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nipreps / fmriprep

fMRIPrep is a robust and easy-to-use pipeline for preprocessing of diverse fMRI data. The transparent workflow dispenses of manual intervention, thereby ensuring the reproducibility of the results.
https://fmriprep.org
Apache License 2.0
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fmriprep-docker hanging with no output or error #2353

Closed xingyu-liu closed 1 year ago

xingyu-liu commented 3 years ago

Hi,

I'm using fMRIPrep to run both the anat and func preprocessing. I tested first with sub-01 and it worked just perfect. But I came into a problem when I tried to run all sub. After several days of running, it now stuck with something I don't know, and no response in terminal window or output dir or work dir since 2020-12-21 15:24:19 (now 2020-12-23 17:06:06). And the container is not consuming CPU or memory any more.

I can not be sure, but I guess it already passed the long anat preproc period including surface recon and should be running the func preproc part.

I'm using Docker installation (v20.10.0) on Windows

The command was:

fmriprep-docker Z:\server_temp\gump_MEG\mri_bids Z:\server_temp\gump_MEG\mri_bids_fmriprep_output participant --output-spaces MNI152NLin2009cAsym fsaverage --task-id rest --use-aroma --skull-strip-t1w force -w Z:\server_temp\gump_MEG\mri_bids_fmriprep_work --fs-license-file Z:\virtual_hard_disk\license.txt --output-layout bids

The latest log showed in the docker window were:

201221-05:20:01,457 nipype.workflow INFO:
     [Node] Finished "fmriprep_wf.single_subject_05_wf.func_preproc_ses_movie_task_rest_wf.bold_std_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.fixhdr_skullstrip2".
201221-05:20:03,114 nipype.workflow INFO:
     [Node] Setting-up "fmriprep_wf.single_subject_05_wf.func_preproc_ses_movie_task_rest_wf.bold_std_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.combine_masks" in "/scratch/fmriprep_wf/single_subject_05_wf/func_preproc_ses_movie_task_rest_wf/bold_std_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/_std_target_MNI152NLin2009cAsym.resnative/combine_masks".
201221-05:20:03,336 nipype.workflow INFO:
     [Node] Running "combine_masks" ("nipype.interfaces.fsl.maths.BinaryMaths"), a CommandLine Interface with command:
fslmaths /scratch/fmriprep_wf/single_subject_05_wf/func_preproc_ses_movie_task_rest_wf/bold_std_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/_std_target_MNI152NLin2009cAsym.resnative/skullstrip_first_pass/ref_bold_corrected_brain_mask.nii.gz -mul /scratch/fmriprep_wf/single_subject_05_wf/func_preproc_ses_movie_task_rest_wf/bold_std_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/_std_target_MNI152NLin2009cAsym.resnative/fixhdr_skullstrip2/uni_xform_mask_xform.nii.gz /scratch/fmriprep_wf/single_subject_05_wf/func_preproc_ses_movie_task_rest_wf/bold_std_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/_std_target_MNI152NLin2009cAsym.resnative/combine_masks/ref_bold_corrected_brain_mask_maths.nii.gz
201221-05:20:03,700 nipype.workflow INFO:
     [Node] Finished "fmriprep_wf.single_subject_05_wf.func_preproc_ses_movie_task_rest_wf.bold_std_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.combine_masks".
201221-05:20:05,118 nipype.workflow INFO:
     [Node] Setting-up "fmriprep_wf.single_subject_05_wf.func_preproc_ses_movie_task_rest_wf.bold_std_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.apply_mask" in "/scratch/fmriprep_wf/single_subject_05_wf/func_preproc_ses_movie_task_rest_wf/bold_std_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/_std_target_MNI152NLin2009cAsym.resnative/apply_mask".
201221-05:20:05,317 nipype.workflow INFO:
     [Node] Running "apply_mask" ("nipype.interfaces.fsl.maths.ApplyMask"), a CommandLine Interface with command:
fslmaths /scratch/fmriprep_wf/single_subject_05_wf/func_preproc_ses_movie_task_rest_wf/bold_std_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/_std_target_MNI152NLin2009cAsym.resnative/fixhdr_unifize/uni_xform.nii.gz -mas /scratch/fmriprep_wf/single_subject_05_wf/func_preproc_ses_movie_task_rest_wf/bold_std_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/_std_target_MNI152NLin2009cAsym.resnative/combine_masks/ref_bold_corrected_brain_mask_maths.nii.gz /scratch/fmriprep_wf/single_subject_05_wf/func_preproc_ses_movie_task_rest_wf/bold_std_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/_std_target_MNI152NLin2009cAsym.resnative/apply_mask/uni_xform_masked.nii.gz
201221-05:20:05,706 nipype.workflow INFO:
     [Node] Finished "fmriprep_wf.single_subject_05_wf.func_preproc_ses_movie_task_rest_wf.bold_std_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.apply_mask".
201221-05:20:13,203 nipype.workflow INFO:
     [Node] Finished "_sampler1".
201221-05:20:14,994 nipype.workflow INFO:
     [Node] Setting-up "fmriprep_wf.single_subject_05_wf.func_preproc_ses_movie_task_rest_wf.bold_surf_wf.sampler" in "/scratch/fmriprep_wf/single_subject_05_wf/func_preproc_ses_movie_task_rest_wf/bold_surf_wf/_target_fsaverage/sampler".
201221-05:20:15,153 nipype.workflow INFO:
     [Node] Setting-up "_sampler0" in "/scratch/fmriprep_wf/single_subject_05_wf/func_preproc_ses_movie_task_rest_wf/bold_surf_wf/_target_fsaverage/sampler/mapflow/_sampler0".
201221-05:20:15,210 nipype.workflow INFO:
     [Node] Cached "_sampler0" - collecting precomputed outputs

It seems that the docker window stopped to update the log then. Because I cheched the output of sub-05, I believe the preproc was finished. All sub larger than sub-<05> all have the same output see below, while the func images of sub-04 to sub-01 have not been proprocessed. And the latest modified files were all concerning sub-04. 

sub-05_ses-movie_task-rest_AROMAnoiseICs.csv
sub-05_ses-movie_task-rest_desc-confounds_timeseries.json
sub-05_ses-movie_task-rest_desc-confounds_timeseries.tsv
sub-05_ses-movie_task-rest_desc-MELODIC_mixing.tsv
sub-05_ses-movie_task-rest_from-scanner_to-T1w_mode-image_xfm.txt
sub-05_ses-movie_task-rest_from-T1w_to-scanner_mode-image_xfm.txt
sub-05_ses-movie_task-rest_space-fsaverage_hemi-L_bold.func.gii
sub-05_ses-movie_task-rest_space-fsaverage_hemi-L_bold.json
sub-05_ses-movie_task-rest_space-fsaverage_hemi-R_bold.func.gii
sub-05_ses-movie_task-rest_space-fsaverage_hemi-R_bold.json
sub-05_ses-movie_task-rest_space-MNI152NLin2009cAsym_boldref.nii.gz
sub-05_ses-movie_task-rest_space-MNI152NLin2009cAsym_desc-aparcaseg_dseg.nii.gz
sub-05_ses-movie_task-rest_space-MNI152NLin2009cAsym_desc-aseg_dseg.nii.gz
sub-05_ses-movie_task-rest_space-MNI152NLin2009cAsym_desc-brain_mask.json
sub-05_ses-movie_task-rest_space-MNI152NLin2009cAsym_desc-brain_mask.nii.gz
sub-05_ses-movie_task-rest_space-MNI152NLin2009cAsym_desc-preproc_bold.json
sub-05_ses-movie_task-rest_space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz
sub-05_ses-movie_task-rest_space-MNI152NLin6Asym_desc-smoothAROMAnonaggr_bold.json
sub-05_ses-movie_task-rest_space-MNI152NLin6Asym_desc-smoothAROMAnonaggr_bold.nii.gz

The 5 latest modified files in the output dir were:

2020-12-21 14:07:11.6909885000 ./sub-04/figures/sub-04_ses-movie_task-rest_desc-rois_bold.svg
2020-12-21 14:07:19.1995497000 ./sub-04/figures/sub-04_ses-movie_task-rest_desc-compcorvar_bold.svg
2020-12-21 14:07:23.6740945000 ./sub-04/figures/sub-04_ses-movie_task-rest_desc-confoundcorr_bold.svg
2020-12-21 14:20:42.8340335000 ./sourcedata/freesurfer/sub-04/surf/lh.midthickness
2020-12-21 14:20:43.7460521000 ./sourcedata/freesurfer/sub-04/surf/rh.midthickness

I cheched the recon-all.log for all the subs (the latest finished one was sub-04) and the last line in recon-all.log all said: recon-all -s sub-04 finished without error at Mon Dec 21 06:03:32 UTC 2020

The 5 latest modified files in the work dir were:

2020-12-21 14:23:59.7182659000 ./fmriprep_wf/single_subject_04_wf/anat_preproc_wf/anat_norm_wf/_template_MNI152NLin2009cAsym/registration/command.txt
2020-12-21 15:24:01.0129393000 ./fmriprep_wf/single_subject_04_wf/anat_preproc_wf/anat_norm_wf/_template_MNI152NLin2009cAsym/registration/ants_t1_to_mniComposite.h5
2020-12-21 15:24:05.3209425000 ./fmriprep_wf/single_subject_04_wf/anat_preproc_wf/anat_norm_wf/_template_MNI152NLin2009cAsym/registration/ants_t1_to_mniInverseComposite.h5
2020-12-21 15:24:19.1499344000 ./fmriprep_wf/single_subject_04_wf/anat_preproc_wf/anat_norm_wf/_template_MNI152NLin2009cAsym/registration/result_registration.pklz
2020-12-21 15:24:19.1759348000 ./fmriprep_wf/single_subject_04_wf/anat_preproc_wf/anat_norm_wf/_template_MNI152NLin2009cAsym/registration/_report/report.rst

I also checked that there was enough disk space.

Should I just wait cause there is no error popped, or something might be wrong and I need to terminate it?

Thank you very much for your advices and help!

Xingyu

oesteban commented 3 years ago

Hi @xingyu-liu, yeah, everything looks okay. Could you post the full log?

xingyu-liu commented 3 years ago

Hi @oesteban, I'm using the windows docker, and I can't find the full log of fmriprep, could you enlighen me a bit?

A weird update. The log in the docker interface suddenly restarted to record on the 12-31 , 10 days after the cease on the 12-21.

