc-BrainCerebellumExtraction_mask.nii.gz -m Mattes[/gpfs/scratchfs1/shj16108/hw5/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/shj16108/hw5/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 | |
| 200315-19:28:54,563 nipype.workflow INFO: | |
| [Node] Finished "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.brain_extraction_wf.init_aff". | |
| 200315-19:28:55,41 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/shj16108/hw5/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". | |
| 200315-19:28:55,109 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/shj16108/hw5/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/shj16108/hw5/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 | |
| 200315-19:29:00,51 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". | |
| 200315-19:29:01,47 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/shj16108/hw5/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". | |
| 200315-19:29:01,105 nipype.workflow INFO: | |
| [Node] Running "skullstrip_first_pass" ("nipype.interfaces.fsl.preprocess.BET"), a CommandLine Interface with command: | |
| bet /gpfs/scratchfs1/shj16108/hw5/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/shj16108/hw5/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 | |
| 200315-19:29:02,483 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". | |
| 200315-19:29:03,48 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/shj16108/hw5/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". | |
| 200315-19:29:03,53 nipype.workflow INFO: | |
| [Node] Running "skullstrip_first_dilate" ("nipype.interfaces.fsl.maths.DilateImage"), a CommandLine Interface with command: | |
| fslmaths -dt char /gpfs/scratchfs1/shj16108/hw5/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/shj16108/hw5/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 | |
| 200315-19:29:05,38 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". | |
| 200315-19:29:07,49 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/shj16108/hw5/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". | |
| 200315-19:29:07,55 nipype.workflow INFO: | |
| [Node] Running "skullstrip_first_mask" ("nipype.interfaces.fsl.maths.ApplyMask"), a CommandLine Interface with command: | |
| fslmaths /gpfs/scratchfs1/shj16108/hw5/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/shj16108/hw5/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/shj16108/hw5/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 | |
| 200315-19:29:07,169 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". | |
| 200315-19:29:09,54 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/shj16108/hw5/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". | |
| 200315-19:29:09,92 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/shj16108/hw5/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 | |
| 200315-19:29:11,903 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". | |
| 200315-19:29:13,58 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/shj16108/hw5/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". | |
| 200315-19:29:13,93 nipype.workflow INFO: | |
| [Node] Running "fixhdr_unifize" ("niworkflows.interfaces.utils.CopyXForm") | |
| 200315-19:29:13,169 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". | |
| 200315-19:29:15,60 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/shj16108/hw5/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". | |
| 200315-19:29:15,66 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/shj16108/hw5/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 | |
| 200315-19:29:15,379 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". | |
| 200315-19:29:17,62 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/shj16108/hw5/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". | |
| 200315-19:29:17,68 nipype.workflow INFO: | |
| [Node] Running "fixhdr_skullstrip2" ("niworkflows.interfaces.utils.CopyXForm") | |
| 200315-19:29:17,99 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". | |
| 200315-19:29:19,64 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/shj16108/hw5/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". | |
| 200315-19:29:19,107 nipype.workflow INFO: | |
| [Node] Running "combine_masks" ("nipype.interfaces.fsl.maths.BinaryMaths"), a CommandLine Interface with command: | |
| fslmaths /gpfs/scratchfs1/shj16108/hw5/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/shj16108/hw5/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/shj16108/hw5/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 | |
| 200315-19:29:19,309 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". | |
| 200315-19:29:21,66 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/shj16108/hw5/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/bold_confounds_wf/dvars". | |
| 200315-19:29:21,66 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/shj16108/hw5/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". | |
| 200315-19:29:21,92 nipype.workflow INFO: | |
| [Node] Running "apply_mask" ("nipype.interfaces.fsl.maths.ApplyMask"), a CommandLine Interface with command: | |
| fslmaths /gpfs/scratchfs1/shj16108/hw5/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/shj16108/hw5/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/shj16108/hw5/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 | |
| 200315-19:29:21,97 nipype.workflow INFO: | |
| [Node] Running "dvars" ("nipype.algorithms.confounds.ComputeDVARS") | |
| 200315-19:29:21,298 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". | |
| 200315-19:29:58,240 nipype.workflow INFO: | |
| [Node] Finished "fmriprep_wf.single_subject_01_wf.func_preproc_ses_01_task_Stroop_run_01_wf.bold_confounds_wf.dvars". | |
| 200315-19:29:59,293 nipype.workflow INFO: | |
| [Node] Setting-up "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.brain_extraction_wf.norm" in "/gpfs/scratchfs1/shj16108/hw5/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/brain_extraction_wf/norm". | |
| 200315-19:29:59,341 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/shj16108/hw5/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/shj16108/.cache/templateflow/tpl-OASIS30ANTs/tpl-OASIS30ANTs_res-01_T1w.nii.gz, /gpfs/scratchfs1/shj16108/hw5/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/shj16108/.cache/templateflow/tpl-OASIS30ANTs/tpl-OASIS30ANTs_res-01_desc-BrainCerebellumExtraction_mask.nii.gz, NULL ] --transform Affine[ 0.1 ] --metric MI[ /home/shj16108/.cache/templateflow/tpl-OASIS30ANTs/tpl-OASIS30ANTs_res-01_T1w.nii.gz, /gpfs/scratchfs1/shj16108/hw5/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/shj16108/.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/shj16108/.cache/templateflow/tpl-OASIS30ANTs/tpl-OASIS30ANTs_res-01_T1w.nii.gz, /gpfs/scratchfs1/shj16108/hw5/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/shj16108/hw5/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/shj16108/hw5/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/shj16108/.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 | |
| 200315-19:43:03,336 nipype.workflow INFO: | |
| [Node] Finished "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.brain_extraction_wf.norm". | |
| 200315-19:43:03,892 nipype.workflow INFO: | |
| [Node] Setting-up "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.brain_extraction_wf.map_brainmask" in "/gpfs/scratchfs1/shj16108/hw5/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/brain_extraction_wf/map_brainmask". | |
| 200315-19:43:03,912 nipype.workflow INFO: | |
| [Node] Running "map_brainmask" ("niworkflows.interfaces.fixes.FixHeaderApplyTransforms"), a CommandLine Interface with command: | |
| antsApplyTransforms --default-value 0 --float 1 --input /home/shj16108/.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/shj16108/hw5/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/brain_extraction_wf/norm/anat_to_template0GenericAffine.mat, 1 ] --transform [ /gpfs/scratchfs1/shj16108/hw5/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/brain_extraction_wf/norm/anat_to_template1InverseWarp.nii.gz, 0 ] | |
| 200315-19:43:56,545 nipype.workflow INFO: | |
| [Node] Finished "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.brain_extraction_wf.map_brainmask". | |
| 200315-19:43:57,944 nipype.workflow INFO: | |
| [Node] Setting-up "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.brain_extraction_wf.thr_brainmask" in "/gpfs/scratchfs1/shj16108/hw5/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/brain_extraction_wf/thr_brainmask". | |
| 200315-19:43:57,951 nipype.workflow INFO: | |
| [Node] Running "thr_brainmask" ("niworkflows.interfaces.ants.ThresholdImage"), a CommandLine Interface with command: | |
| ThresholdImage 3 /gpfs/scratchfs1/shj16108/hw5/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 | |
| 200315-19:43:59,242 nipype.workflow INFO: | |
| [Node] Finished "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.brain_extraction_wf.thr_brainmask". | |
| 200315-19:43:59,946 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/shj16108/hw5/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/03_pad_mask". | |
| 200315-19:43:59,946 nipype.workflow INFO: | |
| [Node] Setting-up "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.brain_extraction_wf.dil_brainmask" in "/gpfs/scratchfs1/shj16108/hw5/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/brain_extraction_wf/dil_brainmask". | |
| 200315-19:43:59,951 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/shj16108/hw5/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 | |
| 200315-19:43:59,952 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/shj16108/hw5/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 | |
| 200315-19:44:01,442 nipype.workflow INFO: | |
| [Node] Finished "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.03_pad_mask". | |
| 200315-19:44:02,94 nipype.workflow INFO: | |
| [Node] Finished "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.brain_extraction_wf.dil_brainmask". | |
| 200315-19:44:03,954 nipype.workflow INFO: | |
| [Node] Setting-up "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.brain_extraction_wf.get_brainmask" in "/gpfs/scratchfs1/shj16108/hw5/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/brain_extraction_wf/get_brainmask". | |
| 200315-19:44:03,959 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/shj16108/hw5/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 | |
| 200315-19:44:05,824 nipype.workflow INFO: | |
| [Node] Finished "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.brain_extraction_wf.get_brainmask". | |
| 200315-19:44:05,952 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/shj16108/hw5/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/01_atropos". | |
| 200315-19:44:05,958 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/shj16108/hw5/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/shj16108/hw5/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 | |
| 200315-19:45:35,689 nipype.workflow INFO: | |
| [Node] Finished "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.01_atropos". | |
| 200315-19:45:36,47 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/shj16108/hw5/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/02_pad_segm". | |
| 200315-19:45:36,58 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/shj16108/hw5/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 | |
| 200315-19:45:37,917 nipype.workflow INFO: | |
| [Node] Finished "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.02_pad_segm". | |
| 200315-19:45:38,49 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/shj16108/hw5/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/04_sel_labels". | |
| 200315-19:45:38,56 nipype.workflow INFO: | |
| [Node] Running "04_sel_labels" ("nipype.interfaces.utility.wrappers.Function") | |
| 200315-19:45:38,497 nipype.workflow INFO: | |
| [Node] Finished "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.04_sel_labels". | |
| 200315-19:45:40,52 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/shj16108/hw5/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/27_depad_csf". | |
| 200315-19:45:40,53 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/shj16108/hw5/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/10_me_csf". | |
| 200315-19:45:40,53 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/shj16108/hw5/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/06_get_gm". | |
| 200315-19:45:40,53 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/shj16108/hw5/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/05_get_wm". | |
| 200315-19:45:40,57 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/shj16108/hw5/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 | |
| 200315-19:45:40,58 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/shj16108/hw5/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 | |
| 200315-19:45:40,59 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/shj16108/hw5/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 | |
| 200315-19:45:40,59 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/shj16108/hw5/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 | |
| 200315-19:45:41,377 nipype.workflow INFO: | |
| [Node] Finished "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.27_depad_csf". | |
| 200315-19:45:42,415 nipype.workflow INFO: | |
| [Node] Finished "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.05_get_wm". | |
| 200315-19:45:42,482 nipype.workflow INFO: | |
| [Node] Finished "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.06_get_gm". | |
| 200315-19:45:44,58 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/shj16108/hw5/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/07_fill_gm". | |
| 200315-19:45:44,58 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/shj16108/hw5/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/09_relabel_wm". | |
| 200315-19:45:44,62 nipype.workflow INFO: | |
| [Node] Running "09_relabel_wm" ("nipype.interfaces.ants.utils.MultiplyImages"), a CommandLine Interface with command: | |
| MultiplyImages 3 /gpfs/scratchfs1/shj16108/hw5/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 | |
| 200315-19:45:44,62 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/shj16108/hw5/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 | |
| 200315-19:45:45,335 nipype.workflow INFO: | |
| [Node] Finished "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.09_relabel_wm". | |
| 200315-19:45:46,64 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/shj16108/hw5/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/26_depad_wm". | |
| 200315-19:45:46,80 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/shj16108/hw5/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 | |
| 200315-19:45:46,550 nipype.workflow INFO: | |
| [Node] Finished "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.10_me_csf". | |
| 200315-19:45:47,634 nipype.workflow INFO: | |
| [Node] Finished "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.26_depad_wm". | |
| 200315-19:45:56,369 nipype.workflow INFO: | |
| [Node] Finished "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.07_fill_gm". | |
| 200315-19:45:58,70 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/shj16108/hw5/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/08_mult_gm". | |
| 200315-19:45:58,74 nipype.workflow INFO: | |
| [Node] Running "08_mult_gm" ("nipype.interfaces.ants.utils.MultiplyImages"), a CommandLine Interface with command: | |
| MultiplyImages 3 /gpfs/scratchfs1/shj16108/hw5/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/shj16108/hw5/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 | |
| 200315-19:45:59,444 nipype.workflow INFO: | |
| [Node] Finished "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.08_mult_gm". | |
| 200315-19:46:00,72 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/shj16108/hw5/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/11_add_gm". | |
| 200315-19:46:00,77 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/shj16108/hw5/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/shj16108/hw5/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 | |
| 200315-19:46:05,629 nipype.workflow INFO: | |
| [Node] Finished "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.11_add_gm". | |
| 200315-19:46:06,78 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/shj16108/hw5/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/12_relabel_gm". | |
| 200315-19:46:06,82 nipype.workflow INFO: | |
| [Node] Running "12_relabel_gm" ("nipype.interfaces.ants.utils.MultiplyImages"), a CommandLine Interface with command: | |
| MultiplyImages 3 /gpfs/scratchfs1/shj16108/hw5/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 | |
| 200315-19:46:07,181 nipype.workflow INFO: | |
| [Node] Finished "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.12_relabel_gm". | |
| 200315-19:46:08,80 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/shj16108/hw5/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/25_depad_gm". | |
| 200315-19:46:08,80 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/shj16108/hw5/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/13_add_gm_wm". | |
| 200315-19:46:08,84 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/shj16108/hw5/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 | |
| 200315-19:46:08,85 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/shj16108/hw5/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/shj16108/hw5/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/12_relabel_gm/12_relabel_gm.nii.gz | |
| 200315-19:46:09,735 nipype.workflow INFO: | |
| [Node] Finished "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.25_depad_gm". | |
| 200315-19:46:10,83 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/shj16108/hw5/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/merge_tpms". | |
| 200315-19:46:10,89 nipype.workflow INFO: | |
| [Node] Running "merge_tpms" ("nipype.interfaces.utility.base.Merge") | |
| 200315-19:46:10,92 nipype.workflow INFO: | |
| [Node] Finished "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.merge_tpms". | |
| 200315-19:46:13,925 nipype.workflow INFO: | |
| [Node] Finished "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.13_add_gm_wm". | |
| 200315-19:46:14,86 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/shj16108/hw5/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/24_depad_segm". | |
| 200315-19:46:14,86 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/shj16108/hw5/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/14_sel_labels2". | |
| 200315-19:46:14,92 nipype.workflow INFO: | |
| [Node] Running "14_sel_labels2" ("nipype.interfaces.utility.wrappers.Function") | |
| 200315-19:46:14,95 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/shj16108/hw5/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 | |
| 200315-19:46:14,392 nipype.workflow INFO: | |
| [Node] Finished "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.14_sel_labels2". | |
| 200315-19:46:15,621 nipype.workflow INFO: | |
| [Node] Finished "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.24_depad_segm". | |
| 200315-19:46:16,89 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/shj16108/hw5/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/15_add_7". | |
| 200315-19:46:16,93 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/shj16108/hw5/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/shj16108/hw5/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 | |
| 200315-19:46:21,287 nipype.workflow INFO: | |
| [Node] Finished "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.15_add_7". | |
| 200315-19:46:22,94 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/shj16108/hw5/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/16_me_7". | |
| 200315-19:46:22,99 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/shj16108/hw5/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 | |
| 200315-19:46:26,382 nipype.workflow INFO: | |
| [Node] Finished "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.16_me_7". | |
| 200315-19:46:28,100 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/shj16108/hw5/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/17_comp_7". | |
| 200315-19:46:28,108 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/shj16108/hw5/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 | |
| 200315-19:46:30,387 nipype.workflow INFO: | |
| [Node] Finished "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.17_comp_7". | |
| 200315-19:46:32,104 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/shj16108/hw5/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/18_md_7". | |
| 200315-19:46:32,108 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/shj16108/hw5/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 | |
| 200315-19:46:34,769 nipype.workflow INFO: | |
| [Node] Finished "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.18_md_7". | |
| 200315-19:46:36,108 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/shj16108/hw5/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/19_fill_7". | |
| 200315-19:46:36,116 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/shj16108/hw5/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 | |
| 200315-19:46:47,4 nipype.workflow INFO: | |
| [Node] Finished "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.19_fill_7". | |
| 200315-19:46:48,121 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/shj16108/hw5/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/20_add_7_2". | |
| 200315-19:46:48,126 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/shj16108/hw5/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/shj16108/hw5/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 | |
| 200315-19:46:53,443 nipype.workflow INFO: | |
| [Node] Finished "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.20_add_7_2". | |
| 200315-19:46:54,127 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/shj16108/hw5/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/21_md_7_2". | |
| 200315-19:46:54,134 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/shj16108/hw5/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 | |
| 200315-19:46:56,693 nipype.workflow INFO: | |
| [Node] Finished "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.21_md_7_2". | |
| 200315-19:46:58,131 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/shj16108/hw5/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/22_me_7_2". | |
| 200315-19:46:58,135 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/shj16108/hw5/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 | |
| 200315-19:47:02,419 nipype.workflow INFO: | |
| [Node] Finished "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.22_me_7_2". | |
| 200315-19:47:04,137 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/shj16108/hw5/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/23_depad_mask". | |
| 200315-19:47:04,141 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/shj16108/hw5/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 | |
| 200315-19:47:05,422 nipype.workflow INFO: | |
| [Node] Finished "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.23_depad_mask". | |
| 200315-19:47:06,138 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/shj16108/hw5/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/msk_conform". | |
| 200315-19:47:06,143 nipype.workflow INFO: | |
| [Node] Running "msk_conform" ("nipype.interfaces.utility.wrappers.Function") | |
| 200315-19:47:06,358 nipype.workflow INFO: | |
| [Node] Finished "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.brain_extraction_wf.atropos_wf.msk_conform". | |
| 200315-19:47:09,749 nipype.workflow INFO: | |
| [Node] Setting-up "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.surface_recon_wf.autorecon1" in "/gpfs/scratchfs1/shj16108/hw5/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/surface_recon_wf/autorecon1". | |
| 200315-19:47:09,782 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 8 -subjid sub-01 -sd /out/freesurfer -expert /gpfs/scratchfs1/shj16108/hw5/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/surface_recon_wf/autorecon1/expert.opts | |
| 200315-19:59:46,823 nipype.workflow INFO: | |
| [Node] Finished "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.surface_recon_wf.autorecon1". | |
| 200315-19:59:47,40 nipype.workflow INFO: | |
| [Node] Setting-up "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.surface_recon_wf.fsnative2t1w_xfm" in "/gpfs/scratchfs1/shj16108/hw5/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/surface_recon_wf/fsnative2t1w_xfm". | |
| 200315-19:59:47,52 nipype.workflow INFO: | |
| [Node] Running "fsnative2t1w_xfm" ("niworkflows.interfaces.freesurfer.PatchedRobustRegister"), a CommandLine Interface with command: | |
| mri_robust_register --satit --iscale --lta /gpfs/scratchfs1/shj16108/hw5/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 | |
| 200315-20:01:11,521 nipype.workflow INFO: | |
| [Node] Finished "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.surface_recon_wf.fsnative2t1w_xfm". | |
| 200315-20:01:13,39 nipype.workflow INFO: | |
| [Node] Setting-up "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.brain_extraction_wf.inu_n4_final" in "/gpfs/scratchfs1/shj16108/hw5/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/brain_extraction_wf/inu_n4_final". | |
| 200315-20:01:13,44 nipype.workflow INFO: | |
| [Node] Setting-up "_inu_n4_final0" in "/gpfs/scratchfs1/shj16108/hw5/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/brain_extraction_wf/inu_n4_final/mapflow/_inu_n4_final0". | |
| 200315-20:01:13,48 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/shj16108/hw5/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 | |
| 200315-20:02:06,188 nipype.workflow INFO: | |
| [Node] Finished "_inu_n4_final0". | |
| 200315-20:02:06,191 nipype.workflow INFO: | |
| [Node] Finished "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.brain_extraction_wf.inu_n4_final". | |
| 200315-20:02:07,94 nipype.workflow INFO: | |
| [Node] Setting-up "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.brain_extraction_wf.apply_mask" in "/gpfs/scratchfs1/shj16108/hw5/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/brain_extraction_wf/apply_mask". | |
| 200315-20:02:07,95 nipype.workflow INFO: | |
| [Node] Setting-up "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.anat_derivatives_wf.lta2itk_inv" in "/gpfs/scratchfs1/shj16108/hw5/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/anat_derivatives_wf/lta2itk_inv". | |
| 200315-20:02:07,95 nipype.workflow INFO: | |
| [Node] Setting-up "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.surface_recon_wf.t1w2fsnative_xfm" in "/gpfs/scratchfs1/shj16108/hw5/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/surface_recon_wf/t1w2fsnative_xfm". | |
| 200315-20:02:07,98 nipype.workflow INFO: | |
| [Node] Setting-up "_apply_mask0" in "/gpfs/scratchfs1/shj16108/hw5/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/brain_extraction_wf/apply_mask/mapflow/_apply_mask0". | |
| 200315-20:02:07,99 nipype.workflow INFO: | |
| [Node] Running "t1w2fsnative_xfm" ("niworkflows.interfaces.freesurfer.PatchedLTAConvert"), a CommandLine Interface with command: | |
| lta_convert --inlta /gpfs/scratchfs1/shj16108/hw5/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/surface_recon_wf/fsnative2t1w_xfm/T1_robustreg.lta --invert --outlta /gpfs/scratchfs1/shj16108/hw5/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/surface_recon_wf/t1w2fsnative_xfm/out.lta | |
| 200315-20:02:07,99 nipype.workflow INFO: | |
| [Node] Running "lta2itk_inv" ("niworkflows.interfaces.freesurfer.PatchedLTAConvert"), a CommandLine Interface with command: | |
| lta_convert --inlta /gpfs/scratchfs1/shj16108/hw5/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/surface_recon_wf/fsnative2t1w_xfm/T1_robustreg.lta --outitk /gpfs/scratchfs1/shj16108/hw5/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/anat_derivatives_wf/lta2itk_inv/out.txt | |
| 200315-20:02:07,104 nipype.workflow INFO: | |
| [Node] Running "_apply_mask0" ("nipype.interfaces.fsl.maths.ApplyMask"), a CommandLine Interface with command: | |
| fslmaths /gpfs/scratchfs1/shj16108/hw5/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/shj16108/hw5/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/shj16108/hw5/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 | |
| 200315-20:02:07,185 nipype.workflow INFO: | |
| [Node] Finished "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.surface_recon_wf.t1w2fsnative_xfm". | |
| 200315-20:02:07,185 nipype.workflow INFO: | |
| [Node] Finished "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.anat_derivatives_wf.lta2itk_inv". | |
| 200315-20:02:09,179 nipype.workflow INFO: | |
| [Node] Finished "_apply_mask0". | |
| 200315-20:02:09,180 nipype.workflow INFO: | |
| [Node] Finished "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.brain_extraction_wf.apply_mask". | |
| 200315-20:02:09,261 nipype.workflow INFO: | |
| [Node] Setting-up "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.anat_derivatives_wf.lta2itk_fwd" in "/gpfs/scratchfs1/shj16108/hw5/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/anat_derivatives_wf/lta2itk_fwd". | |
| 200315-20:02:09,277 nipype.workflow INFO: | |
| [Node] Running "lta2itk_fwd" ("niworkflows.interfaces.freesurfer.PatchedLTAConvert"), a CommandLine Interface with command: | |
| lta_convert --inlta /gpfs/scratchfs1/shj16108/hw5/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/surface_recon_wf/t1w2fsnative_xfm/out.lta --outitk /gpfs/scratchfs1/shj16108/hw5/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/anat_derivatives_wf/lta2itk_fwd/out.txt | |
| 200315-20:02:09,346 nipype.workflow INFO: | |
| [Node] Finished "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.anat_derivatives_wf.lta2itk_fwd". | |
| 200315-20:02:26,302 nipype.workflow INFO: | |
| [Node] Setting-up "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.anat_norm_wf.trunc_mov" in "/gpfs/scratchfs1/shj16108/hw5/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/anat_norm_wf/trunc_mov". | |
| 200315-20:02:26,303 nipype.workflow INFO: | |
| [Node] Setting-up "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.surface_recon_wf.skull_strip_extern" in "/gpfs/scratchfs1/shj16108/hw5/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/surface_recon_wf/skull_strip_extern". | |
| 200315-20:02:26,308 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/shj16108/hw5/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 | |
| 200315-20:02:26,309 nipype.workflow INFO: | |
| [Node] Running "skull_strip_extern" ("niworkflows.interfaces.freesurfer.FSInjectBrainExtracted") | |
| 200315-20:02:28,436 nipype.workflow INFO: | |
| [Node] Finished "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.surface_recon_wf.skull_strip_extern". | |
| 200315-20:02:35,194 nipype.workflow INFO: | |
| [Node] Finished "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.anat_norm_wf.trunc_mov". | |
| 200315-20:02:36,405 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/shj16108/hw5/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/surface_recon_wf/autorecon_resume_wf/autorecon2_vol". | |
| 200315-20:02:36,410 nipype.interface INFO: | |
| resume recon-all : recon-all -autorecon2-volonly -openmp 8 -subjid sub-01 -sd /out/freesurfer | |
| 200315-20:02:36,410 nipype.workflow INFO: | |
| [Node] Running "autorecon2_vol" ("smriprep.interfaces.freesurfer.ReconAll"), a CommandLine Interface with command: | |
| recon-all -autorecon2-volonly -openmp 8 -subjid sub-01 -sd /out/freesurfer | |
| 200315-20:02:36,411 nipype.interface INFO: | |
| resume recon-all : recon-all -autorecon2-volonly -openmp 8 -subjid sub-01 -sd /out/freesurfer | |
| 200315-22:54:06,663 nipype.workflow INFO: | |
| [Node] Finished "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.surface_recon_wf.autorecon_resume_wf.autorecon2_vol". | |
| 200315-22:54:09,495 nipype.workflow INFO: | |
| [Node] Setting-up "_autorecon_surfs0" in "/gpfs/scratchfs1/shj16108/hw5/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/surface_recon_wf/autorecon_resume_wf/autorecon_surfs/mapflow/_autorecon_surfs0". | |
| 200315-22:54:09,500 nipype.interface INFO: | |
| resume recon-all : recon-all -autorecon-hemi lh -noparcstats -noparcstats2 -noparcstats3 -nohyporelabel -nobalabels -openmp 8 -subjid sub-01 -sd /out/freesurfer | |
| 200315-22:54:09,500 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 8 -subjid sub-01 -sd /out/freesurfer | |
| 200315-22:54:09,501 nipype.interface INFO: | |
| resume recon-all : recon-all -autorecon-hemi lh -noparcstats -noparcstats2 -noparcstats3 -nohyporelabel -nobalabels -openmp 8 -subjid sub-01 -sd /out/freesurfer | |
| 200316-00:31:48,404 nipype.workflow INFO: | |
| [Node] Finished "_autorecon_surfs0". | |
| 200316-00:31:49,775 nipype.workflow INFO: | |
| [Node] Setting-up "_autorecon_surfs1" in "/gpfs/scratchfs1/shj16108/hw5/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/surface_recon_wf/autorecon_resume_wf/autorecon_surfs/mapflow/_autorecon_surfs1". | |
| 200316-00:31:49,779 nipype.interface INFO: | |
| resume recon-all : recon-all -autorecon-hemi rh -noparcstats -noparcstats2 -noparcstats3 -nohyporelabel -nobalabels -openmp 8 -subjid sub-01 -sd /out/freesurfer | |
| 200316-00:31:49,779 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 8 -subjid sub-01 -sd /out/freesurfer | |
| 200316-00:31:49,780 nipype.interface INFO: | |
| resume recon-all : recon-all -autorecon-hemi rh -noparcstats -noparcstats2 -noparcstats3 -nohyporelabel -nobalabels -openmp 8 -subjid sub-01 -sd /out/freesurfer | |