201221-05:20:15,210 nipype.workflow INFO:
     [Node] Cached "_sampler0" - collecting precomputed outputs
201221-05:20:15,210 nipype.workflow INFO:
     [Node] "_sampler0" found cached.
201221-05:20:15,244 nipype.workflow INFO:
     [Node] Setting-up "_sampler1" in "/scratch/fmriprep_wf/single_subject_05_wf/func_preproc_ses_movie_task_rest_wf/bold_surf_wf/_target_fsaverage/sampler/mapflow/_sampler1".
201221-05:20:15,302 nipype.workflow INFO:
     [Node] Cached "_sampler1" - collecting precomputed outputs
201221-05:20:15,302 nipype.workflow INFO:
     [Node] "_sampler1" found cached.
201221-05:20:15,338 nipype.workflow INFO:
     [Node] Finished "fmriprep_wf.single_subject_05_wf.func_preproc_ses_movie_task_rest_wf.bold_surf_wf.sampler".
201221-05:20:17,176 nipype.workflow INFO:
     [Node] Setting-up "_parcstats0" in "/scratch/fmriprep_wf/single_subject_04_wf/anat_preproc_wf/surface_recon_wf/autorecon_resume_wf/parcstats/mapflow/_parcstats0".
201221-05:20:17,672 nipype.interface INFO:
     resume recon-all : recon-all -autorecon-hemi lh -nohyporelabel -openmp 3 -subjid sub-04 -sd /out/sourcedata/freesurfer -notessellate -nosmooth1 -noinflate1 -noqsphere -nofix -nowhite -nosmooth2 -noinflate2 -nocurvHK -nocurvstats -nosphere -nosurfreg -nojacobian_white -noavgcurv -nocortparc -nopial -nocortparc2 -nocortparc3 -nopctsurfcon
201221-05:20:17,684 nipype.workflow INFO:
     [Node] Running "_parcstats0" ("smriprep.interfaces.freesurfer.ReconAll"), a CommandLine Interface with command:
recon-all -autorecon-hemi lh -nohyporelabel -openmp 3 -subjid sub-04 -sd /out/sourcedata/freesurfer -notessellate -nosmooth1 -noinflate1 -noqsphere -nofix -nowhite -nosmooth2 -noinflate2 -nocurvHK -nocurvstats -nosphere -nosurfreg -nojacobian_white -noavgcurv -nocortparc -nopial -nocortparc2 -nocortparc3 -nopctsurfcon
201221-05:20:17,823 nipype.interface INFO:
     resume recon-all : recon-all -autorecon-hemi lh -nohyporelabel -openmp 3 -subjid sub-04 -sd /out/sourcedata/freesurfer -notessellate -nosmooth1 -noinflate1 -noqsphere -nofix -nowhite -nosmooth2 -noinflate2 -nocurvHK -nocurvstats -nosphere -nosurfreg -nojacobian_white -noavgcurv -nocortparc -nopial -nocortparc2 -nocortparc3 -nopctsurfcon
201221-05:20:34,232 nipype.workflow INFO:
     [Node] Finished "fmriprep_wf.single_subject_05_wf.func_preproc_ses_movie_task_rest_wf.ica_aroma_wf.rm_nonsteady".
201221-05:20:35,1 nipype.workflow INFO:
     [Node] Setting-up "fmriprep_wf.single_subject_05_wf.func_preproc_ses_movie_task_rest_wf.ica_aroma_wf.calc_bold_mean" in "/scratch/fmriprep_wf/single_subject_05_wf/func_preproc_ses_movie_task_rest_wf/ica_aroma_wf/calc_bold_mean".
201221-05:20:35,176 nipype.workflow INFO:
     [Node] Running "calc_bold_mean" ("nipype.interfaces.fsl.maths.MeanImage"), a CommandLine Interface with command:
fslmaths /scratch/fmriprep_wf/single_subject_05_wf/func_preproc_ses_movie_task_rest_wf/bold_std_trans_wf/_std_target_MNI152NLin6Asym.res2/merge/vol0000_xform-00000_merged_cut.nii.gz -Tmean /scratch/fmriprep_wf/single_subject_05_wf/func_preproc_ses_movie_task_rest_wf/ica_aroma_wf/calc_bold_mean/vol0000_xform-00000_merged_cut_mean.nii.gz
201221-05:20:59,151 nipype.workflow INFO:
     [Node] Finished "fmriprep_wf.single_subject_05_wf.func_preproc_ses_movie_task_rest_wf.ica_aroma_wf.calc_bold_mean".
201221-05:21:01,77 nipype.workflow INFO:
     [Node] Setting-up "fmriprep_wf.single_subject_05_wf.func_preproc_ses_movie_task_rest_wf.ica_aroma_wf.calc_median_val" in "/scratch/fmriprep_wf/single_subject_05_wf/func_preproc_ses_movie_task_rest_wf/ica_aroma_wf/calc_median_val".
201221-05:21:01,281 nipype.workflow INFO:
     [Node] Running "calc_median_val" ("nipype.interfaces.fsl.utils.ImageStats"), a CommandLine Interface with command:
fslstats /scratch/fmriprep_wf/single_subject_05_wf/func_preproc_ses_movie_task_rest_wf/bold_std_trans_wf/_std_target_MNI152NLin6Asym.res2/merge/vol0000_xform-00000_merged_cut.nii.gz -k /scratch/fmriprep_wf/single_subject_05_wf/func_preproc_ses_movie_task_rest_wf/bold_std_trans_wf/_std_target_MNI152NLin6Asym.res2/mask_std_tfm/ref_bold_corrected_brain_mask_maths_trans.nii.gz -p 50 
201221-05:21:31,116 nipype.workflow INFO:
     [Node] Finished "fmriprep_wf.single_subject_05_wf.func_preproc_ses_movie_task_rest_wf.ica_aroma_wf.calc_median_val".
201221-05:21:33,13 nipype.workflow INFO:
     [Node] Setting-up "fmriprep_wf.single_subject_05_wf.func_preproc_ses_movie_task_rest_wf.ica_aroma_wf.getusans" in "/scratch/fmriprep_wf/single_subject_05_wf/func_preproc_ses_movie_task_rest_wf/ica_aroma_wf/getusans".
201221-05:21:33,137 nipype.workflow INFO:
     [Node] Running "getusans" ("nipype.interfaces.utility.wrappers.Function")
201221-05:21:33,209 nipype.workflow INFO:
     [Node] Finished "fmriprep_wf.single_subject_05_wf.func_preproc_ses_movie_task_rest_wf.ica_aroma_wf.getusans".
201221-05:21:35,21 nipype.workflow INFO:
     [Node] Setting-up "fmriprep_wf.single_subject_05_wf.func_preproc_ses_movie_task_rest_wf.ica_aroma_wf.smooth" in "/scratch/fmriprep_wf/single_subject_05_wf/func_preproc_ses_movie_task_rest_wf/ica_aroma_wf/smooth".
201221-05:21:35,186 nipype.workflow INFO:
     [Node] Running "smooth" ("nipype.interfaces.fsl.preprocess.SUSAN"), a CommandLine Interface with command:
susan /scratch/fmriprep_wf/single_subject_05_wf/func_preproc_ses_movie_task_rest_wf/bold_std_trans_wf/_std_target_MNI152NLin6Asym.res2/merge/vol0000_xform-00000_merged_cut.nii.gz 9069.3032227500 2.5479654009 3 1 1 /scratch/fmriprep_wf/single_subject_05_wf/func_preproc_ses_movie_task_rest_wf/ica_aroma_wf/calc_bold_mean/vol0000_xform-00000_merged_cut_mean.nii.gz 12092.4042970000 /scratch/fmriprep_wf/single_subject_05_wf/func_preproc_ses_movie_task_rest_wf/ica_aroma_wf/smooth/vol0000_xform-00000_merged_cut_smooth.nii.gz
201221-05:29:51,677 nipype.workflow INFO:
     [Node] Finished "fmriprep_wf.single_subject_05_wf.func_preproc_ses_movie_task_rest_wf.ica_aroma_wf.smooth".
201221-05:29:53,538 nipype.workflow INFO:
     [Node] Setting-up "fmriprep_wf.single_subject_05_wf.func_preproc_ses_movie_task_rest_wf.ica_aroma_wf.melodic" in "/scratch/fmriprep_wf/single_subject_05_wf/func_preproc_ses_movie_task_rest_wf/ica_aroma_wf/melodic".
201221-05:29:53,726 nipype.workflow INFO:
     [Node] Running "melodic" ("nipype.interfaces.fsl.model.MELODIC"), a CommandLine Interface with command:
melodic -i /scratch/fmriprep_wf/single_subject_05_wf/func_preproc_ses_movie_task_rest_wf/ica_aroma_wf/smooth/vol0000_xform-00000_merged_cut_smooth.nii.gz -d -200 -m /scratch/fmriprep_wf/single_subject_05_wf/func_preproc_ses_movie_task_rest_wf/bold_std_trans_wf/_std_target_MNI152NLin6Asym.res2/mask_std_tfm/ref_bold_corrected_brain_mask_maths_trans.nii.gz --mmthresh=0.500000 --nobet -o /scratch/fmriprep_wf/single_subject_05_wf/func_preproc_ses_movie_task_rest_wf/ica_aroma_wf/melodic --Ostats --tr=2.004000
201221-05:30:40,113 nipype.workflow INFO:
     [Node] Finished "_parcstats0".
201221-05:30:41,597 nipype.workflow INFO:
     [Node] Setting-up "_parcstats1" in "/scratch/fmriprep_wf/single_subject_04_wf/anat_preproc_wf/surface_recon_wf/autorecon_resume_wf/parcstats/mapflow/_parcstats1".
201221-05:30:41,837 nipype.interface INFO:
     resume recon-all : recon-all -autorecon-hemi rh -nohyporelabel -openmp 3 -subjid sub-04 -sd /out/sourcedata/freesurfer -notessellate -nosmooth1 -noinflate1 -noqsphere -nofix -nowhite -nosmooth2 -noinflate2 -nocurvHK -nocurvstats -nosphere -nosurfreg -nojacobian_white -noavgcurv -nocortparc -nopial -nocortparc2 -nocortparc3 -nopctsurfcon
201221-05:30:41,850 nipype.workflow INFO:
     [Node] Running "_parcstats1" ("smriprep.interfaces.freesurfer.ReconAll"), a CommandLine Interface with command:
recon-all -autorecon-hemi rh -nohyporelabel -openmp 3 -subjid sub-04 -sd /out/sourcedata/freesurfer -notessellate -nosmooth1 -noinflate1 -noqsphere -nofix -nowhite -nosmooth2 -noinflate2 -nocurvHK -nocurvstats -nosphere -nosurfreg -nojacobian_white -noavgcurv -nocortparc -nopial -nocortparc2 -nocortparc3 -nopctsurfcon
201221-05:30:41,990 nipype.interface INFO:
     resume recon-all : recon-all -autorecon-hemi rh -nohyporelabel -openmp 3 -subjid sub-04 -sd /out/sourcedata/freesurfer -notessellate -nosmooth1 -noinflate1 -noqsphere -nofix -nowhite -nosmooth2 -noinflate2 -nocurvHK -nocurvstats -nosphere -nosurfreg -nojacobian_white -noavgcurv -nocortparc -nopial -nocortparc2 -nocortparc3 -nopctsurfcon
201221-05:41:02,466 nipype.workflow INFO:
     [Node] Finished "_parcstats1".
201221-05:41:04,240 nipype.workflow INFO:
     [Node] Setting-up "fmriprep_wf.single_subject_04_wf.anat_preproc_wf.surface_recon_wf.autorecon_resume_wf.parcstats" in "/scratch/fmriprep_wf/single_subject_04_wf/anat_preproc_wf/surface_recon_wf/autorecon_resume_wf/parcstats".
201221-05:41:04,337 nipype.workflow INFO:
     [Node] Setting-up "_parcstats0" in "/scratch/fmriprep_wf/single_subject_04_wf/anat_preproc_wf/surface_recon_wf/autorecon_resume_wf/parcstats/mapflow/_parcstats0".
201221-05:41:04,583 nipype.interface INFO:
     recon-all complete : Not running
201221-05:41:04,595 nipype.workflow INFO:
     [Node] Running "_parcstats0" ("smriprep.interfaces.freesurfer.ReconAll"), a CommandLine Interface with command:
echo recon-all: nothing to do
201221-05:41:04,738 nipype.interface INFO:
     recon-all complete : Not running
201221-05:41:05,317 nipype.workflow INFO:
     [Node] Finished "_parcstats0".
201221-05:41:05,336 nipype.workflow INFO:
     [Node] Setting-up "_parcstats1" in "/scratch/fmriprep_wf/single_subject_04_wf/anat_preproc_wf/surface_recon_wf/autorecon_resume_wf/parcstats/mapflow/_parcstats1".
201221-05:41:05,583 nipype.interface INFO:
     recon-all complete : Not running
201221-05:41:05,590 nipype.workflow INFO:
     [Node] Running "_parcstats1" ("smriprep.interfaces.freesurfer.ReconAll"), a CommandLine Interface with command:
echo recon-all: nothing to do
201221-05:41:05,733 nipype.interface INFO:
     recon-all complete : Not running
201221-05:41:06,282 nipype.workflow INFO:
     [Node] Finished "_parcstats1".
201221-05:41:06,359 nipype.workflow INFO:
     [Node] Finished "fmriprep_wf.single_subject_04_wf.anat_preproc_wf.surface_recon_wf.autorecon_resume_wf.parcstats".
201221-05:41:08,247 nipype.workflow INFO:
     [Node] Setting-up "fmriprep_wf.single_subject_04_wf.anat_preproc_wf.surface_recon_wf.autorecon_resume_wf.autorecon3" in "/scratch/fmriprep_wf/single_subject_04_wf/anat_preproc_wf/surface_recon_wf/autorecon_resume_wf/autorecon3".
201221-05:41:08,499 nipype.interface INFO:
     resume recon-all : recon-all -autorecon3 -openmp 3 -subjid sub-04 -sd /out/sourcedata/freesurfer -nosphere -nosurfreg -nojacobian_white -noavgcurv -nocortparc -nopial -noparcstats -nocortparc2 -noparcstats2 -nocortparc3 -noparcstats3 -nopctsurfcon -nocortribbon -nobalabels
201221-05:41:08,510 nipype.workflow INFO:
     [Node] Running "autorecon3" ("smriprep.interfaces.freesurfer.ReconAll"), a CommandLine Interface with command:
recon-all -autorecon3 -openmp 3 -subjid sub-04 -sd /out/sourcedata/freesurfer -nosphere -nosurfreg -nojacobian_white -noavgcurv -nocortparc -nopial -noparcstats -nocortparc2 -noparcstats2 -nocortparc3 -noparcstats3 -nopctsurfcon -nocortribbon -nobalabels
201221-05:41:08,685 nipype.interface INFO:
     resume recon-all : recon-all -autorecon3 -openmp 3 -subjid sub-04 -sd /out/sourcedata/freesurfer -nosphere -nosurfreg -nojacobian_white -noavgcurv -nocortparc -nopial -noparcstats -nocortparc2 -noparcstats2 -nocortparc3 -noparcstats3 -nopctsurfcon -nocortribbon -nobalabels
201221-05:41:54,499 nipype.workflow INFO:
     [Node] Finished "fmriprep_wf.single_subject_05_wf.func_preproc_ses_movie_task_rest_wf.ica_aroma_wf.melodic".
201221-05:41:56,254 nipype.workflow INFO:
     [Node] Setting-up "fmriprep_wf.single_subject_05_wf.func_preproc_ses_movie_task_rest_wf.ica_aroma_wf.ica_aroma" in "/scratch/fmriprep_wf/single_subject_05_wf/func_preproc_ses_movie_task_rest_wf/ica_aroma_wf/ica_aroma".
201221-05:41:56,521 nipype.workflow INFO:
     [Node] Running "ica_aroma" ("niworkflows.interfaces.segmentation.ICA_AROMARPT"), a CommandLine Interface with command:
ICA_AROMA.py -tr 2.004 -np -den nonaggr -i /scratch/fmriprep_wf/single_subject_05_wf/func_preproc_ses_movie_task_rest_wf/ica_aroma_wf/smooth/vol0000_xform-00000_merged_cut_smooth.nii.gz -m /scratch/fmriprep_wf/single_subject_05_wf/func_preproc_ses_movie_task_rest_wf/bold_std_trans_wf/_std_target_MNI152NLin6Asym.res2/mask_std_tfm/ref_bold_corrected_brain_mask_maths_trans.nii.gz -meldir /scratch/fmriprep_wf/single_subject_05_wf/func_preproc_ses_movie_task_rest_wf/ica_aroma_wf/melodic -mc /scratch/fmriprep_wf/single_subject_05_wf/func_preproc_ses_movie_task_rest_wf/bold_hmc_wf/normalize_motion/motion_params.txt -o /scratch/fmriprep_wf/single_subject_05_wf/func_preproc_ses_movie_task_rest_wf/ica_aroma_wf/ica_aroma/out
201221-05:45:17,90 nipype.workflow INFO:
     [Node] Finished "fmriprep_wf.single_subject_05_wf.func_preproc_ses_movie_task_rest_wf.ica_aroma_wf.ica_aroma".
201221-05:45:19,853 nipype.workflow INFO:
     [Node] Setting-up "fmriprep_wf.single_subject_05_wf.func_preproc_ses_movie_task_rest_wf.ica_aroma_wf.add_nonsteady" in "/scratch/fmriprep_wf/single_subject_05_wf/func_preproc_ses_movie_task_rest_wf/ica_aroma_wf/add_nonsteady".
201221-05:45:19,997 nipype.workflow INFO:
     [Node] Running "add_nonsteady" ("nipype.interfaces.utility.wrappers.Function")
201221-05:46:00,972 nipype.workflow INFO:
     [Node] Finished "fmriprep_wf.single_subject_05_wf.func_preproc_ses_movie_task_rest_wf.ica_aroma_wf.add_nonsteady".
201221-05:48:15,673 nipype.workflow INFO:
     [Node] Setting-up "fmriprep_wf.single_subject_05_wf.func_preproc_ses_movie_task_rest_wf.ica_aroma_wf.ica_aroma_confound_extraction" in "/scratch/fmriprep_wf/single_subject_05_wf/func_preproc_ses_movie_task_rest_wf/ica_aroma_wf/ica_aroma_confound_extraction".
201221-05:48:15,818 nipype.workflow INFO:
     [Node] Running "ica_aroma_confound_extraction" ("fmriprep.interfaces.confounds.ICAConfounds")
201221-05:48:16,19 nipype.workflow INFO:
     [Node] Finished "fmriprep_wf.single_subject_05_wf.func_preproc_ses_movie_task_rest_wf.ica_aroma_wf.ica_aroma_confound_extraction".
201221-05:48:19,952 nipype.workflow INFO:
     [Node] Setting-up "fmriprep_wf.single_subject_05_wf.func_preproc_ses_movie_task_rest_wf.aroma_confounds" in "/scratch/fmriprep_wf/single_subject_05_wf/func_preproc_ses_movie_task_rest_wf/aroma_confounds".
201221-05:48:20,87 nipype.workflow INFO:
     [Node] Running "aroma_confounds" ("nipype.interfaces.utility.wrappers.Function")
201221-05:48:20,206 nipype.workflow INFO:
     [Node] Finished "fmriprep_wf.single_subject_05_wf.func_preproc_ses_movie_task_rest_wf.aroma_confounds".
201221-05:48:23,406 nipype.workflow INFO:
     [Node] Setting-up "fmriprep_wf.single_subject_05_wf.func_preproc_ses_movie_task_rest_wf.ica_aroma_wf.ica_aroma_metadata_fmt" in "/scratch/fmriprep_wf/single_subject_05_wf/func_preproc_ses_movie_task_rest_wf/ica_aroma_wf/ica_aroma_metadata_fmt".
201221-05:48:23,524 nipype.workflow INFO:
     [Node] Running "ica_aroma_metadata_fmt" ("niworkflows.interfaces.utils.TSV2JSON")
201221-05:48:23,654 nipype.workflow INFO:
     [Node] Finished "fmriprep_wf.single_subject_05_wf.func_preproc_ses_movie_task_rest_wf.ica_aroma_wf.ica_aroma_metadata_fmt".
201221-05:48:26,406 nipype.workflow INFO:
     [Node] Setting-up "_update_metadata0" in "/scratch/fmriprep_wf/single_subject_05_wf/func_preproc_ses_movie_task_rest_wf/bold_surf_wf/_target_fsaverage/update_metadata/mapflow/_update_metadata0".
201221-05:48:26,502 nipype.workflow INFO:
     [Node] Running "_update_metadata0" ("niworkflows.interfaces.surf.GiftiSetAnatomicalStructure")
201221-05:48:49,950 nipype.workflow INFO:
     [Node] Finished "_update_metadata0".
201221-05:48:52,97 nipype.workflow INFO:
     [Node] Setting-up "_update_metadata1" in "/scratch/fmriprep_wf/single_subject_05_wf/func_preproc_ses_movie_task_rest_wf/bold_surf_wf/_target_fsaverage/update_metadata/mapflow/_update_metadata1".
201221-05:48:52,292 nipype.workflow INFO:
     [Node] Running "_update_metadata1" ("niworkflows.interfaces.surf.GiftiSetAnatomicalStructure")
201221-05:49:15,780 nipype.workflow INFO:
     [Node] Finished "_update_metadata1".
201221-05:49:18,251 nipype.workflow INFO:
     [Node] Setting-up "fmriprep_wf.single_subject_05_wf.func_preproc_ses_movie_task_rest_wf.bold_surf_wf.update_metadata" in "/scratch/fmriprep_wf/single_subject_05_wf/func_preproc_ses_movie_task_rest_wf/bold_surf_wf/_target_fsaverage/update_metadata".
201221-05:49:18,402 nipype.workflow INFO:
     [Node] Setting-up "_update_metadata0" in "/scratch/fmriprep_wf/single_subject_05_wf/func_preproc_ses_movie_task_rest_wf/bold_surf_wf/_target_fsaverage/update_metadata/mapflow/_update_metadata0".
201221-05:49:18,452 nipype.workflow INFO:
     [Node] Cached "_update_metadata0" - collecting precomputed outputs
201221-05:49:18,452 nipype.workflow INFO:
     [Node] "_update_metadata0" found cached.
201221-05:49:18,473 nipype.workflow INFO:
     [Node] Setting-up "_update_metadata1" in "/scratch/fmriprep_wf/single_subject_05_wf/func_preproc_ses_movie_task_rest_wf/bold_surf_wf/_target_fsaverage/update_metadata/mapflow/_update_metadata1".
201221-05:49:18,524 nipype.workflow INFO:
     [Node] Cached "_update_metadata1" - collecting precomputed outputs
201221-05:49:18,524 nipype.workflow INFO:
     [Node] "_update_metadata1" found cached.
201221-05:49:18,569 nipype.workflow INFO:
     [Node] Finished "fmriprep_wf.single_subject_05_wf.func_preproc_ses_movie_task_rest_wf.bold_surf_wf.update_metadata".
201221-05:49:21,27 nipype.workflow INFO:
     [Node] Setting-up "fmriprep_wf.single_subject_05_wf.func_preproc_ses_movie_task_rest_wf.bold_surf_wf.outputnode" in "/scratch/fmriprep_wf/single_subject_05_wf/func_preproc_ses_movie_task_rest_wf/bold_surf_wf/outputnode".
201221-05:49:21,136 nipype.workflow INFO:
     [Node] Running "outputnode" ("nipype.interfaces.utility.base.IdentityInterface")
201221-05:49:21,217 nipype.workflow INFO:
     [Node] Finished "fmriprep_wf.single_subject_05_wf.func_preproc_ses_movie_task_rest_wf.bold_surf_wf.outputnode".
201221-06:03:32,869 nipype.workflow INFO:
     [Node] Finished "fmriprep_wf.single_subject_04_wf.anat_preproc_wf.surface_recon_wf.autorecon_resume_wf.autorecon3".
201221-06:03:34,698 nipype.workflow INFO:
     [Node] Setting-up "fmriprep_wf.single_subject_04_wf.anat_preproc_wf.anat_reports_wf.recon_report" in "/scratch/fmriprep_wf/single_subject_04_wf/anat_preproc_wf/anat_reports_wf/recon_report".
201221-06:03:34,779 nipype.workflow INFO:
     [Node] Running "recon_report" ("smriprep.interfaces.reports.FSSurfaceReport")
201221-06:03:35,684 nipype.workflow INFO:
     [Node] Setting-up "fmriprep_wf.single_subject_04_wf.func_preproc_ses_movie_task_rest_wf.bold_reg_wf.bbreg_wf.mri_coreg" in "/scratch/fmriprep_wf/single_subject_04_wf/func_preproc_ses_movie_task_rest_wf/bold_reg_wf/bbreg_wf/mri_coreg".
201221-06:03:35,955 nipype.workflow INFO:
     [Node] Running "mri_coreg" ("niworkflows.interfaces.freesurfer.PatchedMRICoregRPT"), a CommandLine Interface with command:
mri_coreg --s sub-04 --dof 6 --ftol 1.000000e-04 --linmintol 1.000000e-02 --threads 3 --lta /scratch/fmriprep_wf/single_subject_04_wf/func_preproc_ses_movie_task_rest_wf/bold_reg_wf/bbreg_wf/mri_coreg/registration.lta --sep 4 --mov /scratch/fmriprep_wf/single_subject_04_wf/func_preproc_ses_movie_task_rest_wf/bold_reg_wf/bbreg_wf/mri_coreg/uni_xform_masked.nii.gz --sd /out/sourcedata/freesurfer
201221-06:03:46,380 nipype.workflow INFO:
     [Node] Finished "fmriprep_wf.single_subject_04_wf.anat_preproc_wf.anat_reports_wf.recon_report".
201221-06:03:49,399 nipype.workflow INFO:
     [Node] Setting-up "fmriprep_wf.single_subject_04_wf.anat_preproc_wf.surface_recon_wf.segs_to_native_aparc_aseg.fs_datasource" in "/scratch/fmriprep_wf/single_subject_04_wf/anat_preproc_wf/surface_recon_wf/segs_to_native_aparc_aseg/fs_datasource".
201221-06:03:49,527 nipype.workflow INFO:
     [Node] Running "fs_datasource" ("nipype.interfaces.io.FreeSurferSource")
201221-06:03:50,215 nipype.workflow INFO:
     [Node] Finished "fmriprep_wf.single_subject_04_wf.anat_preproc_wf.surface_recon_wf.segs_to_native_aparc_aseg.fs_datasource".
201221-06:03:52,322 nipype.workflow INFO:
     [Node] Setting-up "fmriprep_wf.single_subject_04_wf.anat_preproc_wf.surface_recon_wf.segs_to_native_aparc_aseg.resample" in "/scratch/fmriprep_wf/single_subject_04_wf/anat_preproc_wf/surface_recon_wf/segs_to_native_aparc_aseg/resample".
201221-06:03:52,771 nipype.workflow INFO:
     [Node] Running "resample" ("nipype.interfaces.freesurfer.preprocess.ApplyVolTransform"), a CommandLine Interface with command:
mri_vol2vol --lta /scratch/fmriprep_wf/single_subject_04_wf/anat_preproc_wf/surface_recon_wf/fsnative2t1w_xfm/T1_robustreg.lta --mov /scratch/fmriprep_wf/single_subject_04_wf/anat_preproc_wf/surface_recon_wf/segs_to_native_aparc_aseg/resample/aparc+aseg.mgz --targ /scratch/fmriprep_wf/single_subject_04_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/copy_xform/sub-04_ses-movie_T1w_corrected_xform.nii.gz --o seg.nii.gz
201221-06:03:56,516 nipype.workflow INFO:
     [Node] Finished "fmriprep_wf.single_subject_04_wf.anat_preproc_wf.surface_recon_wf.segs_to_native_aparc_aseg.resample".
201221-06:04:00,776 nipype.interface WARNING:
     Changing /out/sub-04/ses-movie/anat/sub-04_ses-movie_desc-aparcaseg_dseg.nii.gz dtype from float32 to int16
201221-06:04:01,745 nipype.workflow INFO:
     [Node] Setting-up "fmriprep_wf.single_subject_04_wf.anat_preproc_wf.surface_recon_wf.segs_to_native_aseg.fs_datasource" in "/scratch/fmriprep_wf/single_subject_04_wf/anat_preproc_wf/surface_recon_wf/segs_to_native_aseg/fs_datasource".
201221-06:04:01,823 nipype.workflow INFO:
     [Node] Running "fs_datasource" ("nipype.interfaces.io.FreeSurferSource")
201221-06:04:02,542 nipype.workflow INFO:
     [Node] Finished "fmriprep_wf.single_subject_04_wf.anat_preproc_wf.surface_recon_wf.segs_to_native_aseg.fs_datasource".
201221-06:04:04,401 nipype.workflow INFO:
     [Node] Setting-up "fmriprep_wf.single_subject_04_wf.anat_preproc_wf.surface_recon_wf.segs_to_native_aseg.resample" in "/scratch/fmriprep_wf/single_subject_04_wf/anat_preproc_wf/surface_recon_wf/segs_to_native_aseg/resample".
201221-06:04:04,621 nipype.workflow INFO:
     [Node] Running "resample" ("nipype.interfaces.freesurfer.preprocess.ApplyVolTransform"), a CommandLine Interface with command:
mri_vol2vol --lta /scratch/fmriprep_wf/single_subject_04_wf/anat_preproc_wf/surface_recon_wf/fsnative2t1w_xfm/T1_robustreg.lta --mov /scratch/fmriprep_wf/single_subject_04_wf/anat_preproc_wf/surface_recon_wf/segs_to_native_aseg/resample/aseg.mgz --targ /scratch/fmriprep_wf/single_subject_04_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/copy_xform/sub-04_ses-movie_T1w_corrected_xform.nii.gz --o seg.nii.gz
201221-06:04:08,173 nipype.workflow INFO:
     [Node] Finished "fmriprep_wf.single_subject_04_wf.anat_preproc_wf.surface_recon_wf.segs_to_native_aseg.resample".
201221-06:04:13,536 nipype.interface WARNING:
     Changing /out/sub-04/ses-movie/anat/sub-04_ses-movie_desc-aseg_dseg.nii.gz dtype from float32 to int16
201221-06:04:14,452 nipype.workflow INFO:
     [Node] Setting-up "fmriprep_wf.single_subject_04_wf.anat_preproc_wf.lut_t1w_dseg" in "/scratch/fmriprep_wf/single_subject_04_wf/anat_preproc_wf/lut_t1w_dseg".
201221-06:04:14,580 nipype.workflow INFO:
     [Node] Running "lut_t1w_dseg" ("nipype.interfaces.utility.wrappers.Function")
201221-06:04:15,87 nipype.workflow INFO:
     [Node] Finished "fmriprep_wf.single_subject_04_wf.anat_preproc_wf.lut_t1w_dseg".
201221-06:04:17,584 nipype.interface INFO:
     stdout 2020-12-21T06:04:17.584149:
201221-06:04:17,584 nipype.interface INFO:
     stdout 2020-12-21T06:04:17.584149:Matrix from LTA:
201221-06:04:17,584 nipype.interface INFO:
     stdout 2020-12-21T06:04:17.584149: 0.99990   0.00787   0.01180   0.05095;
201221-06:04:17,584 nipype.interface INFO:
     stdout 2020-12-21T06:04:17.584149:-0.00934  -0.26068   0.96538  -28.92477;
201221-06:04:17,584 nipype.interface INFO:
     stdout 2020-12-21T06:04:17.584149: 0.01067  -0.96539  -0.26058  -2.63668;
201221-06:04:17,585 nipype.interface INFO:
     stdout 2020-12-21T06:04:17.584149: 0.00000   0.00000   0.00000   1.00000;
201221-06:04:17,818 nipype.interface INFO:
     stdout 2020-12-21T06:04:17.818232:
201221-06:04:17,818 nipype.interface INFO:
     stdout 2020-12-21T06:04:17.818232:/scratch/fmriprep_wf/single_subject_04_wf/func_preproc_ses_movie_task_rest_wf/bold_reg_wf/bbreg_wf/mri_coreg/uni_xform_masked.nii.gz /out/sourcedata/freesurfer/sub-04/mri/brainmask.mgz
201221-06:04:17,818 nipype.interface INFO:
     stdout 2020-12-21T06:04:17.818232:movvol /scratch/fmriprep_wf/single_subject_04_wf/func_preproc_ses_movie_task_rest_wf/bold_reg_wf/bbreg_wf/mri_coreg/uni_xform_masked.nii.gz
201221-06:04:17,818 nipype.interface INFO:
     stdout 2020-12-21T06:04:17.818232:targvol /out/sourcedata/freesurfer/sub-04/mri/brainmask.mgz
201221-06:04:17,818 nipype.interface INFO:
     stdout 2020-12-21T06:04:17.818232:outvol /scratch/fmriprep_wf/single_subject_04_wf/func_preproc_ses_movie_task_rest_wf/bold_reg_wf/bbreg_wf/mri_coreg/uni_xform_masked_warped.nii.gz
201221-06:04:17,818 nipype.interface INFO:
     stdout 2020-12-21T06:04:17.818232:regfile /scratch/fmriprep_wf/single_subject_04_wf/func_preproc_ses_movie_task_rest_wf/bold_reg_wf/bbreg_wf/mri_coreg/registration.lta
201221-06:04:17,818 nipype.interface INFO:
     stdout 2020-12-21T06:04:17.818232:invert 0
201221-06:04:17,819 nipype.interface INFO:
     stdout 2020-12-21T06:04:17.818232:tal    0
201221-06:04:17,819 nipype.interface INFO:
     stdout 2020-12-21T06:04:17.818232:talres 2
201221-06:04:17,819 nipype.interface INFO:
     stdout 2020-12-21T06:04:17.818232:regheader 0
201221-06:04:17,819 nipype.interface INFO:
     stdout 2020-12-21T06:04:17.818232:noresample 0
201221-06:04:17,819 nipype.interface INFO:
     stdout 2020-12-21T06:04:17.818232:interp  nearest (0)
201221-06:04:17,819 nipype.interface INFO:
     stdout 2020-12-21T06:04:17.818232:precision  float (3)
201221-06:04:17,819 nipype.interface INFO:
     stdout 2020-12-21T06:04:17.818232:Gdiag_no  -1
201221-06:04:17,819 nipype.interface INFO:
     stdout 2020-12-21T06:04:17.818232:Synth      0
201221-06:04:17,819 nipype.interface INFO:
     stdout 2020-12-21T06:04:17.818232:SynthSeed  1609223662
201221-06:04:17,819 nipype.interface INFO:
     stdout 2020-12-21T06:04:17.818232:
201221-06:04:17,819 nipype.interface INFO:
     stdout 2020-12-21T06:04:17.818232:Final tkRAS-to-tkRAS Matrix is:
201221-06:04:17,819 nipype.interface INFO:
     stdout 2020-12-21T06:04:17.818232: 0.99990   0.00787   0.01180   0.05092;
201221-06:04:17,819 nipype.interface INFO:
     stdout 2020-12-21T06:04:17.818232:-0.00934  -0.26068   0.96538  -28.92477;
201221-06:04:17,820 nipype.interface INFO:
     stdout 2020-12-21T06:04:17.818232: 0.01067  -0.96539  -0.26058  -2.63669;
201221-06:04:17,820 nipype.interface INFO:
     stdout 2020-12-21T06:04:17.818232: 0.00000   0.00000   0.00000   1.00000;
201221-06:04:17,820 nipype.interface INFO:
     stdout 2020-12-21T06:04:17.820223:
201221-06:04:17,820 nipype.interface INFO:
     stdout 2020-12-21T06:04:17.820223:
201221-06:04:17,820 nipype.interface INFO:
     stdout 2020-12-21T06:04:17.820223:Vox2Vox Matrix is:
201221-06:04:17,820 nipype.interface INFO:
     stdout 2020-12-21T06:04:17.820223: 0.44638   0.00527  -0.00351  -7.38431;
201221-06:04:17,820 nipype.interface INFO:
     stdout 2020-12-21T06:04:17.820223: 0.00476  -0.11633   0.43098   10.29246;
201221-06:04:17,820 nipype.interface INFO:
     stdout 2020-12-21T06:04:17.820223: 0.00226  -0.23375  -0.06312   45.70606;
201221-06:04:17,820 nipype.interface INFO:
     stdout 2020-12-21T06:04:17.820223: 0.00000   0.00000   0.00000   1.00000;
201221-06:04:18,760 nipype.interface INFO:
     stdout 2020-12-21T06:04:18.760378:
201221-06:04:18,760 nipype.interface INFO:
     stdout 2020-12-21T06:04:18.760378:Resampling
201221-06:04:18,760 nipype.interface INFO:
     stdout 2020-12-21T06:04:18.760378:Output registration matrix is identity
201221-06:04:18,760 nipype.interface INFO:
     stdout 2020-12-21T06:04:18.760378:
201221-06:04:18,760 nipype.interface INFO:
     stdout 2020-12-21T06:04:18.760378:mri_vol2vol done
201221-06:04:20,8 nipype.workflow INFO:
     [Node] Setting-up "fmriprep_wf.single_subject_04_wf.anat_preproc_wf.split_seg" in "/scratch/fmriprep_wf/single_subject_04_wf/anat_preproc_wf/split_seg".
201221-06:04:20,93 nipype.workflow INFO:
     [Node] Running "split_seg" ("nipype.interfaces.utility.wrappers.Function")
201221-06:04:20,475 nipype.workflow INFO:
     [Node] Finished "fmriprep_wf.single_subject_04_wf.anat_preproc_wf.split_seg".
201221-06:04:24,110 nipype.interface WARNING:
     Changing /out/sub-04/ses-movie/anat/sub-04_ses-movie_label-GM_probseg.nii.gz dtype from uint8 to float32
201221-06:04:25,767 nipype.interface WARNING:
     Changing /out/sub-04/ses-movie/anat/sub-04_ses-movie_label-WM_probseg.nii.gz dtype from uint8 to float32
201221-06:04:26,530 nipype.interface WARNING:
     Changing /out/sub-04/ses-movie/anat/sub-04_ses-movie_label-CSF_probseg.nii.gz dtype from uint8 to float32
201221-06:04:27,429 nipype.workflow INFO:
     [Node] Setting-up "fmriprep_wf.single_subject_04_wf.func_preproc_ses_movie_task_rest_wf.bold_confounds_wf.acc_masks" in "/scratch/fmriprep_wf/single_subject_04_wf/func_preproc_ses_movie_task_rest_wf/bold_confounds_wf/acc_masks".
201221-06:04:27,698 nipype.workflow INFO:
     [Node] Running "acc_masks" ("fmriprep.interfaces.confounds.aCompCorMasks")
201221-06:04:33,552 nipype.workflow INFO:
     [Node] Finished "fmriprep_wf.single_subject_04_wf.func_preproc_ses_movie_task_rest_wf.bold_confounds_wf.acc_masks".
201221-06:04:36,62 nipype.workflow INFO:
     [Node] Setting-up "fmriprep_wf.single_subject_04_wf.anat_preproc_wf.surface_recon_wf.refine" in "/scratch/fmriprep_wf/single_subject_04_wf/anat_preproc_wf/surface_recon_wf/refine".
201221-06:04:36,205 nipype.workflow INFO:
     [Node] Running "refine" ("niworkflows.interfaces.freesurfer.RefineBrainMask")
201221-06:04:39,216 nipype.workflow INFO:
     [Node] Finished "fmriprep_wf.single_subject_04_wf.func_preproc_ses_movie_task_rest_wf.bold_reg_wf.bbreg_wf.mri_coreg".
201221-06:04:40,10 nipype.workflow INFO:
     [Node] Setting-up "fmriprep_wf.single_subject_04_wf.func_preproc_ses_movie_task_rest_wf.bold_reg_wf.bbreg_wf.bbregister" in "/scratch/fmriprep_wf/single_subject_04_wf/func_preproc_ses_movie_task_rest_wf/bold_reg_wf/bbreg_wf/bbregister".
201221-06:04:40,10 nipype.workflow INFO:
     [Node] Setting-up "fmriprep_wf.single_subject_04_wf.anat_preproc_wf.surface_recon_wf.gifti_surface_wf.get_surfaces" in "/scratch/fmriprep_wf/single_subject_04_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/get_surfaces".
201221-06:04:40,100 nipype.workflow INFO:
     [Node] Running "get_surfaces" ("nipype.interfaces.io.FreeSurferSource")
201221-06:04:40,235 nipype.workflow INFO:
     [Node] Running "bbregister" ("niworkflows.interfaces.freesurfer.PatchedBBRegisterRPT"), a CommandLine Interface with command:
bbregister --t2 --6 --init-reg /scratch/fmriprep_wf/single_subject_04_wf/func_preproc_ses_movie_task_rest_wf/bold_reg_wf/bbreg_wf/mri_coreg/registration.lta --lta /scratch/fmriprep_wf/single_subject_04_wf/func_preproc_ses_movie_task_rest_wf/bold_reg_wf/bbreg_wf/bbregister/uni_xform_masked_bbreg_sub-04.lta --reg /scratch/fmriprep_wf/single_subject_04_wf/func_preproc_ses_movie_task_rest_wf/bold_reg_wf/bbreg_wf/bbregister/uni_xform_masked_bbreg_sub-04.dat --o /scratch/fmriprep_wf/single_subject_04_wf/func_preproc_ses_movie_task_rest_wf/bold_reg_wf/bbreg_wf/bbregister/uni_xform_masked_bbreg.nii.gz --mov /scratch/fmriprep_wf/single_subject_04_wf/func_preproc_ses_movie_task_rest_wf/bold_reg_wf/bbreg_wf/bbregister/uni_xform_masked.nii.gz --s sub-04
201221-06:04:40,924 nipype.workflow INFO:
     [Node] Finished "fmriprep_wf.single_subject_04_wf.anat_preproc_wf.surface_recon_wf.gifti_surface_wf.get_surfaces".
201221-06:04:44,147 nipype.workflow INFO:
     [Node] Setting-up "_midthickness0" in "/scratch/fmriprep_wf/single_subject_04_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/midthickness/mapflow/_midthickness0".
201221-06:04:44,158 nipype.workflow INFO:
     [Node] Setting-up "_midthickness1" in "/scratch/fmriprep_wf/single_subject_04_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/midthickness/mapflow/_midthickness1".
201221-06:04:44,288 nipype.workflow INFO:
     [Node] Running "_midthickness0" ("niworkflows.interfaces.freesurfer.MakeMidthickness"), a CommandLine Interface with command:
mris_expand -pial /scratch/fmriprep_wf/single_subject_04_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/midthickness/mapflow/_midthickness0/lh.pial -thickness -thickness_name /scratch/fmriprep_wf/single_subject_04_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/midthickness/mapflow/_midthickness0/lh.thickness /scratch/fmriprep_wf/single_subject_04_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/midthickness/mapflow/_midthickness0/lh.smoothwm 0.5 midthickness
201221-06:04:44,314 nipype.workflow INFO:
     [Node] Running "_midthickness1" ("niworkflows.interfaces.freesurfer.MakeMidthickness"), a CommandLine Interface with command:
mris_expand -pial /scratch/fmriprep_wf/single_subject_04_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/midthickness/mapflow/_midthickness1/rh.pial -thickness -thickness_name /scratch/fmriprep_wf/single_subject_04_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/midthickness/mapflow/_midthickness1/rh.thickness /scratch/fmriprep_wf/single_subject_04_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/midthickness/mapflow/_midthickness1/rh.smoothwm 0.5 midthickness
201221-06:05:33,21 nipype.workflow INFO:
     [Node] Finished "fmriprep_wf.single_subject_04_wf.anat_preproc_wf.surface_recon_wf.refine".
201221-06:05:35,784 nipype.workflow INFO:
     [Node] Setting-up "fmriprep_wf.single_subject_04_wf.anat_preproc_wf.anat_reports_wf.seg_rpt" in "/scratch/fmriprep_wf/single_subject_04_wf/anat_preproc_wf/anat_reports_wf/seg_rpt".
201221-06:05:35,897 nipype.workflow INFO:
     [Node] Running "seg_rpt" ("niworkflows.interfaces.masks.ROIsPlot")
201221-06:05:42,999 nipype.interface INFO:
     stdout 2020-12-21T06:05:42.998923:
201221-06:05:43,0 nipype.interface INFO:
     stdout 2020-12-21T06:05:42.998923:Matrix from LTA:
201221-06:05:43,0 nipype.interface INFO:
     stdout 2020-12-21T06:05:42.998923: 0.99993   0.01126   0.00406  -0.02516;
201221-06:05:43,0 nipype.interface INFO:
     stdout 2020-12-21T06:05:42.998923:-0.00069  -0.28446   0.95869  -31.77698;
201221-06:05:43,0 nipype.interface INFO:
     stdout 2020-12-21T06:05:42.998923: 0.01195  -0.95862  -0.28444  -0.23319;
201221-06:05:43,0 nipype.interface INFO:
     stdout 2020-12-21T06:05:42.998923: 0.00000   0.00000   0.00000   1.00000;
201221-06:05:43,291 nipype.interface INFO:
     stdout 2020-12-21T06:05:43.291305:
201221-06:05:43,291 nipype.interface INFO:
     stdout 2020-12-21T06:05:43.291305:/scratch/fmriprep_wf/single_subject_04_wf/func_preproc_ses_movie_task_rest_wf/bold_reg_wf/bbreg_wf/bbregister/uni_xform_masked.nii.gz /out/sourcedata/freesurfer/sub-04/mri/brainmask.mgz
201221-06:05:43,291 nipype.interface INFO:
     stdout 2020-12-21T06:05:43.291305:movvol /scratch/fmriprep_wf/single_subject_04_wf/func_preproc_ses_movie_task_rest_wf/bold_reg_wf/bbreg_wf/bbregister/uni_xform_masked.nii.gz
201221-06:05:43,292 nipype.interface INFO:
     stdout 2020-12-21T06:05:43.291305:targvol /out/sourcedata/freesurfer/sub-04/mri/brainmask.mgz
201221-06:05:43,292 nipype.interface INFO:
     stdout 2020-12-21T06:05:43.291305:outvol /scratch/fmriprep_wf/single_subject_04_wf/func_preproc_ses_movie_task_rest_wf/bold_reg_wf/bbreg_wf/bbregister/uni_xform_masked_warped.nii.gz
201221-06:05:43,292 nipype.interface INFO:
     stdout 2020-12-21T06:05:43.291305:regfile /scratch/fmriprep_wf/single_subject_04_wf/func_preproc_ses_movie_task_rest_wf/bold_reg_wf/bbreg_wf/bbregister/uni_xform_masked_bbreg_sub-04.lta
201221-06:05:43,292 nipype.interface INFO:
     stdout 2020-12-21T06:05:43.291305:invert 0
201221-06:05:43,292 nipype.interface INFO:
     stdout 2020-12-21T06:05:43.291305:tal    0
201221-06:05:43,292 nipype.interface INFO:
     stdout 2020-12-21T06:05:43.291305:talres 2
201221-06:05:43,293 nipype.interface INFO:
     stdout 2020-12-21T06:05:43.291305:regheader 0
201221-06:05:43,293 nipype.interface INFO:
     stdout 2020-12-21T06:05:43.291305:noresample 0
201221-06:05:43,293 nipype.interface INFO:
     stdout 2020-12-21T06:05:43.291305:interp  nearest (0)
201221-06:05:43,293 nipype.interface INFO:
     stdout 2020-12-21T06:05:43.291305:precision  float (3)
201221-06:05:43,293 nipype.interface INFO:
     stdout 2020-12-21T06:05:43.291305:Gdiag_no  -1
201221-06:05:43,293 nipype.interface INFO:
     stdout 2020-12-21T06:05:43.291305:Synth      0