| 200316-02:20:14,104 nipype.workflow INFO: | |
| [Node] Finished "_autorecon_surfs1". | |
| 200316-02:20:14,582 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/shj16108/hw5/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/surface_recon_wf/autorecon_resume_wf/autorecon_surfs". | |
| 200316-02:20:14,589 nipype.workflow INFO: | |
| [Node] Setting-up "_autorecon_surfs0" in "/gpfs/scratchfs1/shj16108/hw5/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/surface_recon_wf/autorecon_resume_wf/autorecon_surfs/mapflow/_autorecon_surfs0". | |
| 200316-02:20:14,595 nipype.interface INFO: | |
| recon-all complete : Not running | |
| 200316-02:20:14,596 nipype.workflow INFO: | |
| [Node] Running "_autorecon_surfs0" ("smriprep.interfaces.freesurfer.ReconAll"), a CommandLine Interface with command: | |
| echo recon-all: nothing to do | |
| 200316-02:20:14,597 nipype.interface INFO: | |
| recon-all complete : Not running | |
| 200316-02:20:14,678 nipype.workflow INFO: | |
| [Node] Finished "_autorecon_surfs0". | |
| 200316-02:20:14,681 nipype.workflow INFO: | |
| [Node] Setting-up "_autorecon_surfs1" in "/gpfs/scratchfs1/shj16108/hw5/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/surface_recon_wf/autorecon_resume_wf/autorecon_surfs/mapflow/_autorecon_surfs1". | |
| 200316-02:20:14,685 nipype.interface INFO: | |
| recon-all complete : Not running | |
| 200316-02:20:14,686 nipype.workflow INFO: | |
| [Node] Running "_autorecon_surfs1" ("smriprep.interfaces.freesurfer.ReconAll"), a CommandLine Interface with command: | |
| echo recon-all: nothing to do | |
| 200316-02:20:14,687 nipype.interface INFO: | |
| recon-all complete : Not running | |
| 200316-02:20:14,753 nipype.workflow INFO: | |
| [Node] Finished "_autorecon_surfs1". | |
| 200316-02:20:14,758 nipype.workflow INFO: | |
| [Node] Finished "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.surface_recon_wf.autorecon_resume_wf.autorecon_surfs". | |
| 200316-02:20:16,446 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/shj16108/hw5/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/surface_recon_wf/autorecon_resume_wf/cortribbon". | |
| 200316-02:20:16,451 nipype.interface INFO: | |
| resume recon-all : recon-all -parallel -subjid sub-01 -sd /out/freesurfer -T2pial -cortribbon | |
| 200316-02:20:16,451 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 | |
| 200316-02:20:16,452 nipype.interface INFO: | |
| resume recon-all : recon-all -parallel -subjid sub-01 -sd /out/freesurfer -T2pial -cortribbon | |
| 200316-03:26:02,909 nipype.workflow INFO: | |
| [Node] Finished "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.surface_recon_wf.autorecon_resume_wf.cortribbon". | |
| 200316-03:26:06,608 nipype.workflow INFO: | |
| [Node] Setting-up "_parcstats0" in "/gpfs/scratchfs1/shj16108/hw5/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/surface_recon_wf/autorecon_resume_wf/parcstats/mapflow/_parcstats0". | |
| 200316-03:26:06,614 nipype.interface INFO: | |
| resume recon-all : recon-all -autorecon-hemi lh -nohyporelabel -openmp 8 -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 | |
| 200316-03:26:06,615 nipype.workflow INFO: | |
| [Node] Running "_parcstats0" ("smriprep.interfaces.freesurfer.ReconAll"), a CommandLine Interface with command: | |
| recon-all -autorecon-hemi lh -nohyporelabel -openmp 8 -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 | |
| 200316-03:26:06,616 nipype.interface INFO: | |
| resume recon-all : recon-all -autorecon-hemi lh -nohyporelabel -openmp 8 -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 | |
| 200316-03:33:47,528 nipype.workflow INFO: | |
| [Node] Finished "_parcstats0". | |
| 200316-03:33:48,948 nipype.workflow INFO: | |
| [Node] Setting-up "_parcstats1" in "/gpfs/scratchfs1/shj16108/hw5/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/surface_recon_wf/autorecon_resume_wf/parcstats/mapflow/_parcstats1". | |
| 200316-03:33:48,964 nipype.interface INFO: | |
| resume recon-all : recon-all -autorecon-hemi rh -nohyporelabel -openmp 8 -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 | |
| 200316-03:33:48,964 nipype.workflow INFO: | |
| [Node] Running "_parcstats1" ("smriprep.interfaces.freesurfer.ReconAll"), a CommandLine Interface with command: | |
| recon-all -autorecon-hemi rh -nohyporelabel -openmp 8 -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 | |
| 200316-03:33:48,966 nipype.interface INFO: | |
| resume recon-all : recon-all -autorecon-hemi rh -nohyporelabel -openmp 8 -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 | |
| 200316-03:41:37,619 nipype.workflow INFO: | |
| [Node] Finished "_parcstats1". | |
| 200316-03:41:39,574 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/shj16108/hw5/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/surface_recon_wf/autorecon_resume_wf/parcstats". | |
| 200316-03:41:39,583 nipype.workflow INFO: | |
| [Node] Setting-up "_parcstats0" in "/gpfs/scratchfs1/shj16108/hw5/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/surface_recon_wf/autorecon_resume_wf/parcstats/mapflow/_parcstats0". | |
| 200316-03:41:39,594 nipype.interface INFO: | |
| recon-all complete : Not running | |
| 200316-03:41:39,599 nipype.workflow INFO: | |
| [Node] Running "_parcstats0" ("smriprep.interfaces.freesurfer.ReconAll"), a CommandLine Interface with command: | |
| echo recon-all: nothing to do | |
| 200316-03:41:39,601 nipype.interface INFO: | |
| recon-all complete : Not running | |
| 200316-03:41:39,684 nipype.workflow INFO: | |
| [Node] Finished "_parcstats0". | |
| 200316-03:41:39,686 nipype.workflow INFO: | |
| [Node] Setting-up "_parcstats1" in "/gpfs/scratchfs1/shj16108/hw5/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/surface_recon_wf/autorecon_resume_wf/parcstats/mapflow/_parcstats1". | |
| 200316-03:41:39,694 nipype.interface INFO: | |
| recon-all complete : Not running | |
| 200316-03:41:39,695 nipype.workflow INFO: | |
| [Node] Running "_parcstats1" ("smriprep.interfaces.freesurfer.ReconAll"), a CommandLine Interface with command: | |
| echo recon-all: nothing to do | |
| 200316-03:41:39,697 nipype.interface INFO: | |
| recon-all complete : Not running | |
| 200316-03:41:39,766 nipype.workflow INFO: | |
| [Node] Finished "_parcstats1". | |
| 200316-03:41:39,770 nipype.workflow INFO: | |
| [Node] Finished "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.surface_recon_wf.autorecon_resume_wf.parcstats". | |
| 200316-03:41:41,437 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/shj16108/hw5/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/surface_recon_wf/autorecon_resume_wf/autorecon3". | |
| 200316-03:41:41,442 nipype.interface INFO: | |
| resume recon-all : recon-all -autorecon3 -openmp 8 -subjid sub-01 -sd /out/freesurfer -nosphere -nosurfreg -nojacobian_white -noavgcurv -nocortparc -nopial -noparcstats -nocortparc2 -noparcstats2 -nocortparc3 -noparcstats3 -nopctsurfcon -nocortribbon -nobalabels | |
| 200316-03:41:41,442 nipype.workflow INFO: | |
| [Node] Running "autorecon3" ("smriprep.interfaces.freesurfer.ReconAll"), a CommandLine Interface with command: | |
| recon-all -autorecon3 -openmp 8 -subjid sub-01 -sd /out/freesurfer -nosphere -nosurfreg -nojacobian_white -noavgcurv -nocortparc -nopial -noparcstats -nocortparc2 -noparcstats2 -nocortparc3 -noparcstats3 -nopctsurfcon -nocortribbon -nobalabels | |
| 200316-03:41:41,443 nipype.interface INFO: | |
| resume recon-all : recon-all -autorecon3 -openmp 8 -subjid sub-01 -sd /out/freesurfer -nosphere -nosurfreg -nojacobian_white -noavgcurv -nocortparc -nopial -noparcstats -nocortparc2 -noparcstats2 -nocortparc3 -noparcstats3 -nopctsurfcon -nocortribbon -nobalabels | |
| 200316-04:11:16,367 nipype.workflow INFO: | |
| [Node] Finished "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.surface_recon_wf.autorecon_resume_wf.autorecon3". | |
| 200316-04:11:17,341 nipype.workflow INFO: | |
| [Node] Setting-up "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.anat_reports_wf.recon_report" in "/gpfs/scratchfs1/shj16108/hw5/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/anat_reports_wf/recon_report". | |
| 200316-04:11:17,344 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/shj16108/hw5/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/bold_surf_wf/targets". | |
| 200316-04:11:17,344 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/shj16108/hw5/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/surface_recon_wf/segs_to_native_aparc_aseg/fs_datasource". | |
| 200316-04:11:17,344 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/shj16108/hw5/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/surface_recon_wf/segs_to_native_aseg/fs_datasource". | |
| 200316-04:11:17,345 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/shj16108/hw5/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/get_surfaces". | |
| 200316-04:11:17,349 nipype.workflow INFO: | |
| [Node] Running "recon_report" ("smriprep.interfaces.reports.FSSurfaceReport") | |
| 200316-04:11:17,351 nipype.workflow INFO: | |
| [Node] Setting-up "_targets0" in "/gpfs/scratchfs1/shj16108/hw5/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/bold_surf_wf/targets/mapflow/_targets0". | |
| 200316-04:11:17,353 nipype.workflow INFO: | |
| [Node] Running "fs_datasource" ("nipype.interfaces.io.FreeSurferSource") | |
| 200316-04:11:17,353 nipype.workflow INFO: | |
| [Node] Running "fs_datasource" ("nipype.interfaces.io.FreeSurferSource") | |
| 200316-04:11:17,354 nipype.workflow INFO: | |
| [Node] Running "_targets0" ("nipype.interfaces.utility.wrappers.Function") | |
| 200316-04:11:17,355 nipype.workflow INFO: | |
| [Node] Running "get_surfaces" ("nipype.interfaces.io.FreeSurferSource") | |
| 200316-04:11:17,360 nipype.workflow INFO: | |
| [Node] Finished "_targets0". | |
| 200316-04:11:17,364 nipype.workflow INFO: | |
| [Node] Finished "fmriprep_wf.single_subject_01_wf.func_preproc_ses_01_task_Stroop_run_01_wf.bold_surf_wf.targets". | |
| 200316-04:11:17,366 nipype.workflow INFO: | |
| [Node] Finished "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.surface_recon_wf.segs_to_native_aseg.fs_datasource". | |
| 200316-04:11:17,369 nipype.workflow INFO: | |
| [Node] Finished "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.surface_recon_wf.segs_to_native_aparc_aseg.fs_datasource". | |
| 200316-04:11:17,370 nipype.workflow INFO: | |
| [Node] Finished "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.surface_recon_wf.gifti_surface_wf.get_surfaces". | |
| 200316-04:11:19,357 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/shj16108/hw5/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/surface_recon_wf/segs_to_native_aparc_aseg/tonative". | |
| 200316-04:11:19,357 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/shj16108/hw5/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/surface_recon_wf/segs_to_native_aseg/tonative". | |
| 200316-04:11:19,363 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/shj16108/hw5/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/shj16108/hw5/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/surface_recon_wf/segs_to_native_aseg/tonative/aseg_vol.nii.gz | |
| 200316-04:11:19,363 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/shj16108/hw5/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/shj16108/hw5/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 | |
| 200316-04:11:21,359 nipype.workflow INFO: | |
| [Node] Setting-up "_midthickness0" in "/gpfs/scratchfs1/shj16108/hw5/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/midthickness/mapflow/_midthickness0". | |
| 200316-04:11:21,360 nipype.workflow INFO: | |
| [Node] Setting-up "_midthickness1" in "/gpfs/scratchfs1/shj16108/hw5/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/midthickness/mapflow/_midthickness1". | |
| 200316-04:11:21,364 nipype.workflow INFO: | |
| [Node] Running "_midthickness0" ("niworkflows.interfaces.freesurfer.MakeMidthickness"), a CommandLine Interface with command: | |
| mris_expand -pial /gpfs/scratchfs1/shj16108/hw5/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/shj16108/hw5/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/midthickness/mapflow/_midthickness0/rh.thickness /gpfs/scratchfs1/shj16108/hw5/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 | |
| 200316-04:11:21,365 nipype.workflow INFO: | |
| [Node] Running "_midthickness1" ("niworkflows.interfaces.freesurfer.MakeMidthickness"), a CommandLine Interface with command: | |
| mris_expand -pial /gpfs/scratchfs1/shj16108/hw5/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/shj16108/hw5/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/midthickness/mapflow/_midthickness1/lh.thickness /gpfs/scratchfs1/shj16108/hw5/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 | |
| 200316-04:11:28,985 nipype.workflow INFO: | |
| [Node] Finished "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.anat_reports_wf.recon_report". | |
| 200316-04:11:30,636 nipype.workflow INFO: | |
| [Node] Finished "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.surface_recon_wf.segs_to_native_aparc_aseg.tonative". | |
| 200316-04:11:30,660 nipype.workflow INFO: | |
| [Node] Finished "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.surface_recon_wf.segs_to_native_aseg.tonative". | |
| 200316-04:11:31,359 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/shj16108/hw5/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/surface_recon_wf/segs_to_native_aparc_aseg/tonii". | |
| 200316-04:11:31,359 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/shj16108/hw5/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/surface_recon_wf/segs_to_native_aseg/tonii". | |
| 200316-04:11:31,365 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/shj16108/hw5/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/shj16108/hw5/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/shj16108/hw5/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 | |
| 200316-04:11:31,365 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/shj16108/hw5/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/shj16108/hw5/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/shj16108/hw5/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/surface_recon_wf/segs_to_native_aseg/tonii/aseg_vol_out.nii.gz | |
| 200316-04:11:32,949 nipype.workflow INFO: | |
| [Node] Finished "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.surface_recon_wf.segs_to_native_aseg.tonii". | |
| 200316-04:11:32,950 nipype.workflow INFO: | |
| [Node] Finished "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.surface_recon_wf.segs_to_native_aparc_aseg.tonii". | |
| 200316-04:11:39,224 nipype.workflow INFO: | |
| [Node] Setting-up "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.surface_recon_wf.refine" in "/gpfs/scratchfs1/shj16108/hw5/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/surface_recon_wf/refine". | |
| 200316-04:11:39,229 nipype.workflow INFO: | |
| [Node] Running "refine" ("niworkflows.interfaces.freesurfer.RefineBrainMask") | |
| 200316-04:12:42,562 nipype.workflow INFO: | |
| [Node] Finished "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.surface_recon_wf.refine". | |
| 200316-04:12:44,203 nipype.workflow INFO: | |
| [Node] Setting-up "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.applyrefined" in "/gpfs/scratchfs1/shj16108/hw5/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/applyrefined". | |
| 200316-04:12:44,208 nipype.workflow INFO: | |
| [Node] Running "applyrefined" ("nipype.interfaces.fsl.maths.ApplyMask"), a CommandLine Interface with command: | |
| fslmaths /gpfs/scratchfs1/shj16108/hw5/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/shj16108/hw5/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/shj16108/hw5/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/applyrefined/sub-01_ses-01_T1w_corrected_xform_masked.nii.gz | |
| 200316-04:12:46,373 nipype.workflow INFO: | |
| [Node] Finished "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.applyrefined". | |
| 200316-04:12:47,395 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/shj16108/hw5/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/bold_t1_trans_wf/gen_ref". | |
| 200316-04:12:47,395 nipype.workflow INFO: | |
| [Node] Setting-up "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.t1w_dseg" in "/gpfs/scratchfs1/shj16108/hw5/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/t1w_dseg". | |
| 200316-04:12:47,399 nipype.workflow INFO: | |
| [Node] Running "gen_ref" ("niworkflows.interfaces.utils.GenerateSamplingReference") | |
| 200316-04:12:47,400 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/shj16108/hw5/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/t1w_dseg/sub-01_ses-01_T1w_corrected_xform_masked.nii.gz | |
| 200316-04:12:48,415 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". | |
| 200316-04:12:49,399 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/shj16108/hw5/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/bold_t1_trans_wf/aparc_t1w_tfm". | |
| 200316-04:12:49,399 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/shj16108/hw5/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/bold_t1_trans_wf/aseg_t1w_tfm". | |
| 200316-04:12:49,404 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/shj16108/hw5/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/shj16108/hw5/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 | |
| 200316-04:12:49,404 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/shj16108/hw5/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/shj16108/hw5/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 | |
| 200316-04:12:53,244 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". | |
| 200316-04:12:53,282 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". | |
| 200316-04:15:58,223 nipype.workflow INFO: | |
| [Node] Finished "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.t1w_dseg". | |
| 200316-04:16:06,825 nipype.workflow INFO: | |
| [Node] Setting-up "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.anat_derivatives_wf.lut_t1w_dseg" in "/gpfs/scratchfs1/shj16108/hw5/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/anat_derivatives_wf/lut_t1w_dseg". | |
| 200316-04:16:06,826 nipype.workflow INFO: | |
| [Node] Setting-up "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.anat_reports_wf.seg_rpt" in "/gpfs/scratchfs1/shj16108/hw5/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/anat_reports_wf/seg_rpt". | |
| 200316-04:16:06,826 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/shj16108/hw5/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/bold_confounds_wf/wm_roi". | |
| 200316-04:16:06,827 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/shj16108/hw5/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/bold_confounds_wf/csf_roi". | |
| 200316-04:16:06,827 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/shj16108/hw5/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/bold_confounds_wf/tpms_add_csf_wm". | |
| 200316-04:16:06,840 nipype.workflow INFO: | |
| [Node] Running "lut_t1w_dseg" ("nipype.interfaces.utility.wrappers.Function") | |
| 200316-04:16:06,842 nipype.workflow INFO: | |
| [Node] Running "wm_roi" ("niworkflows.interfaces.utils.TPM2ROI") | |
| 200316-04:16:06,842 nipype.workflow INFO: | |
| [Node] Running "seg_rpt" ("niworkflows.interfaces.masks.ROIsPlot") | |
| 200316-04:16:06,842 nipype.workflow INFO: | |
| [Node] Running "tpms_add_csf_wm" ("niworkflows.interfaces.utils.AddTPMs") | |
| 200316-04:16:06,849 nipype.workflow INFO: | |
| [Node] Running "csf_roi" ("niworkflows.interfaces.utils.TPM2ROI") | |
| 200316-04:16:07,450 nipype.workflow INFO: | |
| [Node] Finished "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.anat_derivatives_wf.lut_t1w_dseg". | |
| 200316-04:16:08,127 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". | |
| 200316-04:16:08,487 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". | |
| 200316-04:16:12,319 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/shj16108/hw5/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/bold_confounds_wf/acc_roi". | |
| 200316-04:16:12,324 nipype.workflow INFO: | |
| [Node] Running "acc_roi" ("niworkflows.interfaces.utils.TPM2ROI") | |
| 200316-04:16:13,587 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". | |
| 200316-04:16:18,704 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". | |
| 200316-04:17:20,802 nipype.workflow INFO: | |
| [Node] Finished "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.anat_reports_wf.seg_rpt". | |
| 200316-04:31:35,62 nipype.workflow INFO: | |
| [Node] Finished "_midthickness1". | |
| 200316-04:31:37,679 nipype.workflow INFO: | |
| [Node] Finished "_midthickness0". | |
| 200316-04:31:39,359 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/shj16108/hw5/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/bold_reg_wf/bbreg_wf/mri_coreg". | |
| 200316-04:31:39,366 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 8 --lta /gpfs/scratchfs1/shj16108/hw5/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/shj16108/hw5/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 | |
| 200316-04:32:17,560 nipype.interface INFO: | |
| stdout 2020-03-16T04:32:17.560768: | |
| 200316-04:32:17,561 nipype.interface INFO: | |
| stdout 2020-03-16T04:32:17.560768:Matrix from LTA: | |
| 200316-04:32:17,561 nipype.interface INFO: | |
| stdout 2020-03-16T04:32:17.560768: 0.99875 -0.04553 -0.02054 0.65331; | |
| 200316-04:32:17,561 nipype.interface INFO: | |
| stdout 2020-03-16T04:32:17.560768: 0.00258 -0.36378 0.93148 -6.52174; | |
| 200316-04:32:17,561 nipype.interface INFO: | |
| stdout 2020-03-16T04:32:17.560768:-0.04988 -0.93037 -0.36321 -0.28841; | |
| 200316-04:32:17,561 nipype.interface INFO: | |
| stdout 2020-03-16T04:32:17.560768: 0.00000 0.00000 0.00000 1.00000; | |
| 200316-04:32:17,792 nipype.interface INFO: | |
| stdout 2020-03-16T04:32:17.792005: | |
| 200316-04:32:17,792 nipype.interface INFO: | |
| stdout 2020-03-16T04:32:17.792005:/gpfs/scratchfs1/shj16108/hw5/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 | |
| 200316-04:32:17,792 nipype.interface INFO: | |
| stdout 2020-03-16T04:32:17.792005:movvol /gpfs/scratchfs1/shj16108/hw5/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 | |
| 200316-04:32:17,792 nipype.interface INFO: | |
| stdout 2020-03-16T04:32:17.792005:targvol /out/freesurfer/sub-01/mri/brainmask.mgz | |
| 200316-04:32:17,792 nipype.interface INFO: | |
| stdout 2020-03-16T04:32:17.792005:outvol /gpfs/scratchfs1/shj16108/hw5/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 | |
| 200316-04:32:17,792 nipype.interface INFO: | |
| stdout 2020-03-16T04:32:17.792005:regfile /gpfs/scratchfs1/shj16108/hw5/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 | |
| 200316-04:32:17,792 nipype.interface INFO: | |
| stdout 2020-03-16T04:32:17.792005:invert 0 | |
| 200316-04:32:17,792 nipype.interface INFO: | |
| stdout 2020-03-16T04:32:17.792005:tal 0 | |
| 200316-04:32:17,792 nipype.interface INFO: | |
| stdout 2020-03-16T04:32:17.792005:talres 2 | |
| 200316-04:32:17,792 nipype.interface INFO: | |
| stdout 2020-03-16T04:32:17.792005:regheader 0 | |
| 200316-04:32:17,792 nipype.interface INFO: | |
| stdout 2020-03-16T04:32:17.792005:noresample 0 | |
| 200316-04:32:17,792 nipype.interface INFO: | |
| stdout 2020-03-16T04:32:17.792005:interp nearest (0) | |
| 200316-04:32:17,792 nipype.interface INFO: | |
| stdout 2020-03-16T04:32:17.792005:precision float (3) | |
| 200316-04:32:17,792 nipype.interface INFO: | |
| stdout 2020-03-16T04:32:17.792005:Gdiag_no -1 | |
| 200316-04:32:17,792 nipype.interface INFO: | |
| stdout 2020-03-16T04:32:17.792005:Synth 0 | |
| 200316-04:32:17,792 nipype.interface INFO: | |
| stdout 2020-03-16T04:32:17.792005:SynthSeed 1585018921 | |
| 200316-04:32:17,792 nipype.interface INFO: | |
| stdout 2020-03-16T04:32:17.792005: | |
| 200316-04:32:17,792 nipype.interface INFO: | |
| stdout 2020-03-16T04:32:17.792005:Final tkRAS-to-tkRAS Matrix is: | |
| 200316-04:32:17,792 nipype.interface INFO: | |
| stdout 2020-03-16T04:32:17.792005: 0.99875 -0.04553 -0.02054 0.65331; | |
| 200316-04:32:17,792 nipype.interface INFO: | |
| stdout 2020-03-16T04:32:17.792005: 0.00258 -0.36378 0.93148 -6.52171; | |
| 200316-04:32:17,793 nipype.interface INFO: | |
| stdout 2020-03-16T04:32:17.792005:-0.04988 -0.93037 -0.36321 -0.28844; | |
| 200316-04:32:17,793 nipype.interface INFO: | |
| stdout 2020-03-16T04:32:17.792005: 0.00000 0.00000 0.00000 1.00000; | |
| 200316-04:32:17,793 nipype.interface INFO: | |
| stdout 2020-03-16T04:32:17.792005: | |
| 200316-04:32:17,793 nipype.interface INFO: | |
| stdout 2020-03-16T04:32:17.792005: | |
| 200316-04:32:17,793 nipype.interface INFO: | |
| stdout 2020-03-16T04:32:17.792005:Vox2Vox Matrix is: | |
| 200316-04:32:17,793 nipype.interface INFO: | |
| stdout 2020-03-16T04:32:17.792005: 0.33292 -0.00685 0.01518 -9.87149; | |
| 200316-04:32:17,793 nipype.interface INFO: | |
| stdout 2020-03-16T04:32:17.792005:-0.01663 -0.12107 0.31012 17.53187; | |
| 200316-04:32:17,793 nipype.interface INFO: | |
| stdout 2020-03-16T04:32:17.792005:-0.00086 -0.31049 -0.12126 96.50066; | |
| 200316-04:32:17,793 nipype.interface INFO: | |
| stdout 2020-03-16T04:32:17.792005: 0.00000 0.00000 0.00000 1.00000; | |
| 200316-04:32:19,173 nipype.interface INFO: | |
| stdout 2020-03-16T04:32:19.173548: | |
| 200316-04:32:19,173 nipype.interface INFO: | |
| stdout 2020-03-16T04:32:19.173548:Resampling | |
| 200316-04:32:19,173 nipype.interface INFO: | |
| stdout 2020-03-16T04:32:19.173548:Output registration matrix is identity | |
| 200316-04:32:19,173 nipype.interface INFO: | |
| stdout 2020-03-16T04:32:19.173548: | |
| 200316-04:32:19,173 nipype.interface INFO: | |
| stdout 2020-03-16T04:32:19.173548:mri_vol2vol done | |
| 200316-04:32:39,185 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". | |
| 200316-04:32:39,424 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/shj16108/hw5/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/bold_reg_wf/bbreg_wf/bbregister". | |
| 200316-04:32:39,426 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/shj16108/hw5/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/midthickness". | |
| 200316-04:32:39,430 nipype.workflow INFO: | |
| [Node] Setting-up "_midthickness0" in "/gpfs/scratchfs1/shj16108/hw5/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/midthickness/mapflow/_midthickness0". | |
| 200316-04:32:39,431 nipype.workflow INFO: | |
| [Node] Running "bbregister" ("niworkflows.interfaces.freesurfer.PatchedBBRegisterRPT"), a CommandLine Interface with command: | |
| bbregister --t2 --6 --init-reg /gpfs/scratchfs1/shj16108/hw5/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/shj16108/hw5/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/shj16108/hw5/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/shj16108/hw5/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/shj16108/hw5/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 | |
| 200316-04:32:39,431 nipype.workflow INFO: | |
| [Node] Cached "_midthickness0" - collecting precomputed outputs | |
| 200316-04:32:39,431 nipype.workflow INFO: | |
| [Node] "_midthickness0" found cached. | |
| 200316-04:32:39,432 nipype.workflow INFO: | |
| [Node] Setting-up "_midthickness1" in "/gpfs/scratchfs1/shj16108/hw5/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/midthickness/mapflow/_midthickness1". | |
| 200316-04:32:39,433 nipype.workflow INFO: | |
| [Node] Cached "_midthickness1" - collecting precomputed outputs | |
| 200316-04:32:39,433 nipype.workflow INFO: | |
| [Node] "_midthickness1" found cached. | |
| 200316-04:32:39,435 nipype.workflow INFO: | |
| [Node] Finished "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.surface_recon_wf.gifti_surface_wf.midthickness". | |
| 200316-04:32:41,432 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/shj16108/hw5/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/save_midthickness". | |
| 200316-04:32:41,437 nipype.workflow INFO: | |
| [Node] Running "save_midthickness" ("nipype.interfaces.io.DataSink") | |
| 200316-04:32:41,611 nipype.workflow INFO: | |
| [Node] Finished "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.surface_recon_wf.gifti_surface_wf.save_midthickness". | |
| 200316-04:32:47,442 nipype.workflow INFO: | |
| [Node] Setting-up "_fs2gii0" in "/gpfs/scratchfs1/shj16108/hw5/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/fs2gii/mapflow/_fs2gii0". | |
| 200316-04:32:47,443 nipype.workflow INFO: | |
| [Node] Setting-up "_fs2gii1" in "/gpfs/scratchfs1/shj16108/hw5/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/fs2gii/mapflow/_fs2gii1". | |
| 200316-04:32:47,444 nipype.workflow INFO: | |
| [Node] Setting-up "_fs2gii2" in "/gpfs/scratchfs1/shj16108/hw5/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/fs2gii/mapflow/_fs2gii2". | |
| 200316-04:32:47,445 nipype.workflow INFO: | |
| [Node] Setting-up "_fs2gii3" in "/gpfs/scratchfs1/shj16108/hw5/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/fs2gii/mapflow/_fs2gii3". | |
| 200316-04:32:47,446 nipype.workflow INFO: | |
| [Node] Setting-up "_fs2gii4" in "/gpfs/scratchfs1/shj16108/hw5/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/fs2gii/mapflow/_fs2gii4". | |
| 200316-04:32:47,446 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/shj16108/hw5/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/fs2gii/mapflow/_fs2gii0/rh.smoothwm_converted.gii | |
| 200316-04:32:47,447 nipype.workflow INFO: | |
| [Node] Setting-up "_fs2gii5" in "/gpfs/scratchfs1/shj16108/hw5/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/fs2gii/mapflow/_fs2gii5". | |
| 200316-04:32:47,447 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/shj16108/hw5/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/fs2gii/mapflow/_fs2gii1/lh.smoothwm_converted.gii | |
| 200316-04:32:47,448 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/shj16108/hw5/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/fs2gii/mapflow/_fs2gii3/lh.pial_converted.gii | |
| 200316-04:32:47,449 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/shj16108/hw5/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/fs2gii/mapflow/_fs2gii2/rh.pial_converted.gii | |
| 200316-04:32:47,451 nipype.workflow INFO: | |
| [Node] Setting-up "_fs2gii6" in "/gpfs/scratchfs1/shj16108/hw5/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/fs2gii/mapflow/_fs2gii6". | |
| 200316-04:32:47,456 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/shj16108/hw5/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/fs2gii/mapflow/_fs2gii6/rh.midthickness_converted.gii | |
| 200316-04:32:47,457 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/shj16108/hw5/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/fs2gii/mapflow/_fs2gii5/lh.inflated_converted.gii | |
| 200316-04:32:47,458 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/shj16108/hw5/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/fs2gii/mapflow/_fs2gii4/rh.inflated_converted.gii | |
| 200316-04:32:49,795 nipype.workflow INFO: | |
| [Node] Finished "_fs2gii3". | |
| 200316-04:32:49,817 nipype.workflow INFO: | |
| [Node] Finished "_fs2gii0". | |
| 200316-04:32:49,818 nipype.workflow INFO: | |
| [Node] Finished "_fs2gii2". | |
| 200316-04:32:49,825 nipype.workflow INFO: | |
| [Node] Finished "_fs2gii6". | |
| 200316-04:32:49,825 nipype.workflow INFO: | |
| [Node] Finished "_fs2gii5". | |
| 200316-04:32:49,825 nipype.workflow INFO: | |
| [Node] Finished "_fs2gii1". | |
| 200316-04:32:49,863 nipype.workflow INFO: | |
| [Node] Finished "_fs2gii4". | |
| 200316-04:32:51,441 nipype.workflow INFO: | |
| [Node] Setting-up "_fs2gii7" in "/gpfs/scratchfs1/shj16108/hw5/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/fs2gii/mapflow/_fs2gii7". | |
| 200316-04:32:51,446 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/shj16108/hw5/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/fs2gii/mapflow/_fs2gii7/lh.midthickness_converted.gii | |
| 200316-04:32:53,468 nipype.workflow INFO: | |
| [Node] Finished "_fs2gii7". | |
| 200316-04:32:55,452 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/shj16108/hw5/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/fs2gii". | |
| 200316-04:32:55,458 nipype.workflow INFO: | |
| [Node] Setting-up "_fs2gii0" in "/gpfs/scratchfs1/shj16108/hw5/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/fs2gii/mapflow/_fs2gii0". | |
| 200316-04:32:55,458 nipype.workflow INFO: | |
| [Node] Cached "_fs2gii0" - collecting precomputed outputs | |
| 200316-04:32:55,459 nipype.workflow INFO: | |
| [Node] "_fs2gii0" found cached. | |
| 200316-04:32:55,459 nipype.workflow INFO: | |
| [Node] Setting-up "_fs2gii1" in "/gpfs/scratchfs1/shj16108/hw5/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/fs2gii/mapflow/_fs2gii1". | |
| 200316-04:32:55,460 nipype.workflow INFO: | |
| [Node] Cached "_fs2gii1" - collecting precomputed outputs | |
| 200316-04:32:55,460 nipype.workflow INFO: | |
| [Node] "_fs2gii1" found cached. | |
| 200316-04:32:55,461 nipype.workflow INFO: | |
| [Node] Setting-up "_fs2gii2" in "/gpfs/scratchfs1/shj16108/hw5/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/fs2gii/mapflow/_fs2gii2". | |
| 200316-04:32:55,462 nipype.workflow INFO: | |
| [Node] Cached "_fs2gii2" - collecting precomputed outputs | |
| 200316-04:32:55,462 nipype.workflow INFO: | |
| [Node] "_fs2gii2" found cached. | |
| 200316-04:32:55,463 nipype.workflow INFO: | |
| [Node] Setting-up "_fs2gii3" in "/gpfs/scratchfs1/shj16108/hw5/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/fs2gii/mapflow/_fs2gii3". | |
| 200316-04:32:55,464 nipype.workflow INFO: | |
| [Node] Cached "_fs2gii3" - collecting precomputed outputs | |
| 200316-04:32:55,464 nipype.workflow INFO: | |
| [Node] "_fs2gii3" found cached. | |