201221-06:05:43,293 nipype.interface INFO:
     stdout 2020-12-21T06:05:43.291305:SynthSeed  1608666049
201221-06:05:43,293 nipype.interface INFO:
     stdout 2020-12-21T06:05:43.291305:
201221-06:05:43,294 nipype.interface INFO:
     stdout 2020-12-21T06:05:43.291305:Final tkRAS-to-tkRAS Matrix is:
201221-06:05:43,294 nipype.interface INFO:
     stdout 2020-12-21T06:05:43.291305: 0.99993   0.01126   0.00406  -0.02516;
201221-06:05:43,294 nipype.interface INFO:
     stdout 2020-12-21T06:05:43.291305:-0.00069  -0.28446   0.95869  -31.77696;
201221-06:05:43,294 nipype.interface INFO:
     stdout 2020-12-21T06:05:43.291305: 0.01195  -0.95862  -0.28444  -0.23319;
201221-06:05:43,294 nipype.interface INFO:
     stdout 2020-12-21T06:05:43.291305: 0.00000   0.00000   0.00000   1.00000;
201221-06:05:43,294 nipype.interface INFO:
     stdout 2020-12-21T06:05:43.294871:
201221-06:05:43,295 nipype.interface INFO:
     stdout 2020-12-21T06:05:43.294871:
201221-06:05:43,295 nipype.interface INFO:
     stdout 2020-12-21T06:05:43.294871:Vox2Vox Matrix is:
201221-06:05:43,295 nipype.interface INFO:
     stdout 2020-12-21T06:05:43.294871: 0.44640   0.00181  -0.00503  -6.71630;
201221-06:05:43,295 nipype.interface INFO:
     stdout 2020-12-21T06:05:43.294871: 0.00534  -0.12698   0.42796   10.89623;
201221-06:05:43,295 nipype.interface INFO:
     stdout 2020-12-21T06:05:43.294871: 0.00017  -0.23213  -0.06888   45.81297;
201221-06:05:43,295 nipype.interface INFO:
     stdout 2020-12-21T06:05:43.294871: 0.00000   0.00000   0.00000   1.00000;
201221-06:05:44,441 nipype.interface INFO:
     stdout 2020-12-21T06:05:44.441317:
201221-06:05:44,441 nipype.interface INFO:
     stdout 2020-12-21T06:05:44.441317:Resampling
201221-06:05:44,441 nipype.interface INFO:
     stdout 2020-12-21T06:05:44.441317:Output registration matrix is identity
201221-06:05:44,441 nipype.interface INFO:
     stdout 2020-12-21T06:05:44.441317:
201221-06:05:44,442 nipype.interface INFO:
     stdout 2020-12-21T06:05:44.441317:mri_vol2vol done
201221-06:05:48,56 nipype.workflow INFO:
     [Node] Finished "fmriprep_wf.single_subject_04_wf.anat_preproc_wf.anat_reports_wf.seg_rpt".
201221-06:05:51,898 nipype.workflow INFO:
     [Node] Setting-up "fmriprep_wf.single_subject_04_wf.func_preproc_ses_movie_task_rest_wf.t1w_brain" in "/scratch/fmriprep_wf/single_subject_04_wf/func_preproc_ses_movie_task_rest_wf/t1w_brain".
201221-06:05:51,992 nipype.workflow INFO:
     [Node] Running "t1w_brain" ("niworkflows.interfaces.nibabel.ApplyMask")
201221-06:05:53,133 nipype.workflow INFO:
     [Node] Finished "fmriprep_wf.single_subject_04_wf.func_preproc_ses_movie_task_rest_wf.t1w_brain".
201221-06:05:54,535 nipype.workflow INFO:
     [Node] Setting-up "fmriprep_wf.single_subject_04_wf.func_preproc_ses_movie_task_rest_wf.bold_t1_trans_wf.gen_ref" in "/scratch/fmriprep_wf/single_subject_04_wf/func_preproc_ses_movie_task_rest_wf/bold_t1_trans_wf/gen_ref".
201221-06:05:54,660 nipype.workflow INFO:
     [Node] Running "gen_ref" ("niworkflows.interfaces.utils.GenerateSamplingReference")
201221-06:05:55,526 nipype.workflow INFO:
     [Node] Finished "fmriprep_wf.single_subject_04_wf.func_preproc_ses_movie_task_rest_wf.bold_t1_trans_wf.gen_ref".
201221-06:05:56,516 nipype.workflow INFO:
     [Node] Setting-up "fmriprep_wf.single_subject_04_wf.func_preproc_ses_movie_task_rest_wf.bold_t1_trans_wf.aparc_t1w_tfm" in "/scratch/fmriprep_wf/single_subject_04_wf/func_preproc_ses_movie_task_rest_wf/bold_t1_trans_wf/aparc_t1w_tfm".
201221-06:05:56,631 nipype.workflow INFO:
     [Node] Running "aparc_t1w_tfm" ("niworkflows.interfaces.fixes.FixHeaderApplyTransforms"), a CommandLine Interface with command:
antsApplyTransforms --default-value 0 --float 0 --input /scratch/fmriprep_wf/single_subject_04_wf/anat_preproc_wf/surface_recon_wf/segs_to_native_aparc_aseg/resample/seg.nii.gz --interpolation MultiLabel --output seg_trans.nii.gz --reference-image /scratch/fmriprep_wf/single_subject_04_wf/func_preproc_ses_movie_task_rest_wf/bold_t1_trans_wf/gen_ref/sub-04_ses-movie_T1w_corrected_xform_masked_reference.nii.gz --transform identity
201221-06:06:04,729 nipype.workflow INFO:
     [Node] Finished "fmriprep_wf.single_subject_04_wf.func_preproc_ses_movie_task_rest_wf.bold_t1_trans_wf.aparc_t1w_tfm".
201221-06:06:06,144 nipype.workflow INFO:
     [Node] Finished "fmriprep_wf.single_subject_04_wf.func_preproc_ses_movie_task_rest_wf.bold_reg_wf.bbreg_wf.bbregister".
201221-06:06:06,522 nipype.workflow INFO:
     [Node] Setting-up "fmriprep_wf.single_subject_04_wf.func_preproc_ses_movie_task_rest_wf.bold_t1_trans_wf.aseg_t1w_tfm" in "/scratch/fmriprep_wf/single_subject_04_wf/func_preproc_ses_movie_task_rest_wf/bold_t1_trans_wf/aseg_t1w_tfm".
201221-06:06:06,637 nipype.workflow INFO:
     [Node] Running "aseg_t1w_tfm" ("niworkflows.interfaces.fixes.FixHeaderApplyTransforms"), a CommandLine Interface with command:
antsApplyTransforms --default-value 0 --float 0 --input /scratch/fmriprep_wf/single_subject_04_wf/anat_preproc_wf/surface_recon_wf/segs_to_native_aseg/resample/seg.nii.gz --interpolation MultiLabel --output seg_trans.nii.gz --reference-image /scratch/fmriprep_wf/single_subject_04_wf/func_preproc_ses_movie_task_rest_wf/bold_t1_trans_wf/gen_ref/sub-04_ses-movie_T1w_corrected_xform_masked_reference.nii.gz --transform identity
201221-06:06:09,976 nipype.workflow INFO:
     [Node] Setting-up "fmriprep_wf.single_subject_04_wf.anat_preproc_wf.applyrefined" in "/scratch/fmriprep_wf/single_subject_04_wf/anat_preproc_wf/applyrefined".
201221-06:06:10,172 nipype.workflow INFO:
     [Node] Running "applyrefined" ("nipype.interfaces.fsl.maths.ApplyMask"), a CommandLine Interface with command:
fslmaths /scratch/fmriprep_wf/single_subject_04_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/copy_xform/sub-04_ses-movie_T1w_corrected_xform.nii.gz -mas /scratch/fmriprep_wf/single_subject_04_wf/anat_preproc_wf/surface_recon_wf/refine/sub-04_ses-movie_T1w_corrected_xform_rbrainmask.nii.gz /scratch/fmriprep_wf/single_subject_04_wf/anat_preproc_wf/applyrefined/sub-04_ses-movie_T1w_corrected_xform_masked.nii.gz
201221-06:06:12,133 nipype.workflow INFO:
     [Node] Finished "fmriprep_wf.single_subject_04_wf.anat_preproc_wf.applyrefined".
201221-06:06:14,305 nipype.workflow INFO:
     [Node] Finished "fmriprep_wf.single_subject_04_wf.func_preproc_ses_movie_task_rest_wf.bold_t1_trans_wf.aseg_t1w_tfm".
201221-06:06:16,564 nipype.workflow INFO:
     [Node] Setting-up "_lta_ras2ras0" in "/scratch/fmriprep_wf/single_subject_04_wf/func_preproc_ses_movie_task_rest_wf/bold_reg_wf/bbreg_wf/lta_ras2ras/mapflow/_lta_ras2ras0".
201221-06:06:16,571 nipype.workflow INFO:
     [Node] Setting-up "_lta_ras2ras1" in "/scratch/fmriprep_wf/single_subject_04_wf/func_preproc_ses_movie_task_rest_wf/bold_reg_wf/bbreg_wf/lta_ras2ras/mapflow/_lta_ras2ras1".
201221-06:06:16,659 nipype.workflow INFO:
     [Node] Running "_lta_ras2ras0" ("niworkflows.interfaces.freesurfer.PatchedLTAConvert"), a CommandLine Interface with command:
lta_convert --inlta /scratch/fmriprep_wf/single_subject_04_wf/func_preproc_ses_movie_task_rest_wf/bold_reg_wf/bbreg_wf/bbregister/uni_xform_masked_bbreg_sub-04.lta --outlta /scratch/fmriprep_wf/single_subject_04_wf/func_preproc_ses_movie_task_rest_wf/bold_reg_wf/bbreg_wf/lta_ras2ras/mapflow/_lta_ras2ras0/out.lta
201221-06:06:16,717 nipype.workflow INFO:
     [Node] Running "_lta_ras2ras1" ("niworkflows.interfaces.freesurfer.PatchedLTAConvert"), a CommandLine Interface with command:
lta_convert --inlta /scratch/fmriprep_wf/single_subject_04_wf/func_preproc_ses_movie_task_rest_wf/bold_reg_wf/bbreg_wf/mri_coreg/registration.lta --outlta /scratch/fmriprep_wf/single_subject_04_wf/func_preproc_ses_movie_task_rest_wf/bold_reg_wf/bbreg_wf/lta_ras2ras/mapflow/_lta_ras2ras1/out.lta
201221-06:06:16,873 nipype.workflow INFO:
     [Node] Finished "_lta_ras2ras0".
201221-06:06:16,974 nipype.workflow INFO:
     [Node] Finished "_lta_ras2ras1".
201221-06:06:18,567 nipype.workflow INFO:
     [Node] Setting-up "fmriprep_wf.single_subject_04_wf.func_preproc_ses_movie_task_rest_wf.bold_reg_wf.bbreg_wf.lta_ras2ras" in "/scratch/fmriprep_wf/single_subject_04_wf/func_preproc_ses_movie_task_rest_wf/bold_reg_wf/bbreg_wf/lta_ras2ras".
201221-06:06:18,684 nipype.workflow INFO:
     [Node] Setting-up "_lta_ras2ras0" in "/scratch/fmriprep_wf/single_subject_04_wf/func_preproc_ses_movie_task_rest_wf/bold_reg_wf/bbreg_wf/lta_ras2ras/mapflow/_lta_ras2ras0".
201221-06:06:18,733 nipype.workflow INFO:
     [Node] Cached "_lta_ras2ras0" - collecting precomputed outputs
201221-06:06:18,733 nipype.workflow INFO:
     [Node] "_lta_ras2ras0" found cached.
201221-06:06:18,750 nipype.workflow INFO:
     [Node] Setting-up "_lta_ras2ras1" in "/scratch/fmriprep_wf/single_subject_04_wf/func_preproc_ses_movie_task_rest_wf/bold_reg_wf/bbreg_wf/lta_ras2ras/mapflow/_lta_ras2ras1".
201221-06:06:18,801 nipype.workflow INFO:
     [Node] Cached "_lta_ras2ras1" - collecting precomputed outputs
201221-06:06:18,801 nipype.workflow INFO:
     [Node] "_lta_ras2ras1" found cached.
201221-06:06:18,843 nipype.workflow INFO:
     [Node] Finished "fmriprep_wf.single_subject_04_wf.func_preproc_ses_movie_task_rest_wf.bold_reg_wf.bbreg_wf.lta_ras2ras".
201221-06:06:20,543 nipype.workflow INFO:
     [Node] Setting-up "fmriprep_wf.single_subject_04_wf.func_preproc_ses_movie_task_rest_wf.bold_reg_wf.bbreg_wf.compare_transforms" in "/scratch/fmriprep_wf/single_subject_04_wf/func_preproc_ses_movie_task_rest_wf/bold_reg_wf/bbreg_wf/compare_transforms".
201221-06:06:20,648 nipype.workflow INFO:
     [Node] Running "compare_transforms" ("nipype.interfaces.utility.wrappers.Function")
201221-06:06:20,726 nipype.workflow INFO:
     [Node] Finished "fmriprep_wf.single_subject_04_wf.func_preproc_ses_movie_task_rest_wf.bold_reg_wf.bbreg_wf.compare_transforms".
201221-06:06:27,139 nipype.workflow INFO:
     [Node] Setting-up "fmriprep_wf.single_subject_04_wf.func_preproc_ses_movie_task_rest_wf.bold_reg_wf.bbreg_wf.concat_xfm" in "/scratch/fmriprep_wf/single_subject_04_wf/func_preproc_ses_movie_task_rest_wf/bold_reg_wf/bbreg_wf/concat_xfm".
201221-06:06:27,246 nipype.workflow INFO:
     [Node] Running "concat_xfm" ("niworkflows.interfaces.nitransforms.ConcatenateXFMs")
201221-06:06:27,356 nipype.workflow INFO:
     [Node] Finished "fmriprep_wf.single_subject_04_wf.func_preproc_ses_movie_task_rest_wf.bold_reg_wf.bbreg_wf.concat_xfm".
201221-06:06:31,785 nipype.workflow INFO:
     [Node] Setting-up "fmriprep_wf.single_subject_04_wf.func_preproc_ses_movie_task_
rest_wf.bold_t1_trans_wf.mask_t1w_tfm" in "/scratch/fmriprep_wf/single_subject_04_wf/func_preproc_ses_movie_task_rest_wf/bold_t1_trans_wf/mask_t1w_tfm".
201221-06:06:31,999 nipype.workflow INFO:
     [Node] Running "mask_t1w_tfm" ("niworkflows.interfaces.fixes.FixHeaderApplyTransforms"), a CommandLine Interface with command:
antsApplyTransforms --default-value 0 --float 0 --input /scratch/fmriprep_wf/single_subject_04_wf/func_preproc_ses_movie_task_rest_wf/initial_boldref_wf/enhance_and_skullstrip_bold_wf/combine_masks/ref_bold_corrected_brain_mask_maths.nii.gz --interpolation MultiLabel --output ref_bold_corrected_brain_mask_maths_trans.nii.gz --reference-image /scratch/fmriprep_wf/single_subject_04_wf/func_preproc_ses_movie_task_rest_wf/bold_t1_trans_wf/gen_ref/sub-04_ses-movie_T1w_corrected_xform_masked_reference.nii.gz --transform /scratch/fmriprep_wf/single_subject_04_wf/func_preproc_ses_movie_task_rest_wf/bold_reg_wf/bbreg_wf/concat_xfm/out_fwd.tfm
201221-06:06:32,448 nipype.workflow INFO:
     [Node] Setting-up "_acc_msk_tfm0" in "/scratch/fmriprep_wf/single_subject_04_wf/func_preproc_ses_movie_task_rest_wf/bold_confounds_wf/acc_msk_tfm/mapflow/_acc_msk_tfm0".
201221-06:06:32,566 nipype.workflow INFO:
     [Node] Running "_acc_msk_tfm0" ("niworkflows.interfaces.fixes.FixHeaderApplyTransforms"), a CommandLine Interface with command:
antsApplyTransforms --default-value 0 --float 0 --input /scratch/fmriprep_wf/single_subject_04_wf/func_preproc_ses_movie_task_rest_wf/bold_confounds_wf/acc_masks/acompcor_csf.nii.gz --interpolation Gaussian --output acompcor_csf_trans.nii.gz --reference-image /scratch/fmriprep_wf/single_subject_04_wf/func_preproc_ses_movie_task_rest_wf/final_boldref_wf/enhance_and_skullstrip_bold_wf/combine_masks/ref_bold_corrected_brain_mask_maths.nii.gz --transform /scratch/fmriprep_wf/single_subject_04_wf/func_preproc_ses_movie_task_rest_wf/bold_reg_wf/bbreg_wf/concat_xfm/out_inv.tfm