| 200316-04:32:55,464 nipype.workflow INFO: | |
| [Node] Setting-up "_fs2gii4" in "/gpfs/scratchfs1/shj16108/hw5/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/fs2gii/mapflow/_fs2gii4". | |
| 200316-04:32:55,465 nipype.workflow INFO: | |
| [Node] Cached "_fs2gii4" - collecting precomputed outputs | |
| 200316-04:32:55,465 nipype.workflow INFO: | |
| [Node] "_fs2gii4" found cached. | |
| 200316-04:32:55,466 nipype.workflow INFO: | |
| [Node] Setting-up "_fs2gii5" in "/gpfs/scratchfs1/shj16108/hw5/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/fs2gii/mapflow/_fs2gii5". | |
| 200316-04:32:55,467 nipype.workflow INFO: | |
| [Node] Cached "_fs2gii5" - collecting precomputed outputs | |
| 200316-04:32:55,467 nipype.workflow INFO: | |
| [Node] "_fs2gii5" found cached. | |
| 200316-04:32:55,468 nipype.workflow INFO: | |
| [Node] Setting-up "_fs2gii6" in "/gpfs/scratchfs1/shj16108/hw5/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/fs2gii/mapflow/_fs2gii6". | |
| 200316-04:32:55,469 nipype.workflow INFO: | |
| [Node] Cached "_fs2gii6" - collecting precomputed outputs | |
| 200316-04:32:55,469 nipype.workflow INFO: | |
| [Node] "_fs2gii6" found cached. | |
| 200316-04:32:55,469 nipype.workflow INFO: | |
| [Node] Setting-up "_fs2gii7" in "/gpfs/scratchfs1/shj16108/hw5/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/fs2gii/mapflow/_fs2gii7". | |
| 200316-04:32:55,470 nipype.workflow INFO: | |
| [Node] Cached "_fs2gii7" - collecting precomputed outputs | |
| 200316-04:32:55,470 nipype.workflow INFO: | |
| [Node] "_fs2gii7" found cached. | |
| 200316-04:32:55,473 nipype.workflow INFO: | |
| [Node] Finished "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.surface_recon_wf.gifti_surface_wf.fs2gii". | |
| 200316-04:32:59,455 nipype.workflow INFO: | |
| [Node] Setting-up "_fix_surfs0" in "/gpfs/scratchfs1/shj16108/hw5/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/fix_surfs/mapflow/_fix_surfs0". | |
| 200316-04:32:59,456 nipype.workflow INFO: | |
| [Node] Setting-up "_fix_surfs1" in "/gpfs/scratchfs1/shj16108/hw5/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/fix_surfs/mapflow/_fix_surfs1". | |
| 200316-04:32:59,457 nipype.workflow INFO: | |
| [Node] Setting-up "_fix_surfs2" in "/gpfs/scratchfs1/shj16108/hw5/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/fix_surfs/mapflow/_fix_surfs2". | |
| 200316-04:32:59,458 nipype.workflow INFO: | |
| [Node] Setting-up "_fix_surfs3" in "/gpfs/scratchfs1/shj16108/hw5/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/fix_surfs/mapflow/_fix_surfs3". | |
| 200316-04:32:59,458 nipype.workflow INFO: | |
| [Node] Running "_fix_surfs0" ("niworkflows.interfaces.surf.NormalizeSurf") | |
| 200316-04:32:59,459 nipype.workflow INFO: | |
| [Node] Setting-up "_fix_surfs4" in "/gpfs/scratchfs1/shj16108/hw5/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/fix_surfs/mapflow/_fix_surfs4". | |
| 200316-04:32:59,459 nipype.workflow INFO: | |
| [Node] Setting-up "_fix_surfs5" in "/gpfs/scratchfs1/shj16108/hw5/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/fix_surfs/mapflow/_fix_surfs5". | |
| 200316-04:32:59,460 nipype.workflow INFO: | |
| [Node] Running "_fix_surfs1" ("niworkflows.interfaces.surf.NormalizeSurf") | |
| 200316-04:32:59,460 nipype.workflow INFO: | |
| [Node] Setting-up "_fix_surfs6" in "/gpfs/scratchfs1/shj16108/hw5/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/fix_surfs/mapflow/_fix_surfs6". | |
| 200316-04:32:59,460 nipype.workflow INFO: | |
| [Node] Running "_fix_surfs2" ("niworkflows.interfaces.surf.NormalizeSurf") | |
| 200316-04:32:59,461 nipype.workflow INFO: | |
| [Node] Running "_fix_surfs3" ("niworkflows.interfaces.surf.NormalizeSurf") | |
| 200316-04:32:59,461 nipype.workflow INFO: | |
| [Node] Running "_fix_surfs4" ("niworkflows.interfaces.surf.NormalizeSurf") | |
| 200316-04:32:59,462 nipype.workflow INFO: | |
| [Node] Running "_fix_surfs6" ("niworkflows.interfaces.surf.NormalizeSurf") | |
| 200316-04:32:59,463 nipype.workflow INFO: | |
| [Node] Running "_fix_surfs5" ("niworkflows.interfaces.surf.NormalizeSurf") | |
| 200316-04:33:00,67 nipype.workflow INFO: | |
| [Node] Finished "_fix_surfs0". | |
| 200316-04:33:00,68 nipype.workflow INFO: | |
| [Node] Finished "_fix_surfs3". | |
| 200316-04:33:00,77 nipype.workflow INFO: | |
| [Node] Finished "_fix_surfs4". | |
| 200316-04:33:00,79 nipype.workflow INFO: | |
| [Node] Finished "_fix_surfs1". | |
| 200316-04:33:00,83 nipype.workflow INFO: | |
| [Node] Finished "_fix_surfs5". | |
| 200316-04:33:00,84 nipype.workflow INFO: | |
| [Node] Finished "_fix_surfs6". | |
| 200316-04:33:00,91 nipype.workflow INFO: | |
| [Node] Finished "_fix_surfs2". | |
| 200316-04:33:01,460 nipype.workflow INFO: | |
| [Node] Setting-up "_fix_surfs7" in "/gpfs/scratchfs1/shj16108/hw5/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/fix_surfs/mapflow/_fix_surfs7". | |
| 200316-04:33:01,463 nipype.workflow INFO: | |
| [Node] Running "_fix_surfs7" ("niworkflows.interfaces.surf.NormalizeSurf") | |
| 200316-04:33:02,11 nipype.workflow INFO: | |
| [Node] Finished "_fix_surfs7". | |
| 200316-04:33:03,460 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/shj16108/hw5/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/fix_surfs". | |
| 200316-04:33:03,465 nipype.workflow INFO: | |
| [Node] Setting-up "_fix_surfs0" in "/gpfs/scratchfs1/shj16108/hw5/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/fix_surfs/mapflow/_fix_surfs0". | |
| 200316-04:33:03,465 nipype.workflow INFO: | |
| [Node] Cached "_fix_surfs0" - collecting precomputed outputs | |
| 200316-04:33:03,465 nipype.workflow INFO: | |
| [Node] "_fix_surfs0" found cached. | |
| 200316-04:33:03,466 nipype.workflow INFO: | |
| [Node] Setting-up "_fix_surfs1" in "/gpfs/scratchfs1/shj16108/hw5/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/fix_surfs/mapflow/_fix_surfs1". | |
| 200316-04:33:03,467 nipype.workflow INFO: | |
| [Node] Cached "_fix_surfs1" - collecting precomputed outputs | |
| 200316-04:33:03,467 nipype.workflow INFO: | |
| [Node] "_fix_surfs1" found cached. | |
| 200316-04:33:03,468 nipype.workflow INFO: | |
| [Node] Setting-up "_fix_surfs2" in "/gpfs/scratchfs1/shj16108/hw5/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/fix_surfs/mapflow/_fix_surfs2". | |
| 200316-04:33:03,468 nipype.workflow INFO: | |
| [Node] Cached "_fix_surfs2" - collecting precomputed outputs | |
| 200316-04:33:03,468 nipype.workflow INFO: | |
| [Node] "_fix_surfs2" found cached. | |
| 200316-04:33:03,469 nipype.workflow INFO: | |
| [Node] Setting-up "_fix_surfs3" in "/gpfs/scratchfs1/shj16108/hw5/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/fix_surfs/mapflow/_fix_surfs3". | |
| 200316-04:33:03,470 nipype.workflow INFO: | |
| [Node] Cached "_fix_surfs3" - collecting precomputed outputs | |
| 200316-04:33:03,470 nipype.workflow INFO: | |
| [Node] "_fix_surfs3" found cached. | |
| 200316-04:33:03,470 nipype.workflow INFO: | |
| [Node] Setting-up "_fix_surfs4" in "/gpfs/scratchfs1/shj16108/hw5/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/fix_surfs/mapflow/_fix_surfs4". | |
| 200316-04:33:03,471 nipype.workflow INFO: | |
| [Node] Cached "_fix_surfs4" - collecting precomputed outputs | |
| 200316-04:33:03,471 nipype.workflow INFO: | |
| [Node] "_fix_surfs4" found cached. | |
| 200316-04:33:03,472 nipype.workflow INFO: | |
| [Node] Setting-up "_fix_surfs5" in "/gpfs/scratchfs1/shj16108/hw5/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/fix_surfs/mapflow/_fix_surfs5". | |
| 200316-04:33:03,473 nipype.workflow INFO: | |
| [Node] Cached "_fix_surfs5" - collecting precomputed outputs | |
| 200316-04:33:03,473 nipype.workflow INFO: | |
| [Node] "_fix_surfs5" found cached. | |
| 200316-04:33:03,473 nipype.workflow INFO: | |
| [Node] Setting-up "_fix_surfs6" in "/gpfs/scratchfs1/shj16108/hw5/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/fix_surfs/mapflow/_fix_surfs6". | |
| 200316-04:33:03,474 nipype.workflow INFO: | |
| [Node] Cached "_fix_surfs6" - collecting precomputed outputs | |
| 200316-04:33:03,474 nipype.workflow INFO: | |
| [Node] "_fix_surfs6" found cached. | |
| 200316-04:33:03,475 nipype.workflow INFO: | |
| [Node] Setting-up "_fix_surfs7" in "/gpfs/scratchfs1/shj16108/hw5/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/fix_surfs/mapflow/_fix_surfs7". | |
| 200316-04:33:03,475 nipype.workflow INFO: | |
| [Node] Cached "_fix_surfs7" - collecting precomputed outputs | |
| 200316-04:33:03,476 nipype.workflow INFO: | |
| [Node] "_fix_surfs7" found cached. | |
| 200316-04:33:03,478 nipype.workflow INFO: | |
| [Node] Finished "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.surface_recon_wf.gifti_surface_wf.fix_surfs". | |
| 200316-04:33:37,648 nipype.interface INFO: | |
| stdout 2020-03-16T04:33:37.648435: | |
| 200316-04:33:37,648 nipype.interface INFO: | |
| stdout 2020-03-16T04:33:37.648435:Matrix from LTA: | |
| 200316-04:33:37,648 nipype.interface INFO: | |
| stdout 2020-03-16T04:33:37.648435: 0.99857 -0.04858 -0.02220 0.86746; | |
| 200316-04:33:37,648 nipype.interface INFO: | |
| stdout 2020-03-16T04:33:37.648435: 0.00233 -0.37571 0.92674 -6.68849; | |
| 200316-04:33:37,648 nipype.interface INFO: | |
| stdout 2020-03-16T04:33:37.648435:-0.05336 -0.92546 -0.37506 0.17295; | |
| 200316-04:33:37,648 nipype.interface INFO: | |
| stdout 2020-03-16T04:33:37.648435: 0.00000 0.00000 0.00000 1.00000; | |
| 200316-04:33:37,880 nipype.interface INFO: | |
| stdout 2020-03-16T04:33:37.880492: | |
| 200316-04:33:37,880 nipype.interface INFO: | |
| stdout 2020-03-16T04:33:37.880492:/gpfs/scratchfs1/shj16108/hw5/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 | |
| 200316-04:33:37,880 nipype.interface INFO: | |
| stdout 2020-03-16T04:33:37.880492:movvol /gpfs/scratchfs1/shj16108/hw5/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 | |
| 200316-04:33:37,880 nipype.interface INFO: | |
| stdout 2020-03-16T04:33:37.880492:targvol /out/freesurfer/sub-01/mri/brainmask.mgz | |
| 200316-04:33:37,880 nipype.interface INFO: | |
| stdout 2020-03-16T04:33:37.880492:outvol /gpfs/scratchfs1/shj16108/hw5/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 | |
| 200316-04:33:37,880 nipype.interface INFO: | |
| stdout 2020-03-16T04:33:37.880492:regfile /gpfs/scratchfs1/shj16108/hw5/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 | |
| 200316-04:33:37,880 nipype.interface INFO: | |
| stdout 2020-03-16T04:33:37.880492:invert 0 | |
| 200316-04:33:37,880 nipype.interface INFO: | |
| stdout 2020-03-16T04:33:37.880492:tal 0 | |
| 200316-04:33:37,880 nipype.interface INFO: | |
| stdout 2020-03-16T04:33:37.880492:talres 2 | |
| 200316-04:33:37,880 nipype.interface INFO: | |
| stdout 2020-03-16T04:33:37.880492:regheader 0 | |
| 200316-04:33:37,881 nipype.interface INFO: | |
| stdout 2020-03-16T04:33:37.880492:noresample 0 | |
| 200316-04:33:37,881 nipype.interface INFO: | |
| stdout 2020-03-16T04:33:37.880492:interp nearest (0) | |
| 200316-04:33:37,881 nipype.interface INFO: | |
| stdout 2020-03-16T04:33:37.880492:precision float (3) | |
| 200316-04:33:37,881 nipype.interface INFO: | |
| stdout 2020-03-16T04:33:37.880492:Gdiag_no -1 | |
| 200316-04:33:37,881 nipype.interface INFO: | |
| stdout 2020-03-16T04:33:37.880492:Synth 0 | |
| 200316-04:33:37,881 nipype.interface INFO: | |
| stdout 2020-03-16T04:33:37.880492:SynthSeed 1585107086 | |
| 200316-04:33:37,881 nipype.interface INFO: | |
| stdout 2020-03-16T04:33:37.880492: | |
| 200316-04:33:37,881 nipype.interface INFO: | |
| stdout 2020-03-16T04:33:37.880492:Final tkRAS-to-tkRAS Matrix is: | |
| 200316-04:33:37,881 nipype.interface INFO: | |
| stdout 2020-03-16T04:33:37.880492: 0.99857 -0.04858 -0.02220 0.86745; | |
| 200316-04:33:37,881 nipype.interface INFO: | |
| stdout 2020-03-16T04:33:37.880492: 0.00233 -0.37571 0.92674 -6.68846; | |
| 200316-04:33:37,881 nipype.interface INFO: | |
| stdout 2020-03-16T04:33:37.880492:-0.05336 -0.92546 -0.37506 0.17293; | |
| 200316-04:33:37,881 nipype.interface INFO: | |
| stdout 2020-03-16T04:33:37.880492: 0.00000 0.00000 0.00000 1.00000; | |
| 200316-04:33:37,881 nipype.interface INFO: | |
| stdout 2020-03-16T04:33:37.880492: | |
| 200316-04:33:37,881 nipype.interface INFO: | |
| stdout 2020-03-16T04:33:37.880492: | |
| 200316-04:33:37,881 nipype.interface INFO: | |
| stdout 2020-03-16T04:33:37.880492:Vox2Vox Matrix is: | |
| 200316-04:33:37,881 nipype.interface INFO: | |
| stdout 2020-03-16T04:33:37.880492: 0.33286 -0.00740 0.01619 -10.02549; | |
| 200316-04:33:37,881 nipype.interface INFO: | |
| stdout 2020-03-16T04:33:37.880492:-0.01779 -0.12502 0.30849 18.41886; | |
| 200316-04:33:37,881 nipype.interface INFO: | |
| stdout 2020-03-16T04:33:37.880492:-0.00078 -0.30891 -0.12524 96.80080; | |
| 200316-04:33:37,881 nipype.interface INFO: | |
| stdout 2020-03-16T04:33:37.880492: 0.00000 0.00000 0.00000 1.00000; | |
| 200316-04:33:39,251 nipype.interface INFO: | |
| stdout 2020-03-16T04:33:39.251494: | |
| 200316-04:33:39,251 nipype.interface INFO: | |
| stdout 2020-03-16T04:33:39.251494:Resampling | |
| 200316-04:33:39,251 nipype.interface INFO: | |
| stdout 2020-03-16T04:33:39.251494:Output registration matrix is identity | |
| 200316-04:33:39,251 nipype.interface INFO: | |
| stdout 2020-03-16T04:33:39.251494: | |
| 200316-04:33:39,251 nipype.interface INFO: | |
| stdout 2020-03-16T04:33:39.251494:mri_vol2vol done | |
| 200316-04:33:59,320 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". | |
| 200316-04:33:59,692 nipype.workflow INFO: | |
| [Node] Setting-up "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.anat_norm_wf.registration" in "/gpfs/scratchfs1/shj16108/hw5/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/anat_norm_wf/_template_MNI152NLin2009cAsym./registration". | |
| 200316-04:33:59,706 nipype.workflow INFO: | |
| [Node] Running "registration" ("niworkflows.interfaces.mni.RobustMNINormalization") | |
| 200316-05:03:10,749 nipype.workflow INFO: | |
| [Node] Finished "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.anat_norm_wf.registration". | |
| 200316-05:03:11,788 nipype.workflow INFO: | |
| [Node] Setting-up "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.anat_norm_wf.std_mask" in "/gpfs/scratchfs1/shj16108/hw5/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/anat_norm_wf/_template_MNI152NLin2009cAsym./std_mask". | |
| 200316-05:03:11,788 nipype.workflow INFO: | |
| [Node] Setting-up "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.anat_norm_wf.tpl_moving" in "/gpfs/scratchfs1/shj16108/hw5/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/anat_norm_wf/_template_MNI152NLin2009cAsym./tpl_moving". | |
| 200316-05:03:11,789 nipype.workflow INFO: | |
| [Node] Setting-up "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.anat_norm_wf.std_dseg" in "/gpfs/scratchfs1/shj16108/hw5/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/anat_norm_wf/_template_MNI152NLin2009cAsym./std_dseg". | |
| 200316-05:03:11,803 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/shj16108/hw5/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/shj16108/.cache/templateflow/tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_res-01_T1w.nii.gz --transform /gpfs/scratchfs1/shj16108/hw5/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/anat_norm_wf/_template_MNI152NLin2009cAsym./registration/ants_t1_to_mniComposite.h5 | |
| 200316-05:03:11,804 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/shj16108/hw5/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/shj16108/.cache/templateflow/tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_res-01_T1w.nii.gz --transform /gpfs/scratchfs1/shj16108/hw5/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/anat_norm_wf/_template_MNI152NLin2009cAsym./registration/ants_t1_to_mniComposite.h5 | |
| 200316-05:03:11,806 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/shj16108/hw5/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/shj16108/.cache/templateflow/tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_res-01_T1w.nii.gz --transform /gpfs/scratchfs1/shj16108/hw5/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/anat_norm_wf/_template_MNI152NLin2009cAsym./registration/ants_t1_to_mniComposite.h5 | |
| 200316-05:03:13,254 nipype.workflow INFO: | |
| [Node] Setting-up "_lta_ras2ras0" in "/gpfs/scratchfs1/shj16108/hw5/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". | |
| 200316-05:03:13,255 nipype.workflow INFO: | |
| [Node] Setting-up "_lta_ras2ras1" in "/gpfs/scratchfs1/shj16108/hw5/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". | |
| 200316-05:03:13,256 nipype.workflow INFO: | |
| [Node] Setting-up "_std_tpms0" in "/gpfs/scratchfs1/shj16108/hw5/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/anat_norm_wf/_template_MNI152NLin2009cAsym./std_tpms/mapflow/_std_tpms0". | |
| 200316-05:03:13,257 nipype.workflow INFO: | |
| [Node] Setting-up "_std_tpms1" in "/gpfs/scratchfs1/shj16108/hw5/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/anat_norm_wf/_template_MNI152NLin2009cAsym./std_tpms/mapflow/_std_tpms1". | |
| 200316-05:03:13,258 nipype.workflow INFO: | |
| [Node] Setting-up "_std_tpms2" in "/gpfs/scratchfs1/shj16108/hw5/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/anat_norm_wf/_template_MNI152NLin2009cAsym./std_tpms/mapflow/_std_tpms2". | |
| 200316-05:03:13,259 nipype.workflow INFO: | |
| [Node] Running "_lta_ras2ras1" ("niworkflows.interfaces.freesurfer.PatchedLTAConvert"), a CommandLine Interface with command: | |
| lta_convert --inlta /gpfs/scratchfs1/shj16108/hw5/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/shj16108/hw5/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 | |
| 200316-05:03:13,261 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/shj16108/hw5/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/shj16108/.cache/templateflow/tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_res-01_T1w.nii.gz --transform /gpfs/scratchfs1/shj16108/hw5/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/anat_norm_wf/_template_MNI152NLin2009cAsym./registration/ants_t1_to_mniComposite.h5 | |
| 200316-05:03:13,261 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/shj16108/hw5/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/shj16108/.cache/templateflow/tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_res-01_T1w.nii.gz --transform /gpfs/scratchfs1/shj16108/hw5/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/anat_norm_wf/_template_MNI152NLin2009cAsym./registration/ants_t1_to_mniComposite.h5 | |
| 200316-05:03:13,262 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/shj16108/hw5/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/shj16108/.cache/templateflow/tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_res-01_T1w.nii.gz --transform /gpfs/scratchfs1/shj16108/hw5/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/anat_norm_wf/_template_MNI152NLin2009cAsym./registration/ants_t1_to_mniComposite.h5 | |
| 200316-05:03:13,264 nipype.workflow INFO: | |
| [Node] Running "_lta_ras2ras0" ("niworkflows.interfaces.freesurfer.PatchedLTAConvert"), a CommandLine Interface with command: | |
| lta_convert --inlta /gpfs/scratchfs1/shj16108/hw5/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/shj16108/hw5/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 | |
| 200316-05:03:13,349 nipype.workflow INFO: | |
| [Node] Finished "_lta_ras2ras1". | |
| 200316-05:03:13,352 nipype.workflow INFO: | |
| [Node] Finished "_lta_ras2ras0". | |
| 200316-05:03:15,259 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/shj16108/hw5/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/bold_reg_wf/bbreg_wf/lta_ras2ras". | |
| 200316-05:03:15,266 nipype.workflow INFO: | |
| [Node] Setting-up "_lta_ras2ras0" in "/gpfs/scratchfs1/shj16108/hw5/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". | |
| 200316-05:03:15,267 nipype.workflow INFO: | |
| [Node] Cached "_lta_ras2ras0" - collecting precomputed outputs | |
| 200316-05:03:15,267 nipype.workflow INFO: | |
| [Node] "_lta_ras2ras0" found cached. | |
| 200316-05:03:15,268 nipype.workflow INFO: | |
| [Node] Setting-up "_lta_ras2ras1" in "/gpfs/scratchfs1/shj16108/hw5/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". | |
| 200316-05:03:15,269 nipype.workflow INFO: | |
| [Node] Cached "_lta_ras2ras1" - collecting precomputed outputs | |
| 200316-05:03:15,269 nipype.workflow INFO: | |
| [Node] "_lta_ras2ras1" found cached. | |
| 200316-05:03:15,271 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". | |
| 200316-05:03:17,260 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/shj16108/hw5/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/bold_reg_wf/bbreg_wf/compare_transforms". | |
| 200316-05:03:17,264 nipype.workflow INFO: | |
| [Node] Running "compare_transforms" ("nipype.interfaces.utility.wrappers.Function") | |
| 200316-05:03:17,366 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". | |
| 200316-05:03:21,374 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/shj16108/hw5/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/bold_reg_wf/bbreg_wf/lta_concat". | |
| 200316-05:03:21,379 nipype.workflow INFO: | |
| [Node] Running "lta_concat" ("niworkflows.interfaces.freesurfer.PatchedConcatenateLTA"), a CommandLine Interface with command: | |
| mri_concatenate_lta /gpfs/scratchfs1/shj16108/hw5/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/shj16108/hw5/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/surface_recon_wf/fsnative2t1w_xfm/T1_robustreg.lta out.lta | |
| 200316-05:03:21,456 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". | |
| 200316-05:03:23,266 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/shj16108/hw5/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/bold_reg_wf/bbreg_wf/lta2fsl_inv". | |
| 200316-05:03:23,267 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/shj16108/hw5/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/bold_reg_wf/bbreg_wf/lta2fsl_fwd". | |
| 200316-05:03:23,271 nipype.workflow INFO: | |
| [Node] Running "lta2fsl_inv" ("niworkflows.interfaces.freesurfer.PatchedLTAConvert"), a CommandLine Interface with command: | |
| lta_convert --inlta /gpfs/scratchfs1/shj16108/hw5/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/shj16108/hw5/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 | |
| 200316-05:03:23,271 nipype.workflow INFO: | |
| [Node] Running "lta2fsl_fwd" ("niworkflows.interfaces.freesurfer.PatchedLTAConvert"), a CommandLine Interface with command: | |
| lta_convert --inlta /gpfs/scratchfs1/shj16108/hw5/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/shj16108/hw5/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 | |
| 200316-05:03:23,357 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". | |
| 200316-05:03:23,358 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". | |
| 200316-05:03:25,269 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/shj16108/hw5/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/bold_reg_wf/bbreg_wf/fsl2itk_fwd". | |
| 200316-05:03:25,270 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/shj16108/hw5/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/bold_reg_wf/bbreg_wf/fsl2itk_inv". | |
| 200316-05:03:25,274 nipype.workflow INFO: | |
| [Node] Running "fsl2itk_fwd" ("nipype.interfaces.c3.C3dAffineTool"), a CommandLine Interface with command: | |
| c3d_affine_tool -ref /gpfs/scratchfs1/shj16108/hw5/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/shj16108/hw5/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/shj16108/hw5/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/shj16108/hw5/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 | |
| 200316-05:03:25,275 nipype.workflow INFO: | |
| [Node] Running "fsl2itk_inv" ("nipype.interfaces.c3.C3dAffineTool"), a CommandLine Interface with command: | |
| c3d_affine_tool -ref /gpfs/scratchfs1/shj16108/hw5/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/shj16108/hw5/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/applyrefined/sub-01_ses-01_T1w_corrected_xform_masked.nii.gz /gpfs/scratchfs1/shj16108/hw5/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/shj16108/hw5/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 | |
| 200316-05:03:25,813 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". | |
| 200316-05:03:25,824 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". | |
| 200316-05:03:27,405 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/shj16108/hw5/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/bold_t1_trans_wf/mask_t1w_tfm". | |
| 200316-05:03:27,405 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/shj16108/hw5/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/sdc_unwarp_report_wf/map_seg". | |
| 200316-05:03:27,417 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/shj16108/hw5/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/shj16108/hw5/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/shj16108/hw5/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 | |
| 200316-05:03:27,420 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/shj16108/hw5/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/shj16108/hw5/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/shj16108/hw5/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 | |
| 200316-05:03:30,547 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". | |
| 200316-05:03:31,274 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/shj16108/hw5/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". | |
| 200316-05:03:31,278 nipype.workflow INFO: | |
| [Node] Running "pre_mask_dilate" ("nipype.interfaces.fsl.maths.DilateImage"), a CommandLine Interface with command: | |
| fslmaths -dt char /gpfs/scratchfs1/shj16108/hw5/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/shj16108/hw5/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 | |
| 200316-05:03:31,508 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". | |
| 200316-05:03:33,40 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". | |
| 200316-05:03:33,276 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/shj16108/hw5/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/sdc_unwarp_report_wf/sel_wm". | |
| 200316-05:03:33,277 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/shj16108/hw5/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/bold_confounds_wf/wm_tfm". | |
| 200316-05:03:33,283 nipype.workflow INFO: | |
| [Node] Running "sel_wm" ("nipype.interfaces.utility.wrappers.Function") | |
| 200316-05:03:33,291 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/shj16108/hw5/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/shj16108/hw5/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/shj16108/hw5/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 | |
| 200316-05:03:33,320 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". | |
| 200316-05:03:33,572 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". | |
| 200316-05:03:35,278 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/shj16108/hw5/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/sdc_unwarp_report_wf/bold_rpt". | |
| 200316-05:03:35,278 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/shj16108/hw5/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/bold_confounds_wf/wm_msk". | |
| 200316-05:03:35,282 nipype.workflow INFO: | |
| [Node] Running "wm_msk" ("nipype.interfaces.utility.wrappers.Function") | |
| 200316-05:03:35,289 nipype.workflow INFO: | |
| [Node] Running "bold_rpt" ("niworkflows.interfaces.registration.SimpleBeforeAfterRPT") | |
| 200316-05:03:35,316 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". | |
| 200316-05:03:37,279 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/shj16108/hw5/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/bold_confounds_wf/tcc_tfm". | |
| 200316-05:03:37,289 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/shj16108/hw5/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/shj16108/hw5/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/shj16108/hw5/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 | |
| 200316-05:03:37,535 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". | |
| 200316-05:03:39,285 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/shj16108/hw5/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/bold_confounds_wf/tcc_msk". | |
| 200316-05:03:39,289 nipype.workflow INFO: | |
| [Node] Running "tcc_msk" ("nipype.interfaces.utility.wrappers.Function") | |
| 200316-05:03:39,324 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". | |
| 200316-05:03:39,493 nipype.workflow INFO: | |
| [Node] Finished "_std_tpms0". | |
| 200316-05:03:39,521 nipype.workflow INFO: | |
| [Node] Finished "_std_tpms2". | |
| 200316-05:03:39,570 nipype.workflow INFO: | |
| [Node] Finished "_std_tpms1". | |
| 200316-05:03:41,294 nipype.workflow INFO: | |
| [Node] Setting-up "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.anat_norm_wf.std_tpms" in "/gpfs/scratchfs1/shj16108/hw5/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/anat_norm_wf/_template_MNI152NLin2009cAsym./std_tpms". | |
| 200316-05:03:41,295 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/shj16108/hw5/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/bold_confounds_wf/tcompcor". | |
| 200316-05:03:41,295 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/shj16108/hw5/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/bold_confounds_wf/csf_tfm". | |
| 200316-05:03:41,295 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/shj16108/hw5/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/bold_confounds_wf/acc_tfm". | |
| 200316-05:03:41,301 nipype.workflow INFO: | |
| [Node] Setting-up "_std_tpms0" in "/gpfs/scratchfs1/shj16108/hw5/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/anat_norm_wf/_template_MNI152NLin2009cAsym./std_tpms/mapflow/_std_tpms0". | |
| 200316-05:03:41,302 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/shj16108/hw5/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/shj16108/hw5/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/shj16108/hw5/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 | |
| 200316-05:03:41,302 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/shj16108/hw5/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/shj16108/hw5/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/shj16108/hw5/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 | |
| 200316-05:03:41,302 nipype.workflow INFO: | |
| [Node] Cached "_std_tpms0" - collecting precomputed outputs | |
| 200316-05:03:41,302 nipype.workflow INFO: | |
| [Node] "_std_tpms0" found cached. | |
| 200316-05:03:41,303 nipype.workflow INFO: | |
| [Node] Setting-up "_std_tpms1" in "/gpfs/scratchfs1/shj16108/hw5/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/anat_norm_wf/_template_MNI152NLin2009cAsym./std_tpms/mapflow/_std_tpms1". | |
| 200316-05:03:41,304 nipype.workflow INFO: | |
| [Node] Cached "_std_tpms1" - collecting precomputed outputs | |
| 200316-05:03:41,304 nipype.workflow INFO: | |
| [Node] "_std_tpms1" found cached. | |
| 200316-05:03:41,305 nipype.workflow INFO: | |
| [Node] Setting-up "_std_tpms2" in "/gpfs/scratchfs1/shj16108/hw5/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/anat_norm_wf/_template_MNI152NLin2009cAsym./std_tpms/mapflow/_std_tpms2". | |
| 200316-05:03:41,306 nipype.workflow INFO: | |
| [Node] Cached "_std_tpms2" - collecting precomputed outputs | |
| 200316-05:03:41,306 nipype.workflow INFO: | |
| [Node] "_std_tpms2" found cached. | |
| 200316-05:03:41,309 nipype.workflow INFO: | |
| [Node] Finished "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.anat_norm_wf.std_tpms". | |
| 200316-05:03:41,349 nipype.workflow INFO: | |
| [Node] Running "tcompcor" ("niworkflows.interfaces.patches.RobustTCompCor") | |
| 200316-05:03:41,543 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". | |
| 200316-05:03:41,547 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". | |
| 200316-05:03:44,813 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". | |
| 200316-05:03:46,266 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/shj16108/hw5/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/bold_confounds_wf/csf_msk". | |
| 200316-05:03:46,267 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/shj16108/hw5/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/bold_confounds_wf/acc_msk". | |
| 200316-05:03:46,273 nipype.workflow INFO: | |
| [Node] Running "acc_msk" ("nipype.interfaces.utility.wrappers.Function") | |
| 200316-05:03:46,275 nipype.workflow INFO: | |
| [Node] Running "csf_msk" ("nipype.interfaces.utility.wrappers.Function") | |
| 200316-05:03:46,309 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". | |
| 200316-05:03:46,309 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". | |
| 200316-05:03:49,747 nipype.workflow INFO: | |
| [Node] Finished "fmriprep_wf.single_subject_01_wf.func_preproc_ses_01_task_Stroop_run_01_wf.bold_confounds_wf.tcompcor". | |
| 200316-05:03:50,367 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/shj16108/hw5/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/bold_confounds_wf/tcc_metadata_fmt". | |
| 200316-05:03:50,367 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/shj16108/hw5/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/bold_confounds_wf/signals". | |
| 200316-05:03:50,372 nipype.workflow INFO: | |
| [Node] Running "tcc_metadata_fmt" ("niworkflows.interfaces.utils.TSV2JSON") | |
| 200316-05:03:50,373 nipype.workflow INFO: | |
| [Node] Running "signals" ("niworkflows.interfaces.images.SignalExtraction") | |
| 200316-05:03:50,429 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". | |
| 200316-05:03:50,480 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/shj16108/hw5/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/bold_confounds_wf/acompcor". | |
| 200316-05:03:50,487 nipype.workflow INFO: | |
| [Node] Running "acompcor" ("niworkflows.interfaces.patches.RobustACompCor") | |
| 200316-05:03:52,378 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/shj16108/hw5/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/bold_confounds_wf/rois_plot". | |
| 200316-05:03:52,383 nipype.workflow INFO: | |
| [Node] Running "rois_plot" ("niworkflows.interfaces.masks.ROIsPlot") | |
| 200316-05:03:55,433 nipype.workflow INFO: | |
| [Node] Finished "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.anat_norm_wf.tpl_moving". | |
| 200316-05:03:55,604 nipype.workflow INFO: | |
| [Node] Finished "fmriprep_wf.single_subject_01_wf.func_preproc_ses_01_task_Stroop_run_01_wf.bold_confounds_wf.signals". | |
| 200316-05:04:00,413 nipype.workflow INFO: | |
| [Node] Finished "fmriprep_wf.single_subject_01_wf.func_preproc_ses_01_task_Stroop_run_01_wf.bold_confounds_wf.acompcor". | |
| 200316-05:04:00,670 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/shj16108/hw5/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/bold_confounds_wf/acc_metadata_fmt". | |
| 200316-05:04:00,674 nipype.workflow INFO: | |
| [Node] Running "acc_metadata_fmt" ("niworkflows.interfaces.utils.TSV2JSON") | |
| 200316-05:04:00,810 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". | |
| 200316-05:04:02,553 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/shj16108/hw5/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/bold_confounds_wf/compcor_plot". | |
| 200316-05:04:02,558 nipype.workflow INFO: | |
| [Node] Running "compcor_plot" ("niworkflows.interfaces.plotting.CompCorVariancePlot") | |
| 200316-05:04:02,915 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". | |
| 200316-05:04:03,368 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/shj16108/hw5/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/bold_confounds_wf/conf_corr_plot". | |
| 200316-05:04:03,368 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/shj16108/hw5/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/bold_confounds_wf/model_expansion". | |
| 200316-05:04:03,382 nipype.workflow INFO: | |
| [Node] Running "model_expansion" ("niworkflows.interfaces.confounds.ExpandModel") | |
| 200316-05:04:03,386 nipype.workflow INFO: | |
| [Node] Running "conf_corr_plot" ("niworkflows.interfaces.plotting.ConfoundsCorrelationPlot") | |
| 200316-05:04:03,513 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". | |
| 200316-05:04:03,839 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". | |
| 200316-05:04:05,564 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/shj16108/hw5/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/bold_confounds_wf/spike_regressors". | |
| 200316-05:04:05,568 nipype.workflow INFO: | |
| [Node] Running "spike_regressors" ("niworkflows.interfaces.confounds.SpikeRegressors") | |
| 200316-05:04:05,908 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". | |
| 200316-05:04:06,463 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". | |
| 200316-05:04:54,606 nipype.workflow INFO: | |
| [Node] Finished "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.anat_norm_wf.std_mask". | |
| 200316-05:04:57,207 nipype.workflow INFO: | |
| [Node] Setting-up "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.anat_reports_wf.norm_msk" in "/gpfs/scratchfs1/shj16108/hw5/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/anat_reports_wf/_template_MNI152NLin2009cAsym./norm_msk". | |
| 200316-05:04:57,224 nipype.workflow INFO: | |
| [Node] Running "norm_msk" ("nipype.interfaces.utility.wrappers.Function") | |
| 200316-05:04:58,329 nipype.workflow INFO: | |
| [Node] Finished "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.anat_reports_wf.norm_msk". | |
| 200316-05:04:58,610 nipype.workflow INFO: | |
| [Node] Setting-up "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.anat_reports_wf.norm_rpt" in "/gpfs/scratchfs1/shj16108/hw5/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/anat_reports_wf/_template_MNI152NLin2009cAsym./norm_rpt". | |
| 200316-05:04:58,617 nipype.workflow INFO: | |
| [Node] Running "norm_rpt" ("niworkflows.interfaces.registration.SimpleBeforeAfterRPT") | |
| 200316-05:05:01,198 nipype.workflow INFO: | |
| [Node] Finished "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.anat_norm_wf.std_dseg". | |
| 200316-05:05:02,627 nipype.workflow INFO: | |
| [Node] Setting-up "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.anat_derivatives_wf.lut_std_dseg" in "/gpfs/scratchfs1/shj16108/hw5/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/anat_derivatives_wf/_template_MNI152NLin2009cAsym./lut_std_dseg". | |
| 200316-05:05:02,628 nipype.workflow INFO: | |
| [Node] Setting-up "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.anat_norm_wf.outputnode" in "/gpfs/scratchfs1/shj16108/hw5/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/anat_norm_wf/outputnode". | |
| 200316-05:05:02,631 nipype.workflow INFO: | |
| [Node] Running "lut_std_dseg" ("nipype.interfaces.utility.wrappers.Function") | |
| 200316-05:05:02,636 nipype.workflow INFO: | |
| [Node] Running "outputnode" ("nipype.interfaces.utility.base.IdentityInterface") | |
| 200316-05:05:02,640 nipype.workflow INFO: | |
| [Node] Finished "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.anat_norm_wf.outputnode". | |
| 200316-05:05:02,853 nipype.workflow INFO: | |
| [Node] Finished "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.anat_derivatives_wf.lut_std_dseg". | |
| 200316-05:05:05,527 nipype.workflow INFO: | |
| [Node] Finished "fmriprep_wf.single_subject_01_wf.anat_preproc_wf.anat_reports_wf.norm_rpt". | |
| 200316-05:05:06,858 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/shj16108/hw5/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". | |
| 200316-05:05:07,852 nipype.workflow INFO: | |
| [Node] Running "bold_to_t1w_transform" ("niworkflows.interfaces.itk.MultiApplyTransforms") | |
| 200316-05:07:09,206 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". | |
| 200316-05:07:10,892 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/shj16108/hw5/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/bold_t1_trans_wf/merge". | |
| 200316-05:07:11,51 nipype.workflow INFO: | |
| [Node] Running "merge" ("niworkflows.interfaces.nilearn.Merge") | |
| 200316-05:07:11,265 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/shj16108/hw5/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/carpetplot_wf/mrg_xfms". | |
| 200316-05:07:11,276 nipype.workflow INFO: | |
| [Node] Running "mrg_xfms" ("nipype.interfaces.utility.base.Merge") | |
| 200316-05:07:11,279 nipype.workflow INFO: | |
| [Node] Finished "fmriprep_wf.single_subject_01_wf.func_preproc_ses_01_task_Stroop_run_01_wf.carpetplot_wf.mrg_xfms". | |
| 200316-05:07:12,889 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/shj16108/hw5/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". | |
| 200316-05:07:12,895 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/shj16108/hw5/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/carpetplot_wf/resample_parc". | |
| 200316-05:07:12,900 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/shj16108/.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/shj16108/hw5/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/shj16108/hw5/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/shj16108/hw5/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/anat_norm_wf/_template_MNI152NLin2009cAsym./registration/ants_t1_to_mniInverseComposite.h5 | |
| 200316-05:07:12,928 nipype.workflow INFO: | |
| [Node] Running "gen_ref" ("niworkflows.interfaces.utils.GenerateSamplingReference") | |
| 200316-05:07:13,205 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". | |
| 200316-05:07:14,888 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/shj16108/hw5/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". | |
| 200316-05:07:14,889 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/shj16108/hw5/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". | |
| 200316-05:07:14,889 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/shj16108/hw5/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". | |
| 200316-05:07:14,894 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/shj16108/hw5/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/shj16108/hw5/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/shj16108/hw5/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/shj16108/hw5/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 | |
| 200316-05:07:14,899 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/shj16108/hw5/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/shj16108/hw5/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/shj16108/hw5/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/anat_norm_wf/_template_MNI152NLin2009cAsym./registration/ants_t1_to_mniComposite.h5 | |
| 200316-05:07:14,900 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/shj16108/hw5/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/shj16108/hw5/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/shj16108/hw5/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/anat_norm_wf/_template_MNI152NLin2009cAsym./registration/ants_t1_to_mniComposite.h5 | |
| 200316-05:07:18,477 nipype.workflow INFO: | |
| [Node] Finished "fmriprep_wf.single_subject_01_wf.func_preproc_ses_01_task_Stroop_run_01_wf.carpetplot_wf.resample_parc". | |
| 200316-05:07:18,903 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/shj16108/hw5/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/carpetplot_wf/conf_plot". | |
| 200316-05:07:18,923 nipype.workflow INFO: | |
| [Node] Running "conf_plot" ("fmriprep.interfaces.confounds.FMRISummary") | |
| 200316-05:07:22,687 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". | |
| 200316-05:07:23,149 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/shj16108/hw5/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". | |
| 200316-05:07:23,161 nipype.workflow INFO: | |
| [Node] Running "pre_mask_dilate" ("nipype.interfaces.fsl.maths.DilateImage"), a CommandLine Interface with command: | |
| fslmaths -dt char /gpfs/scratchfs1/shj16108/hw5/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/shj16108/hw5/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 | |
| 200316-05:07:23,658 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". | |
| 200316-05:07:23,822 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". | |
| 200316-05:07:23,948 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". | |
| 200316-05:07:26,130 nipype.workflow INFO: | |
| [Node] Finished "fmriprep_wf.single_subject_01_wf.func_preproc_ses_01_task_Stroop_run_01_wf.carpetplot_wf.conf_plot". | |
| 200316-05:07:55,287 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". | |
| 200316-05:07:56,921 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/shj16108/hw5/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/bold_surf_wf/resampling_xfm". | |
| 200316-05:07:56,944 nipype.workflow INFO: | |
| [Node] Running "resampling_xfm" ("niworkflows.interfaces.freesurfer.PatchedLTAConvert"), a CommandLine Interface with command: | |
| lta_convert --inlta identity.nofile --outlta /gpfs/scratchfs1/shj16108/hw5/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/shj16108/hw5/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/shj16108/hw5/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 | |
| 200316-05:07:57,60 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/shj16108/hw5/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". | |
| 200316-05:07:57,65 nipype.workflow INFO: | |
| [Node] Running "validate" ("niworkflows.interfaces.images.ValidateImage") | |
| 200316-05:07:57,68 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". | |
| 200316-05:07:57,71 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". | |
| 200316-05:07:58,925 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/shj16108/hw5/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". | |
| 200316-05:07:58,925 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/shj16108/hw5/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/bold_surf_wf/set_xfm_source". | |
| 200316-05:07:58,928 nipype.workflow INFO: | |
| [Node] Running "gen_ref" ("niworkflows.interfaces.registration.EstimateReferenceImage") | |
| 200316-05:07:58,933 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/shj16108/hw5/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/shj16108/hw5/hw5/work/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/surface_recon_wf/t1w2fsnative_xfm/out.lta out_concat.lta | |
| 200316-05:07:59,17 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". | |
| 200316-05:07:59,191 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". | |
| 200316-05:08:00,954 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/shj16108/hw5/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/bold_surf_wf/_hemi_rh/sampler". | |
| 200316-05:08:00,958 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/shj16108/hw5/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/bold_surf_wf/_hemi_lh/sampler". | |
| 200316-05:08:00,961 nipype.workflow INFO: | |
| [Node] Setting-up "_sampler0" in "/gpfs/scratchfs1/shj16108/hw5/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". | |
| 200316-05:08:00,965 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/shj16108/hw5/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/shj16108/hw5/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/shj16108/hw5/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 | |
| 200316-05:08:00,965 nipype.workflow INFO: | |
| [Node] Setting-up "_sampler0" in "/gpfs/scratchfs1/shj16108/hw5/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". | |
| 200316-05:08:00,970 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/shj16108/hw5/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/shj16108/hw5/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/shj16108/hw5/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 | |
| 200316-05:08:02,935 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.n4_correct" in "/gpfs/scratchfs1/shj16108/hw5/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/n4_correct". | |
| 200316-05:08:02,978 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/shj16108/hw5/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/n4_correct/ref_bold_scaled.nii.gz --mask-image /gpfs/scratchfs1/shj16108/hw5/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/check_hdr/ref_sbref_corrected_trans_corrected_brain_mask_maths_trans_dil_hdr.nii.gz --output ref_bold_corrected.nii.gz -r | |
| 200316-05:08:06,245 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.n4_correct". | |
| 200316-05:08:06,938 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.skullstrip_first_pass" in "/gpfs/scratchfs1/shj16108/hw5/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/skullstrip_first_pass". | |
| 200316-05:08:06,944 nipype.workflow INFO: | |
| [Node] Running "skullstrip_first_pass" ("nipype.interfaces.fsl.preprocess.BET"), a CommandLine Interface with command: | |
| bet /gpfs/scratchfs1/shj16108/hw5/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/n4_correct/ref_bold_corrected.nii.gz /gpfs/scratchfs1/shj16108/hw5/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/skullstrip_first_pass/ref_bold_corrected_brain.nii.gz -f 0.20 -m | |
| 200316-05:08:08,428 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.skullstrip_first_pass". | |
| 200316-05:08:08,941 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.skullstrip_first_dilate" in "/gpfs/scratchfs1/shj16108/hw5/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/skullstrip_first_dilate". | |
| 200316-05:08:08,948 nipype.workflow INFO: | |
| [Node] Running "skullstrip_first_dilate" ("nipype.interfaces.fsl.maths.DilateImage"), a CommandLine Interface with command: | |
| fslmaths -dt char /gpfs/scratchfs1/shj16108/hw5/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/skullstrip_first_pass/ref_bold_corrected_brain_mask.nii.gz -kernel sphere 6.0000 -dilF /gpfs/scratchfs1/shj16108/hw5/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/skullstrip_first_dilate/ref_bold_corrected_brain_mask_dil.nii.gz | |
| 200316-05:08:10,26 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.skullstrip_first_dilate". | |
| 200316-05:08:10,943 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.skullstrip_first_mask" in "/gpfs/scratchfs1/shj16108/hw5/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/skullstrip_first_mask". | |
| 200316-05:08:10,948 nipype.workflow INFO: | |
| [Node] Running "skullstrip_first_mask" ("nipype.interfaces.fsl.maths.ApplyMask"), a CommandLine Interface with command: | |
| fslmaths /gpfs/scratchfs1/shj16108/hw5/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/skullstrip_first_pass/ref_bold_corrected_brain.nii.gz -mas /gpfs/scratchfs1/shj16108/hw5/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/skullstrip_first_dilate/ref_bold_corrected_brain_mask_dil.nii.gz /gpfs/scratchfs1/shj16108/hw5/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/skullstrip_first_mask/ref_bold_corrected_brain_masked.nii.gz | |
| 200316-05:08:11,63 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.skullstrip_first_mask". | |
| 200316-05:08:12,944 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.unifize" in "/gpfs/scratchfs1/shj16108/hw5/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/unifize". | |
| 200316-05:08:12,949 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/shj16108/hw5/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/unifize/ref_bold_corrected_brain_masked.nii.gz | |
| 200316-05:08:15,349 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.unifize". | |
| 200316-05:08:16,948 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.fixhdr_unifize" in "/gpfs/scratchfs1/shj16108/hw5/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/fixhdr_unifize". | |
| 200316-05:08:16,954 nipype.workflow INFO: | |
| [Node] Running "fixhdr_unifize" ("niworkflows.interfaces.utils.CopyXForm") | |
| 200316-05:08:17,10 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.fixhdr_unifize". | |
| 200316-05:08:18,950 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.skullstrip_second_pass" in "/gpfs/scratchfs1/shj16108/hw5/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/skullstrip_second_pass". | |
| 200316-05:08:18,954 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/shj16108/hw5/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/skullstrip_second_pass/uni_xform.nii.gz | |
| 200316-05:08:19,128 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.skullstrip_second_pass". | |
| 200316-05:08:20,952 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.fixhdr_skullstrip2" in "/gpfs/scratchfs1/shj16108/hw5/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/fixhdr_skullstrip2". | |
| 200316-05:08:20,956 nipype.workflow INFO: | |
| [Node] Running "fixhdr_skullstrip2" ("niworkflows.interfaces.utils.CopyXForm") | |
| 200316-05:08:20,975 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.fixhdr_skullstrip2". | |
| 200316-05:08:22,953 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.combine_masks" in "/gpfs/scratchfs1/shj16108/hw5/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/combine_masks". | |
| 200316-05:08:22,960 nipype.workflow INFO: | |
| [Node] Running "combine_masks" ("nipype.interfaces.fsl.maths.BinaryMaths"), a CommandLine Interface with command: | |
| fslmaths /gpfs/scratchfs1/shj16108/hw5/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/skullstrip_first_pass/ref_bold_corrected_brain_mask.nii.gz -mul /gpfs/scratchfs1/shj16108/hw5/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/fixhdr_skullstrip2/uni_xform_mask_xform.nii.gz /gpfs/scratchfs1/shj16108/hw5/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/combine_masks/ref_bold_corrected_brain_mask_maths.nii.gz | |
| 200316-05:08:23,57 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.combine_masks". | |
| 200316-05:08:24,957 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.apply_mask" in "/gpfs/scratchfs1/shj16108/hw5/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/apply_mask". | |
| 200316-05:08:24,965 nipype.workflow INFO: | |
| [Node] Running "apply_mask" ("nipype.interfaces.fsl.maths.ApplyMask"), a CommandLine Interface with command: | |
| fslmaths /gpfs/scratchfs1/shj16108/hw5/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/fixhdr_unifize/uni_xform.nii.gz -mas /gpfs/scratchfs1/shj16108/hw5/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/combine_masks/ref_bold_corrected_brain_mask_maths.nii.gz /gpfs/scratchfs1/shj16108/hw5/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/apply_mask/uni_xform_masked.nii.gz | |
| 200316-05:08:25,81 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.apply_mask". | |
| 200316-05:09:33,926 nipype.workflow INFO: | |
| [Node] Finished "_sampler0". | |
| 200316-05:09:33,930 nipype.workflow INFO: | |
| [Node] Finished "fmriprep_wf.single_subject_01_wf.func_preproc_ses_01_task_Stroop_run_01_wf.bold_surf_wf.sampler". | |
| 200316-05:09:39,860 nipype.workflow INFO: | |
| [Node] Finished "_sampler0". | |
| 200316-05:09:39,862 nipype.workflow INFO: | |
| [Node] Finished "fmriprep_wf.single_subject_01_wf.func_preproc_ses_01_task_Stroop_run_01_wf.bold_surf_wf.sampler". | |
| 200316-05:09:41,128 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_to_std_transform" in "/gpfs/scratchfs1/shj16108/hw5/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/bold_std_trans_wf/_key_MNI152NLin2009cAsym/bold_to_std_transform". | |
| 200316-05:09:41,235 nipype.workflow INFO: | |
| [Node] Running "bold_to_std_transform" ("niworkflows.interfaces.itk.MultiApplyTransforms") | |
| 200316-05:14:05,640 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_to_std_transform". | |
| 200316-05:14:07,311 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.merge" in "/gpfs/scratchfs1/shj16108/hw5/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/bold_std_trans_wf/_key_MNI152NLin2009cAsym/merge". | |
| 200316-05:14:07,403 nipype.workflow INFO: | |
| [Node] Running "merge" ("niworkflows.interfaces.nilearn.Merge") | |
| 200316-05:14:09,294 nipype.workflow INFO: | |
| [Node] Setting-up "_update_metadata0" in "/gpfs/scratchfs1/shj16108/hw5/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/bold_surf_wf/update_metadata/mapflow/_update_metadata0". | |
| 200316-05:14:09,295 nipype.workflow INFO: | |
| [Node] Setting-up "_update_metadata1" in "/gpfs/scratchfs1/shj16108/hw5/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/bold_surf_wf/update_metadata/mapflow/_update_metadata1". | |
| 200316-05:14:09,299 nipype.workflow INFO: | |
| [Node] Running "_update_metadata1" ("niworkflows.interfaces.surf.GiftiSetAnatomicalStructure") | |
| 200316-05:14:09,299 nipype.workflow INFO: | |
| [Node] Running "_update_metadata0" ("niworkflows.interfaces.surf.GiftiSetAnatomicalStructure") | |
| 200316-05:14:10,517 nipype.workflow INFO: | |
| [Node] Finished "_update_metadata0". | |
| 200316-05:14:10,562 nipype.workflow INFO: | |
| [Node] Finished "_update_metadata1". | |
| 200316-05:14:11,299 nipype.workflow INFO: | |
| [Node] Setting-up "fmriprep_wf.single_subject_01_wf.func_preproc_ses_01_task_Stroop_run_01_wf.bold_surf_wf.update_metadata" in "/gpfs/scratchfs1/shj16108/hw5/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/bold_surf_wf/update_metadata". | |
| 200316-05:14:11,315 nipype.workflow INFO: | |
| [Node] Setting-up "_update_metadata0" in "/gpfs/scratchfs1/shj16108/hw5/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/bold_surf_wf/update_metadata/mapflow/_update_metadata0". | |
| 200316-05:14:11,316 nipype.workflow INFO: | |
| [Node] Cached "_update_metadata0" - collecting precomputed outputs | |
| 200316-05:14:11,316 nipype.workflow INFO: | |
| [Node] "_update_metadata0" found cached. | |
| 200316-05:14:11,317 nipype.workflow INFO: | |
| [Node] Setting-up "_update_metadata1" in "/gpfs/scratchfs1/shj16108/hw5/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/bold_surf_wf/update_metadata/mapflow/_update_metadata1". | |
| 200316-05:14:11,317 nipype.workflow INFO: | |
| [Node] Cached "_update_metadata1" - collecting precomputed outputs | |
| 200316-05:14:11,317 nipype.workflow INFO: | |
| [Node] "_update_metadata1" found cached. | |
| 200316-05:14:11,319 nipype.workflow INFO: | |
| [Node] Finished "fmriprep_wf.single_subject_01_wf.func_preproc_ses_01_task_Stroop_run_01_wf.bold_surf_wf.update_metadata". | |
| 200316-05:15:46,89 nipype.workflow INFO: | |
| [Node] Finished "fmriprep_wf.single_subject_01_wf.func_preproc_ses_01_task_Stroop_run_01_wf.bold_std_trans_wf.merge". | |
| 200316-05:16:41,695 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.validate" in "/gpfs/scratchfs1/shj16108/hw5/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/bold_std_trans_wf/bold_reference_wf/_key_MNI152NLin2009cAsym/validate". | |
| 200316-05:16:41,706 nipype.workflow INFO: | |
| [Node] Running "validate" ("niworkflows.interfaces.images.ValidateImage") | |
| 200316-05:16:41,725 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.validate". | |
| 200316-05:16:43,792 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.gen_ref" in "/gpfs/scratchfs1/shj16108/hw5/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/bold_std_trans_wf/bold_reference_wf/_key_MNI152NLin2009cAsym/gen_ref". | |
| 200316-05:16:43,795 nipype.workflow INFO: | |
| [Node] Running "gen_ref" ("niworkflows.interfaces.registration.EstimateReferenceImage") | |
| 200316-05:16:44,909 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.gen_ref". | |
| 200316-05:16:47,794 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.n4_correct" in "/gpfs/scratchfs1/shj16108/hw5/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/n4_correct". | |
| 200316-05:16:47,873 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/shj16108/hw5/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/n4_correct/ref_bold_scaled.nii.gz --mask-image /gpfs/scratchfs1/shj16108/hw5/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/check_hdr/ref_bold_corrected_brain_mask_maths_trans_dil_hdr.nii.gz --output ref_bold_corrected.nii.gz -r | |
| 200316-05:16:52,531 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.n4_correct". | |
| 200316-05:16:53,807 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.outputnode" in "/gpfs/scratchfs1/shj16108/hw5/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/bold_std_trans_wf/outputnode". | |
| 200316-05:16:53,824 nipype.workflow INFO: | |
| [Node] Running "outputnode" ("nipype.interfaces.utility.base.IdentityInterface") | |
| 200316-05:16:53,827 nipype.workflow INFO: | |
| [Node] Finished "fmriprep_wf.single_subject_01_wf.func_preproc_ses_01_task_Stroop_run_01_wf.bold_std_trans_wf.outputnode". | |
| 200316-05:16:54,149 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.skullstrip_first_pass" in "/gpfs/scratchfs1/shj16108/hw5/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/skullstrip_first_pass". | |
| 200316-05:16:54,153 nipype.workflow INFO: | |
| [Node] Running "skullstrip_first_pass" ("nipype.interfaces.fsl.preprocess.BET"), a CommandLine Interface with command: | |
| bet /gpfs/scratchfs1/shj16108/hw5/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/n4_correct/ref_bold_corrected.nii.gz /gpfs/scratchfs1/shj16108/hw5/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/skullstrip_first_pass/ref_bold_corrected_brain.nii.gz -f 0.20 -m | |
| 200316-05:16:55,582 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.skullstrip_first_pass". | |
| 200316-05:16:55,908 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.skullstrip_first_dilate" in "/gpfs/scratchfs1/shj16108/hw5/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/skullstrip_first_dilate". | |
| 200316-05:16:55,912 nipype.workflow INFO: | |
| [Node] Running "skullstrip_first_dilate" ("nipype.interfaces.fsl.maths.DilateImage"), a CommandLine Interface with command: | |
| fslmaths -dt char /gpfs/scratchfs1/shj16108/hw5/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/skullstrip_first_pass/ref_bold_corrected_brain_mask.nii.gz -kernel sphere 6.0000 -dilF /gpfs/scratchfs1/shj16108/hw5/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/skullstrip_first_dilate/ref_bold_corrected_brain_mask_dil.nii.gz | |
| 200316-05:16:57,815 nipype.workflow INFO: | |
| [Node] Setting-up "fmriprep_wf.single_subject_01_wf.func_preproc_ses_01_task_Stroop_run_01_wf.gen_cifti" in "/gpfs/scratchfs1/shj16108/hw5/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/gen_cifti". | |
| 200316-05:16:57,819 nipype.workflow INFO: | |
| [Node] Setting-up "_gen_cifti0" in "/gpfs/scratchfs1/shj16108/hw5/hw5/work/fmriprep_wf/single_subject_01_wf/func_preproc_ses_01_task_Stroop_run_01_wf/gen_cifti/mapflow/_gen_cifti0". | |
| 200316-05:16:57,822 nipype.workflow INFO: | |
| [Node] Running "_gen_cifti0" ("niworkflows.interfaces.cifti.GenerateCifti") | |
| 200316-05:16:58,452 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.skullstrip_first_dilate". | |
| 200316-05:16:59,820 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.skullstrip_first_mask" in "/gpfs/scratchfs1/shj16108/hw5/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/skullstrip_first_mask". | |
| 200316-05:16:59,824 nipype.workflow INFO: | |
| [Node] Running "skullstrip_first_mask" ("nipype.interfaces.fsl.maths.ApplyMask"), a CommandLine Interface with command: | |
| fslmaths /gpfs/scratchfs1/shj16108/hw5/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/skullstrip_first_pass/ref_bold_corrected_brain.nii.gz -mas /gpfs/scratchfs1/shj16108/hw5/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/skullstrip_first_dilate/ref_bold_corrected_brain_mask_dil.nii.gz /gpfs/scratchfs1/shj16108/hw5/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/skullstrip_first_mask/ref_bold_corrected_brain_masked.nii.gz | |
| 200316-05:16:59,967 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.skullstrip_first_mask". | |
| 200316-05:17:01,829 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.unifize" in "/gpfs/scratchfs1/shj16108/hw5/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/unifize". | |
| 200316-05:17:01,838 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/shj16108/hw5/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/unifize/ref_bold_corrected_brain_masked.nii.gz | |
| 200316-05:17:05,931 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.unifize". | |
| 200316-05:17:07,822 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.fixhdr_unifize" in "/gpfs/scratchfs1/shj16108/hw5/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/fixhdr_unifize". | |
| 200316-05:17:07,845 nipype.workflow INFO: | |
| [Node] Running "fixhdr_unifize" ("niworkflows.interfaces.utils.CopyXForm") | |
| 200316-05:17:07,924 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.fixhdr_unifize". | |
| 200316-05:17:09,824 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.skullstrip_second_pass" in "/gpfs/scratchfs1/shj16108/hw5/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/skullstrip_second_pass". | |
| 200316-05:17:09,830 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/shj16108/hw5/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/skullstrip_second_pass/uni_xform.nii.gz | |
| 200316-05:17:10,80 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.skullstrip_second_pass". | |
| 200316-05:17:11,826 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.fixhdr_skullstrip2" in "/gpfs/scratchfs1/shj16108/hw5/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/fixhdr_skullstrip2". | |
| 200316-05:17:11,835 nipype.workflow INFO: | |
| [Node] Running "fixhdr_skullstrip2" ("niworkflows.interfaces.utils.CopyXForm") | |
| 200316-05:17:11,866 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.fixhdr_skullstrip2". | |
| 200316-05:17:13,831 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.combine_masks" in "/gpfs/scratchfs1/shj16108/hw5/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/combine_masks". | |
| 200316-05:17:13,838 nipype.workflow INFO: | |
| [Node] Running "combine_masks" ("nipype.interfaces.fsl.maths.BinaryMaths"), a CommandLine Interface with command: | |
| fslmaths /gpfs/scratchfs1/shj16108/hw5/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/skullstrip_first_pass/ref_bold_corrected_brain_mask.nii.gz -mul /gpfs/scratchfs1/shj16108/hw5/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/fixhdr_skullstrip2/uni_xform_mask_xform.nii.gz /gpfs/scratchfs1/shj16108/hw5/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/combine_masks/ref_bold_corrected_brain_mask_maths.nii.gz | |
| 200316-05:17:13,961 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.combine_masks". | |
| 200316-05:17:15,830 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.apply_mask" in "/gpfs/scratchfs1/shj16108/hw5/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/apply_mask". | |
| 200316-05:17:15,837 nipype.workflow INFO: | |
| [Node] Running "apply_mask" ("nipype.interfaces.fsl.maths.ApplyMask"), a CommandLine Interface with command: | |
| fslmaths /gpfs/scratchfs1/shj16108/hw5/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/fixhdr_unifize/uni_xform.nii.gz -mas /gpfs/scratchfs1/shj16108/hw5/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/combine_masks/ref_bold_corrected_brain_mask_maths.nii.gz /gpfs/scratchfs1/shj16108/hw5/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/apply_mask/uni_xform_masked.nii.gz | |
| 200316-05:17:15,989 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.apply_mask". | |
| 200316-05:20:14,803 nipype.workflow INFO: | |
| [Node] Finished "_gen_cifti0". | |
| 200316-05:20:14,805 nipype.workflow INFO: | |
| [Node] Finished "fmriprep_wf.single_subject_01_wf.func_preproc_ses_01_task_Stroop_run_01_wf.gen_cifti". |