201221-06:06:34,10 nipype.workflow INFO:
     [Node] Finished "_acc_msk_tfm0".
201221-06:06:34,780 nipype.workflow INFO:
     [Node] Finished "fmriprep_wf.single_subject_04_wf.func_preproc_ses_movie_task_rest_wf.bold_t1_trans_wf.mask_t1w_tfm".
201221-06:06:36,346 nipype.workflow INFO:
     [Node] Setting-up "fmriprep_wf.single_subject_04_wf.func_preproc_ses_movie_task_rest_wf.bold_t1_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.pre_mask_dilate" in "/scratch/fmriprep_wf/single_subject_04_wf/func_preproc_ses_movie_task_rest_wf/bold_t1_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/pre_mask_dilate".
201221-06:06:36,384 nipype.workflow INFO:
     [Node] Setting-up "_acc_msk_tfm1" in "/scratch/fmriprep_wf/single_subject_04_wf/func_preproc_ses_movie_task_rest_wf/bold_confounds_wf/acc_msk_tfm/mapflow/_acc_msk_tfm1".
201221-06:06:36,450 nipype.workflow INFO:
     [Node] Running "pre_mask_dilate" ("nipype.interfaces.fsl.maths.DilateImage"), a CommandLine Interface with command:
fslmaths -dt char /scratch/fmriprep_wf/single_subject_04_wf/func_preproc_ses_movie_task_rest_wf/bold_t1_trans_wf/mask_t1w_tfm/ref_bold_corrected_brain_mask_maths_trans.nii.gz -kernel sphere 3.0000 -dilF /scratch/fmriprep_wf/single_subject_04_wf/func_preproc_ses_movie_task_rest_wf/bold_t1_trans_wf/bold_reference_wf/enhance_and_skullstrip_bold_wf/pre_mask_dilate/ref_bold_corrected_brain_mask_maths_trans_dil.nii.gz
201221-06:06:36,513 nipype.workflow INFO:
     [Node] Running "_acc_msk_tfm1" ("niworkflows.interfaces.fixes.FixHeaderApplyTransforms"), a CommandLine Interface with command:
antsApplyTransforms --default-value 0 --float 0 --input /scratch/fmriprep_wf/single_subject_04_wf/func_preproc_ses_movie_task_rest_wf/bold_confounds_wf/acc_masks/acompcor_wm.nii.gz --interpolation Gaussian --output acompcor_wm_trans.nii.gz --reference-image /scratch/fmriprep_wf/single_subject_04_wf/func_preproc_ses_movie_task_rest_wf/final_boldref_wf/enhance_and_skullstrip_bold_wf/combine_masks/ref_bold_corrected_brain_mask_maths.nii.gz --transform /scratch/fmriprep_wf/single_subject_04_wf/func_preproc_ses_movie_task_rest_wf/bold_reg_wf/bbreg_wf/concat_xfm/out_inv.tfm
201221-06:06:36,852 nipype.workflow INFO:
     [Node] Finished "fmriprep_wf.single_subject_04_wf.func_preproc_ses_movie_task_rest_wf.bold_t1_trans_wf.bold_reference_wf.enhance_and_skullstrip_bold_wf.pre_mask_dilate".
201221-06:06:37,671 nipype.workflow INFO:
     [Node] Finished "_acc_msk_tfm1".
201221-06:06:38,374 nipype.workflow INFO:
     [Node] Setting-up "_acc_msk_tfm2" in "/scratch/fmriprep_wf/single_subject_04_wf/func_preproc_ses_movie_task_rest_wf/bold_confounds_wf/acc_msk_tfm/mapflow/_acc_msk_tfm2".
201221-06:06:38,500 nipype.workflow INFO:
     [Node] Running "_acc_msk_tfm2" ("niworkflows.interfaces.fixes.FixHeaderApplyTransforms"), a CommandLine Interface with command:
antsApplyTransforms --default-value 0 --float 0 --input /scratch/fmriprep_wf/single_subject_04_wf/func_preproc_ses_movie_task_rest_wf/bold_confounds_wf/acc_masks/acompcor_wmcsf.nii.gz --interpolation Gaussian --output acompcor_wmcsf_trans.nii.gz --reference-image /scratch/fmriprep_wf/single_subject_04_wf/func_preproc_ses_movie_task_rest_wf/final_boldref_wf/enhance_and_skullstrip_bold_wf/combine_masks/ref_bold_corrected_brain_mask_maths.nii.gz --transform /scratch/fmriprep_wf/single_subject_04_wf/func_preproc_ses_movie_task_rest_wf/bold_reg_wf/bbreg_wf/concat_xfm/out_inv.tfm
201221-06:06:39,612 nipype.workflow INFO:
     [Node] Finished "_acc_msk_tfm2".
201221-06:06:40,424 nipype.workflow INFO:
     [Node] Setting-up "fmriprep_wf.single_subject_04_wf.func_preproc_ses_movie_task_rest_wf.bold_confounds_wf.acc_msk_tfm" in "/scratch/fmriprep_wf/single_subject_04_wf/func_preproc_ses_movie_task_rest_wf/bold_confounds_wf/acc_msk_tfm".
201221-06:06:40,786 nipype.workflow INFO:
     [Node] Setting-up "_acc_msk_tfm0" in "/scratch/fmriprep_wf/single_subject_04_wf/func_preproc_ses_movie_task_rest_wf/bold_confounds_wf/acc_msk_tfm/mapflow/_acc_msk_tfm0".
201221-06:06:40,854 nipype.workflow INFO:
     [Node] Cached "_acc_msk_tfm0" - collecting precomputed outputs
201221-06:06:40,854 nipype.workflow INFO:
     [Node] "_acc_msk_tfm0" found cached.
201221-06:06:40,888 nipype.workflow INFO:
     [Node] Setting-up "_acc_msk_tfm1" in "/scratch/fmriprep_wf/single_subject_04_wf/func_preproc_ses_movie_task_rest_wf/bold_confounds_wf/acc_msk_tfm/mapflow/_acc_msk_tfm1".
201221-06:06:40,956 nipype.workflow INFO:
     [Node] Cached "_acc_msk_tfm1" - collecting precomputed outputs
201221-06:06:40,957 nipype.workflow INFO:
     [Node] "_acc_msk_tfm1" found cached.
201221-06:06:40,989 nipype.workflow INFO:
     [Node] Setting-up "_acc_msk_tfm2" in "/scratch/fmriprep_wf/single_subject_04_wf/func_preproc_ses_movie_task_rest_wf/bold_confounds_wf/acc_msk_tfm/mapflow/_acc_msk_tfm2".
201221-06:06:41,56 nipype.workflow INFO:
     [Node] Cached "_acc_msk_tfm2" - collecting precomputed outputs
201221-06:06:41,56 nipype.workflow INFO:
     [Node] "_acc_msk_tfm2" found cached.
201221-06:06:41,105 nipype.workflow INFO:
     [Node] Finished "fmriprep_wf.single_subject_04_wf.func_preproc_ses_movie_task_rest_wf.bold_confounds_wf.acc_msk_tfm".
201221-06:06:44,374 nipype.workflow INFO:
     [Node] Setting-up "_acc_msk_brain0" in "/scratch/fmriprep_wf/single_subject_04_wf/func_preproc_ses_movie_task_rest_wf/bold_confounds_wf/acc_msk_brain/mapflow/_acc_msk_brain0".
201221-06:06:44,385 nipype.workflow INFO:
     [Node] Setting-up "_acc_msk_brain1" in "/scratch/fmriprep_wf/single_subject_04_wf/func_preproc_ses_movie_task_rest_wf/bold_confounds_wf/acc_msk_brain/mapflow/_acc_msk_brain1".
201221-06:06:44,456 nipype.workflow INFO:
     [Node] Running "_acc_msk_brain0" ("niworkflows.interfaces.nibabel.ApplyMask")
201221-06:06:44,491 nipype.workflow INFO:
     [Node] Running "_acc_msk_brain1" ("niworkflows.interfaces.nibabel.ApplyMask")
201221-06:06:44,657 nipype.workflow INFO:
     [Node] Finished "_acc_msk_brain1".
201221-06:06:44,730 nipype.workflow INFO:
     [Node] Finished "_acc_msk_brain0".
201221-06:06:46,381 nipype.workflow INFO:
     [Node] Setting-up "_acc_msk_brain2" in "/scratch/fmriprep_wf/single_subject_04_wf/func_preproc_ses_movie_task_rest_wf/bold_confounds_wf/acc_msk_brain/mapflow/_acc_msk_brain2".
201221-06:06:46,480 nipype.workflow INFO:
     [Node] Running "_acc_msk_brain2" ("niworkflows.interfaces.nibabel.ApplyMask")
201221-06:06:46,662 nipype.workflow INFO:
     [Node] Finished "_acc_msk_brain2".
201221-06:06:48,415 nipype.workflow INFO:
     [Node] Setting-up "fmriprep_wf.single_subject_04_wf.func_preproc_ses_movie_task_rest_wf.bold_confounds_wf.acc_msk_brain" in "/scratch/fmriprep_wf/single_subject_04_wf/func_preproc_ses_movie_task_rest_wf/bold_confounds_wf/acc_msk_brain".
201221-06:06:48,599 nipype.workflow INFO:
     [Node] Setting-up "_acc_msk_brain0" in "/scratch/fmriprep_wf/single_subject_04_wf/func_preproc_ses_movie_task_rest_wf/bold_confounds_wf/acc_msk_brain/mapflow/_acc_msk_brain0".
201221-06:06:48,659 nipype.workflow INFO:
     [Node] Cached "_acc_msk_brain0" - collecting precomputed outputs
201221-06:06:48,659 nipype.workflow INFO:
     [Node] "_acc_msk_brain0" found cached.
201221-06:06:48,682 nipype.workflow INFO:
     [Node] Setting-up "_acc_msk_brain1" in "/scratch/fmriprep_wf/single_subject_04_wf/func_preproc_ses_movie_task_rest_wf/bold_confounds_wf/acc_msk_brain/mapflow/_acc_msk_brain1".
201221-06:06:48,742 nipype.workflow INFO:
     [Node] Cached "_acc_msk_brain1" - collecting precomputed outputs
201221-06:06:48,742 nipype.workflow INFO:
     [Node] "_acc_msk_brain1" found cached.
201221-06:06:48,764 nipype.workflow INFO:
     [Node] Setting-up "_acc_msk_brain2" in "/scratch/fmriprep_wf/single_subject_04_wf/func_preproc_ses_movie_task_rest_wf/bold_confounds_wf/acc_msk_brain/mapflow/_acc_msk_brain2".
201221-06:06:48,825 nipype.workflow INFO:
     [Node] Cached "_acc_msk_brain2" - collecting precomputed outputs
201221-06:06:48,825 nipype.workflow INFO:
     [Node] "_acc_msk_brain2" found cached.
201221-06:06:48,866 nipype.workflow INFO:
     [Node] Finished "fmriprep_wf.single_subject_04_wf.func_preproc_ses_movie_task_rest_wf.bold_confounds_wf.acc_msk_brain".
201221-06:06:52,379 nipype.workflow INFO:
     [Node] Setting-up "_acc_msk_bin0" in "/scratch/fmriprep_wf/single_subject_04_wf/func_preproc_ses_movie_task_rest_wf/bold_confounds_wf/acc_msk_bin/mapflow/_acc_msk_bin0".
201221-06:06:52,385 nipype.workflow INFO:
     [Node] Setting-up "_acc_msk_bin1" in "/scratch/fmriprep_wf/single_subject_04_wf/func_preproc_ses_movie_task_rest_wf/bold_confounds_wf/acc_msk_bin/mapflow/_acc_msk_bin1".
201221-06:06:52,463 nipype.workflow INFO:
     [Node] Running "_acc_msk_bin0" ("niworkflows.interfaces.nibabel.Binarize")
201221-06:06:52,475 nipype.workflow INFO:
     [Node] Running "_acc_msk_bin1" ("niworkflows.interfaces.nibabel.Binarize")
201221-06:06:52,621 nipype.workflow INFO:
     [Node] Finished "_acc_msk_bin0".
201221-06:06:52,668 nipype.workflow INFO:
     [Node] Finished "_acc_msk_bin1".
201221-06:06:54,376 nipype.workflow INFO:
     [Node] Setting-up "_acc_msk_bin2" in "/scratch/fmriprep_wf/single_subject_04_wf/func_preproc_ses_movie_task_rest_wf/bold_confounds_wf/acc_msk_bin/mapflow/_acc_msk_bin2".
201221-06:06:54,505 nipype.workflow INFO:
     [Node] Running "_acc_msk_bin2" ("niworkflows.interfaces.nibabel.Binarize")
201221-06:06:54,708 nipype.workflow INFO:
     [Node] Finished "_acc_msk_bin2".
201221-06:06:56,369 nipype.workflow INFO:
     [Node] Setting-up "fmriprep_wf.single_subject_04_wf.func_preproc_ses_movie_task_rest_wf.bold_confounds_wf.acc_msk_bin" in "/scratch/fmriprep_wf/single_subject_04_wf/func_preproc_ses_movie_task_rest_wf/bold_confounds_wf/acc_msk_bin".
201221-06:06:56,510 nipype.workflow INFO:
     [Node] Setting-up "_acc_msk_bin0" in "/scratch/fmriprep_wf/single_subject_04_wf/func_preproc_ses_movie_task_rest_wf/bold_confounds_wf/acc_msk_bin/mapflow/_acc_msk_bin0".
201221-06:06:56,557 nipype.workflow INFO:
     [Node] Cached "_acc_msk_bin0" - collecting precomputed outputs
201221-06:06:56,558 nipype.workflow INFO:
     [Node] "_acc_msk_bin0" found cached.
201221-06:06:56,571 nipype.workflow INFO:
     [Node] Setting-up "_acc_msk_bin1" in "/scratch/fmriprep_wf/single_subject_04_wf/func_preproc_ses_movie_task_rest_wf/bold_confounds_wf/acc_msk_bin/mapflow/_acc_msk_bin1".
201221-06:06:56,620 nipype.workflow INFO:
     [Node] Cached "_acc_msk_bin1" - collecting precomputed outputs
201221-06:06:56,620 nipype.workflow INFO:
     [Node] "_acc_msk_bin1" found cached.
201221-06:06:56,634 nipype.workflow INFO:
     [Node] Setting-up "_acc_msk_bin2" in "/scratch/fmriprep_wf/single_subject_04_wf/func_preproc_ses_movie_task_rest_wf/bold_confounds_wf/acc_msk_bin/mapflow/_acc_msk_bin2".
201221-06:06:56,681 nipype.workflow INFO:
     [Node] Cached "_acc_msk_bin2" - collecting precomputed outputs
201221-06:06:56,681 nipype.workflow INFO:
     [Node] "_acc_msk_bin2" found cached.
201221-06:06:56,722 nipype.workflow INFO:
     [Node] Finished "fmriprep_wf.single_subject_04_wf.func_preproc_ses_movie_task_rest_wf.bold_confounds_wf.acc_msk_bin".
201221-06:06:59,982 nipype.workflow INFO:
     [Node] Setting-up "fmriprep_wf.single_subject_04_wf.func_preproc_ses_movie_task_rest_wf.bold_confounds_wf.acompcor" in "/scratch/fmriprep_wf/single_subject_04_wf/func_preproc_ses_movie_task_rest_wf/bold_confounds_wf/acompcor".
201221-06:07:00,233 nipype.workflow INFO:
     [Node] Running "acompcor" ("niworkflows.interfaces.patches.RobustACompCor")
201221-06:07:00,611 nipype.workflow INFO:
     [Node] Setting-up "fmriprep_wf.single_subject_04_wf.func_preproc_ses_movie_task_rest_wf.bold_confounds_wf.rois_plot" in "/scratch/fmriprep_wf/single_subject_04_wf/func_preproc_ses_movie_task_rest_wf/bold_confounds_wf/rois_plot".
201221-06:07:00,747 nipype.workflow INFO:
     [Node] Running "rois_plot" ("niworkflows.interfaces.masks.ROIsPlot")
201221-06:07:07,822 nipype.workflow INFO:
     [Node] Finished "fmriprep_wf.single_subject_04_wf.func_preproc_ses_movie_task_rest_wf.bold_confounds_wf.acompcor".
201221-06:07:08,634 nipype.workflow INFO:
     [Node] Setting-up "fmriprep_wf.single_subject_04_wf.func_preproc_ses_movie_task_rest_wf.bold_confounds_wf.signals" in "/scratch/fmriprep_wf/single_subject_04_wf/func_preproc_ses_movie_task_rest_wf/bold_confounds_wf/signals".
201221-06:07:08,800 nipype.workflow INFO:
     [Node] Running "signals" ("niworkflows.interfaces.images.SignalExtraction")
201221-06:07:09,973 nipype.workflow INFO:
     [Node] Finished "fmriprep_wf.single_subject_04_wf.func_preproc_ses_movie_task_rest_wf.bold_confounds_wf.rois_plot".
201221-06:07:12,494 nipype.workflow INFO:
     [Node] Setting-up "fmriprep_wf.single_subject_04_wf.func_preproc_ses_movie_task_rest_wf.bold_confounds_wf.acc_metadata_fmt" in "/scratch/fmriprep_wf/single_subject_04_wf/func_preproc_ses_movie_task_rest_wf/bold_confounds_wf/acc_metadata_fmt".
201221-06:07:12,554 nipype.workflow INFO:
     [Node] Running "acc_metadata_fmt" ("niworkflows.interfaces.utils.TSV2JSON")
201221-06:07:12,690 nipype.workflow INFO:
     [Node] Finished "fmriprep_wf.single_subject_04_wf.func_preproc_ses_movie_task_rest_wf.bold_confounds_wf.acc_metadata_fmt".
201221-06:07:12,708 nipype.workflow INFO:
     [Node] Finished "fmriprep_wf.single_subject_04_wf.func_preproc_ses_movie_task_rest_wf.bold_confounds_wf.signals".
201221-06:07:15,59 nipype.workflow INFO:
     [Node] Setting-up "fmriprep_wf.single_subject_04_wf.func_preproc_ses_movie_task_rest_wf.bold_confounds_wf.compcor_plot" in "/scratch/fmriprep_wf/single_subject_04_wf/func_preproc_ses_movie_task_rest_wf/bold_confounds_wf/compcor_plot".
201221-06:07:15,148 nipype.workflow INFO:
     [Node] Running "compcor_plot" ("niworkflows.interfaces.plotting.CompCorVariancePlot")
201221-06:07:15,699 nipype.workflow INFO:
     [Node] Finished "fmriprep_wf.single_subject_04_wf.func_preproc_ses_movie_task_rest_wf.bold_confounds_wf.compcor_plot".
201221-06:07:20,142 nipype.workflow INFO:
     [Node] Setting-up "fmriprep_wf.single_subject_04_wf.func_preproc_ses_movie_task_rest_wf.bold_confounds_wf.conf_corr_plot" in "/scratch/fmriprep_wf/single_subject_04_wf/func_preproc_ses_movie_task_rest_wf/bold_confounds_wf/conf_corr_plot".
201221-06:07:20,149 nipype.workflow INFO:
     [Node] Setting-up "fmriprep_wf.single_subject_04_wf.func_preproc_ses_movie_task_rest_wf.bold_confounds_wf.model_expansion" in "/scratch/fmriprep_wf/single_subject_04_wf/func_preproc_ses_movie_task_rest_wf/bold_confounds_wf/model_expansion".
201221-06:07:20,223 nipype.workflow INFO:
     [Node] Running "conf_corr_plot" ("niworkflows.interfaces.plotting.ConfoundsCorrelationPlot")
201221-06:07:20,248 nipype.workflow INFO:
     [Node] Running "model_expansion" ("niworkflows.interfaces.confounds.ExpandModel")
201221-06:07:20,533 nipype.workflow INFO:
     [Node] Finished "fmriprep_wf.single_subject_04_wf.func_preproc_ses_movie_task_rest_wf.bold_confounds_wf.model_expansion".
201221-06:07:21,159 nipype.workflow INFO:
     [Node] Finished "fmriprep_wf.single_subject_04_wf.func_preproc_ses_movie_task_rest_wf.bold_confounds_wf.conf_corr_plot".
201221-06:07:23,521 nipype.workflow INFO:
     [Node] Setting-up "fmriprep_wf.single_subject_04_wf.func_preproc_ses_movie_task_rest_wf.bold_confounds_wf.spike_regressors" in "/scratch/fmriprep_wf/single_subject_04_wf/func_preproc_ses_movie_task_rest_wf/bold_confounds_wf/spike_regressors".
201221-06:07:23,600 nipype.workflow INFO:
     [Node] Running "spike_regressors" ("niworkflows.interfaces.confounds.SpikeRegressors")
201221-06:07:23,798 nipype.workflow INFO:
     [Node] Finished "fmriprep_wf.single_subject_04_wf.func_preproc_ses_movie_task_rest_wf.bold_confounds_wf.spike_regressors".
201221-06:20:32,854 nipype.workflow INFO:
     [Node] Finished "_midthickness1".
201221-06:20:35,326 nipype.workflow INFO:
     [Node] Setting-up "fmriprep_wf.single_subject_04_wf.anat_preproc_wf.anat_norm_wf.registration" in "/scratch/fmriprep_wf/single_subject_04_wf/anat_preproc_wf/anat_norm_wf/_template_MNI152NLin2009cAsym/registration".
201221-06:20:35,553 nipype.workflow INFO:
     [Node] Running "registration" ("niworkflows.interfaces.mni.RobustMNINormalization")
201221-06:20:38,666 nipype.workflow INFO:
     [Node] Finished "_midthickness0".
201221-06:20:39,345 nipype.workflow INFO:
     [Node] Setting-up "fmriprep_wf.single_subject_04_wf.anat_preproc_wf.surface_recon_wf.gifti_surface_wf.midthickness" in "/scratch/fmriprep_wf/single_subject_04_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/midthickness".
201221-06:20:39,454 nipype.workflow INFO:
     [Node] Setting-up "_midthickness0" in "/scratch/fmriprep_wf/single_subject_04_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/midthickness/mapflow/_midthickness0".
201221-06:20:39,491 nipype.workflow INFO:
     [Node] Cached "_midthickness0" - collecting precomputed outputs
201221-06:20:39,491 nipype.workflow INFO:
     [Node] "_midthickness0" found cached.
201221-06:20:39,503 nipype.workflow INFO:
     [Node] Setting-up "_midthickness1" in "/scratch/fmriprep_wf/single_subject_04_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/midthickness/mapflow/_midthickness1".
201221-06:20:39,538 nipype.workflow INFO:
     [Node] Cached "_midthickness1" - collecting precomputed outputs
201221-06:20:39,538 nipype.workflow INFO:
     [Node] "_midthickness1" found cached.
201221-06:20:39,585 nipype.workflow INFO:
     [Node] Finished "fmriprep_wf.single_subject_04_wf.anat_preproc_wf.surface_recon_wf.gifti_surface_wf.midthickness".
201221-06:20:41,392 nipype.workflow INFO:
     [Node] Setting-up "fmriprep_wf.single_subject_04_wf.anat_preproc_wf.surface_recon_wf.gifti_surface_wf.save_midthickness" in "/scratch/fmriprep_wf/single_subject_04_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/save_midthickness".
201221-06:20:41,605 nipype.workflow INFO:
     [Node] Running "save_midthickness" ("nipype.interfaces.io.DataSink")
201221-06:20:44,11 nipype.workflow INFO:
     [Node] Finished "fmriprep_wf.single_subject_04_wf.anat_preproc_wf.surface_recon_wf.gifti_surface_wf.save_midthickness".
201221-06:20:49,394 nipype.workflow INFO:
     [Node] Setting-up "_fs2gii0" in "/scratch/fmriprep_wf/single_subject_04_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/fs2gii/mapflow/_fs2gii0".
201221-06:20:49,512 nipype.workflow INFO:
     [Node] Running "_fs2gii0" ("nipype.interfaces.freesurfer.utils.MRIsConvert"), a CommandLine Interface with command:
mris_convert /out/sourcedata/freesurfer/sub-04/surf/lh.smoothwm /scratch/fmriprep_wf/single_subject_04_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/fs2gii/mapflow/_fs2gii0/lh.smoothwm_converted.gii
201221-06:20:54,514 nipype.workflow INFO:
     [Node] Finished "_fs2gii0".
201221-06:20:55,392 nipype.workflow INFO:
     [Node] Setting-up "_fs2gii1" in "/scratch/fmriprep_wf/single_subject_04_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/fs2gii/mapflow/_fs2gii1".
201221-06:20:55,500 nipype.workflow INFO:
     [Node] Running "_fs2gii1" ("nipype.interfaces.freesurfer.utils.MRIsConvert"), a CommandLine Interface with command:
mris_convert /out/sourcedata/freesurfer/sub-04/surf/rh.smoothwm /scratch/fmriprep_wf/single_subject_04_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/fs2gii/mapflow/_fs2gii1/rh.smoothwm_converted.gii
201221-06:21:00,645 nipype.workflow INFO:
     [Node] Finished "_fs2gii1".
201221-06:21:01,410 nipype.workflow INFO:
     [Node] Setting-up "_fs2gii2" in "/scratch/fmriprep_wf/single_subject_04_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/fs2gii/mapflow/_fs2gii2".
201221-06:21:01,561 nipype.workflow INFO:
     [Node] Running "_fs2gii2" ("nipype.interfaces.freesurfer.utils.MRIsConvert"), a CommandLine Interface with command:
mris_convert /out/sourcedata/freesurfer/sub-04/surf/lh.pial /scratch/fmriprep_wf/single_subject_04_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/fs2gii/mapflow/_fs2gii2/lh.pial_converted.gii
201221-06:21:06,460 nipype.workflow INFO:
     [Node] Finished "_fs2gii2".
201221-06:21:07,470 nipype.workflow INFO:
     [Node] Setting-up "_fs2gii3" in "/scratch/fmriprep_wf/single_subject_04_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/fs2gii/mapflow/_fs2gii3".
201221-06:21:07,588 nipype.workflow INFO:
     [Node] Running "_fs2gii3" ("nipype.interfaces.freesurfer.utils.MRIsConvert"), a CommandLine Interface with command:
mris_convert /out/sourcedata/freesurfer/sub-04/surf/rh.pial /scratch/fmriprep_wf/single_subject_04_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/fs2gii/mapflow/_fs2gii3/rh.pial_converted.gii
201221-06:21:12,419 nipype.workflow INFO:
     [Node] Finished "_fs2gii3".
201221-06:21:13,462 nipype.workflow INFO:
     [Node] Setting-up "_fs2gii4" in "/scratch/fmriprep_wf/single_subject_04_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/fs2gii/mapflow/_fs2gii4".
201221-06:21:13,571 nipype.workflow INFO:
     [Node] Running "_fs2gii4" ("nipype.interfaces.freesurfer.utils.MRIsConvert"), a CommandLine Interface with command:
mris_convert /out/sourcedata/freesurfer/sub-04/surf/lh.inflated /scratch/fmriprep_wf/single_subject_04_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/fs2gii/mapflow/_fs2gii4/lh.inflated_converted.gii
201221-06:21:18,642 nipype.workflow INFO:
     [Node] Finished "_fs2gii4".
201221-06:21:19,491 nipype.workflow INFO:
     [Node] Setting-up "_fs2gii5" in "/scratch/fmriprep_wf/single_subject_04_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/fs2gii/mapflow/_fs2gii5".
201221-06:21:19,590 nipype.workflow INFO:
     [Node] Running "_fs2gii5" ("nipype.interfaces.freesurfer.utils.MRIsConvert"), a CommandLine Interface with command:
mris_convert /out/sourcedata/freesurfer/sub-04/surf/rh.inflated /scratch/fmriprep_wf/single_subject_04_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/fs2gii/mapflow/_fs2gii5/rh.inflated_converted.gii
201221-06:21:24,617 nipype.workflow INFO:
     [Node] Finished "_fs2gii5".
201221-06:21:25,450 nipype.workflow INFO:
     [Node] Setting-up "_fs2gii6" in "/scratch/fmriprep_wf/single_subject_04_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/fs2gii/mapflow/_fs2gii6".
201221-06:21:25,569 nipype.workflow INFO:
     [Node] Running "_fs2gii6" ("nipype.interfaces.freesurfer.utils.MRIsConvert"), a CommandLine Interface with command:
mris_convert /out/sourcedata/freesurfer/sub-04/surf/lh.midthickness /scratch/fmriprep_wf/single_subject_04_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/fs2gii/mapflow/_fs2gii6/lh.midthickness_converted.gii
201221-06:21:30,493 nipype.workflow INFO:
     [Node] Finished "_fs2gii6".
201221-06:21:31,488 nipype.workflow INFO:
     [Node] Setting-up "_fs2gii7" in "/scratch/fmriprep_wf/single_subject_04_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/fs2gii/mapflow/_fs2gii7".
201221-06:21:31,612 nipype.workflow INFO:
     [Node] Running "_fs2gii7" ("nipype.interfaces.freesurfer.utils.MRIsConvert"), a CommandLine Interface with command:
mris_convert /out/sourcedata/freesurfer/sub-04/surf/rh.midthickness /scratch/fmriprep_wf/single_subject_04_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/fs2gii/mapflow/_fs2gii7/rh.midthickness_converted.gii
201221-06:21:36,371 nipype.workflow INFO:
     [Node] Finished "_fs2gii7".
201221-06:21:37,550 nipype.workflow INFO:
     [Node] Setting-up "fmriprep_wf.single_subject_04_wf.anat_preproc_wf.surface_recon_wf.gifti_surface_wf.fs2gii" in "/scratch/fmriprep_wf/single_subject_04_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/fs2gii".
201221-06:21:37,870 nipype.workflow INFO:
     [Node] Setting-up "_fs2gii0" in "/scratch/fmriprep_wf/single_subject_04_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/fs2gii/mapflow/_fs2gii0".
201221-06:21:37,911 nipype.workflow INFO:
     [Node] Cached "_fs2gii0" - collecting precomputed outputs
201221-06:21:37,911 nipype.workflow INFO:
     [Node] "_fs2gii0" found cached.
201221-06:21:37,930 nipype.workflow INFO:
     [Node] Setting-up "_fs2gii1" in "/scratch/fmriprep_wf/single_subject_04_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/fs2gii/mapflow/_fs2gii1".
201221-06:21:37,975 nipype.workflow INFO:
     [Node] Cached "_fs2gii1" - collecting precomputed outputs
201221-06:21:37,975 nipype.workflow INFO:
     [Node] "_fs2gii1" found cached.
201221-06:21:38,3 nipype.workflow INFO:
     [Node] Setting-up "_fs2gii2" in "/scratch/fmriprep_wf/single_subject_04_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/fs2gii/mapflow/_fs2gii2".
201221-06:21:38,66 nipype.workflow INFO:
     [Node] Cached "_fs2gii2" - collecting precomputed outputs
201221-06:21:38,66 nipype.workflow INFO:
     [Node] "_fs2gii2" found cached.
201221-06:21:38,77 nipype.workflow INFO:
     [Node] Setting-up "_fs2gii3" in "/scratch/fmriprep_wf/single_subject_04_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/fs2gii/mapflow/_fs2gii3".
201221-06:21:38,133 nipype.workflow INFO:
     [Node] Cached "_fs2gii3" - collecting precomputed outputs
201221-06:21:38,133 nipype.workflow INFO:
     [Node] "_fs2gii3" found cached.
201221-06:21:38,149 nipype.workflow INFO:
     [Node] Setting-up "_fs2gii4" in "/scratch/fmriprep_wf/single_subject_04_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/fs2gii/mapflow/_fs2gii4".
201221-06:21:38,193 nipype.workflow INFO:
     [Node] Cached "_fs2gii4" - collecting precomputed outputs
201221-06:21:38,194 nipype.workflow INFO:
     [Node] "_fs2gii4" found cached.
201221-06:21:38,230 nipype.workflow INFO:
     [Node] Setting-up "_fs2gii5" in "/scratch/fmriprep_wf/single_subject_04_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/fs2gii/mapflow/_fs2gii5".
201221-06:21:38,283 nipype.workflow INFO:
     [Node] Cached "_fs2gii5" - collecting precomputed outputs
201221-06:21:38,283 nipype.workflow INFO:
     [Node] "_fs2gii5" found cached.
201221-06:21:38,297 nipype.workflow INFO:
     [Node] Setting-up "_fs2gii6" in "/scratch/fmriprep_wf/single_subject_04_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/fs2gii/mapflow/_fs2gii6".
201221-06:21:38,346 nipype.workflow INFO:
     [Node] Cached "_fs2gii6" - collecting precomputed outputs
201221-06:21:38,347 nipype.workflow INFO:
     [Node] "_fs2gii6" found cached.
201221-06:21:38,359 nipype.workflow INFO:
     [Node] Setting-up "_fs2gii7" in "/scratch/fmriprep_wf/single_subject_04_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/fs2gii/mapflow/_fs2gii7".
201221-06:21:38,424 nipype.workflow INFO:
     [Node] Cached "_fs2gii7" - collecting precomputed outputs
201221-06:21:38,425 nipype.workflow INFO:
     [Node] "_fs2gii7" found cached.
201221-06:21:38,495 nipype.workflow INFO:
     [Node] Finished "fmriprep_wf.single_subject_04_wf.anat_preproc_wf.surface_recon_wf.gifti_surface_wf.fs2gii".
201221-06:21:41,475 nipype.workflow INFO:
     [Node] Setting-up "_fix_surfs0" in "/scratch/fmriprep_wf/single_subject_04_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/fix_surfs/mapflow/_fix_surfs0".
201221-06:21:41,587 nipype.workflow INFO:
     [Node] Running "_fix_surfs0" ("niworkflows.interfaces.surf.NormalizeSurf")
201221-06:21:42,626 nipype.workflow INFO:
     [Node] Finished "_fix_surfs0".
201221-06:21:43,487 nipype.workflow INFO:
     [Node] Setting-up "_fix_surfs1" in "/scratch/fmriprep_wf/single_subject_04_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/fix_surfs/mapflow/_fix_surfs1".
201221-06:21:43,581 nipype.workflow INFO:
     [Node] Running "_fix_surfs1" ("niworkflows.interfaces.surf.NormalizeSurf")
201221-06:21:44,500 nipype.workflow INFO:
     [Node] Finished "_fix_surfs1".
201221-06:21:45,513 nipype.workflow INFO:
     [Node] Setting-up "_fix_surfs2" in "/scratch/fmriprep_wf/single_subject_04_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/fix_surfs/mapflow/_fix_surfs2".
201221-06:21:45,606 nipype.workflow INFO:
     [Node] Running "_fix_surfs2" ("niworkflows.interfaces.surf.NormalizeSurf")
201221-06:21:46,528 nipype.workflow INFO:
     [Node] Finished "_fix_surfs2".
201221-06:21:47,489 nipype.workflow INFO:
     [Node] Setting-up "_fix_surfs3" in "/scratch/fmriprep_wf/single_subject_04_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/fix_surfs/mapflow/_fix_surfs3".
201221-06:21:47,592 nipype.workflow INFO:
     [Node] Running "_fix_surfs3" ("niworkflows.interfaces.surf.NormalizeSurf")
201221-06:21:48,509 nipype.workflow INFO:
     [Node] Finished "_fix_surfs3".
201221-06:21:49,527 nipype.workflow INFO:
     [Node] Setting-up "_fix_surfs4" in "/scratch/fmriprep_wf/single_subject_04_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/fix_surfs/mapflow/_fix_surfs4".
201221-06:21:49,639 nipype.workflow INFO:
     [Node] Running "_fix_surfs4" ("niworkflows.interfaces.surf.NormalizeSurf")
201221-06:21:50,578 nipype.workflow INFO:
     [Node] Finished "_fix_surfs4".
201221-06:21:51,514 nipype.workflow INFO:
     [Node] Setting-up "_fix_surfs5" in "/scratch/fmriprep_wf/single_subject_04_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/fix_surfs/mapflow/_fix_surfs5".
201221-06:21:51,623 nipype.workflow INFO:
     [Node] Running "_fix_surfs5" ("niworkflows.interfaces.surf.NormalizeSurf")
201221-06:21:52,527 nipype.workflow INFO:
     [Node] Finished "_fix_surfs5".
201221-06:21:53,500 nipype.workflow INFO:
     [Node] Setting-up "_fix_surfs6" in "/scratch/fmriprep_wf/single_subject_04_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/fix_surfs/mapflow/_fix_surfs6".
201221-06:21:53,596 nipype.workflow INFO:
     [Node] Running "_fix_surfs6" ("niworkflows.interfaces.surf.NormalizeSurf")
201221-06:21:54,474 nipype.workflow INFO:
     [Node] Finished "_fix_surfs6".
201221-06:21:55,500 nipype.workflow INFO:
     [Node] Setting-up "_fix_surfs7" in "/scratch/fmriprep_wf/single_subject_04_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/fix_surfs/mapflow/_fix_surfs7".
201221-06:21:55,607 nipype.workflow INFO:
     [Node] Running "_fix_surfs7" ("niworkflows.interfaces.surf.NormalizeSurf")
201221-06:21:56,580 nipype.workflow INFO:
     [Node] Finished "_fix_surfs7".
201221-06:21:57,582 nipype.workflow INFO:
     [Node] Setting-up "fmriprep_wf.single_subject_04_wf.anat_preproc_wf.surface_recon_wf.gifti_surface_wf.fix_surfs" in "/scratch/fmriprep_wf/single_subject_04_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/fix_surfs".
201221-06:21:57,868 nipype.workflow INFO:
     [Node] Setting-up "_fix_surfs0" in "/scratch/fmriprep_wf/single_subject_04_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/fix_surfs/mapflow/_fix_surfs0".
201221-06:21:57,917 nipype.workflow INFO:
     [Node] Cached "_fix_surfs0" - collecting precomputed outputs
201221-06:21:57,917 nipype.workflow INFO:
     [Node] "_fix_surfs0" found cached.
201221-06:21:57,938 nipype.workflow INFO:
     [Node] Setting-up "_fix_surfs1" in "/scratch/fmriprep_wf/single_subject_04_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/fix_surfs/mapflow/_fix_surfs1".
201221-06:21:57,993 nipype.workflow INFO:
     [Node] Cached "_fix_surfs1" - collecting precomputed outputs
201221-06:21:57,993 nipype.workflow INFO:
     [Node] "_fix_surfs1" found cached.
201221-06:21:58,18 nipype.workflow INFO:
     [Node] Setting-up "_fix_surfs2" in "/scratch/fmriprep_wf/single_subject_04_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/fix_surfs/mapflow/_fix_surfs2".
201221-06:21:58,75 nipype.workflow INFO:
     [Node] Cached "_fix_surfs2" - collecting precomputed outputs
201221-06:21:58,75 nipype.workflow INFO:
     [Node] "_fix_surfs2" found cached.
201221-06:21:58,100 nipype.workflow INFO:
     [Node] Setting-up "_fix_surfs3" in "/scratch/fmriprep_wf/single_subject_04_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/fix_surfs/mapflow/_fix_surfs3".
201221-06:21:58,147 nipype.workflow INFO:
     [Node] Cached "_fix_surfs3" - collecting precomputed outputs
201221-06:21:58,148 nipype.workflow INFO:
     [Node] "_fix_surfs3" found cached.
201221-06:21:58,174 nipype.workflow INFO:
     [Node] Setting-up "_fix_surfs4" in "/scratch/fmriprep_wf/single_subject_04_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/fix_surfs/mapflow/_fix_surfs4".
201221-07:24:18,412 nipype.workflow INFO:
     [Node] Finished "fmriprep_wf.single_subject_04_wf.anat_preproc_wf.anat_norm_wf.registration".
201231-10:42:49,707 nipype.workflow INFO:
     [Node] Cached "_fix_surfs4" - collecting precomputed outputs
201231-10:42:49,716 nipype.workflow INFO:
     [Node] "_fix_surfs4" found cached.
201231-10:42:49,783 nipype.workflow INFO:
     [Node] Setting-up "_fix_surfs5" in "/scratch/fmriprep_wf/single_subject_04_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/fix_surfs/mapflow/_fix_surfs5".
201231-10:42:49,887 nipype.workflow INFO:
     [Node] Cached "_fix_surfs5" - collecting precomputed outputs
201231-10:42:49,887 nipype.workflow INFO:
     [Node] "_fix_surfs5" found cached.
201231-10:42:49,929 nipype.workflow INFO:
     [Node] Setting-up "_fix_surfs6" in "/scratch/fmriprep_wf/single_subject_04_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/fix_surfs/mapflow/_fix_surfs6".
201231-10:42:50,16 nipype.workflow INFO:
     [Node] Cached "_fix_surfs6" - collecting precomputed outputs
201231-10:42:50,17 nipype.workflow INFO:
     [Node] "_fix_surfs6" found cached.
201231-10:42:50,53 nipype.workflow INFO:
     [Node] Setting-up "_fix_surfs7" in "/scratch/fmriprep_wf/single_subject_04_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/fix_surfs/mapflow/_fix_surfs7".
201231-10:42:50,138 nipype.workflow INFO:
     [Node] Cached "_fix_surfs7" - collecting precomputed outputs
201231-10:42:50,139 nipype.workflow INFO:
     [Node] "_fix_surfs7" found cached.
201231-10:42:50,232 nipype.workflow INFO:
     [Node] Finished "fmriprep_wf.single_subject_04_wf.anat_preproc_wf.surface_recon_wf.gifti_surface_wf.fix_surfs".
201231-10:42:52,156 nipype.workflow INFO:
     [Node] Setting-up "fmriprep_wf.single_subject_04_wf.anat_preproc_wf.anat_norm_wf.tpl_moving" in "/scratch/fmriprep_wf/single_subject_04_wf/anat_preproc_wf/anat_norm_wf/_template_MNI152NLin2009cAsym/tpl_moving".
201231-10:42:52,171 nipype.workflow INFO:
     [Node] Setting-up "fmriprep_wf.single_subject_04_wf.anat_preproc_wf.anat_norm_wf.std_mask" in "/scratch/fmriprep_wf/single_subject_04_wf/anat_preproc_wf/anat_norm_wf/_template_MNI152NLin2009cAsym/std_mask".
201231-10:42:52,170 nipype.workflow INFO:
     [Node] Setting-up "fmriprep_wf.single_subject_04_wf.anat_preproc_wf.anat_norm_wf.std_dseg" in "/scratch/fmriprep_wf/single_subject_04_wf/anat_preproc_wf/anat_norm_wf/_template_MNI152NLin2009cAsym/std_dseg".
201231-10:42:52,414 nipype.workflow INFO:
     [Node] Running "std_mask" ("niworkflows.interfaces.fixes.FixHeaderApplyTransforms"), a CommandLine Interface with command:
antsApplyTransforms --default-value 0 --float 0 --input /scratch/fmriprep_wf/single_subject_04_wf/anat_preproc_wf/surface_recon_wf/refine/sub-04_ses-movie_T1w_corrected_xform_rbrainmask.nii.gz --interpolation MultiLabel --output sub-04_ses-movie_T1w_corrected_xform_rbrainmask_trans.nii.gz --reference-image /home/fmriprep/.cache/templateflow/tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_res-01_T1w.nii.gz --transform /scratch/fmriprep_wf/single_subject_04_wf/anat_preproc_wf/anat_norm_wf/_template_MNI152NLin2009cAsym/registration/ants_t1_to_mniComposite.h5
201231-10:42:52,425 nipype.workflow INFO:
     [Node] Running "std_dseg" ("niworkflows.interfaces.fixes.FixHeaderApplyTransforms"), a CommandLine Interface with command:
antsApplyTransforms --default-value 0 --float 0 --input /scratch/fmriprep_wf/single_subject_04_wf/anat_preproc_wf/lut_t1w_dseg/seg_dseg.nii.gz --interpolation MultiLabel --output seg_dseg_trans.nii.gz --reference-image /home/fmriprep/.cache/templateflow/tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_res-01_T1w.nii.gz --transform /scratch/fmriprep_wf/single_subject_04_wf/anat_preproc_wf/anat_norm_wf/_template_MNI152NLin2009cAsym/registration/ants_t1_to_mniComposite.h5
201231-10:42:52,437 nipype.workflow INFO:
     [Node] Running "tpl_moving" ("niworkflows.interfaces.fixes.FixHeaderApplyTransforms"), a CommandLine Interface with command:
antsApplyTransforms --default-value 0 --dimensionality 3 --float 1 --input /scratch/fmriprep_wf/single_subject_04_wf/anat_preproc_wf/brain_extraction_wf/atropos_wf/copy_xform/sub-04_ses-movie_T1w_corrected_xform.nii.gz --interpolation LanczosWindowedSinc --output sub-04_ses-movie_T1w_corrected_xform_trans.nii.gz --reference-image /home/fmriprep/.cache/templateflow/tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_res-01_T1w.nii.gz --transform /scratch/fmriprep_wf/single_subject_04_wf/anat_preproc_wf/anat_norm_wf/_template_MNI152NLin2009cAsym/registration/ants_t1_to_mniComposite.h5
201231-10:42:54,97 nipype.workflow INFO:
     [Node] Setting-up "_std_tpms0" in "/scratch/fmriprep_wf/single_subject_04_wf/anat_preproc_wf/anat_norm_wf/_template_MNI152NLin2009cAsym/std_tpms/mapflow/_std_tpms0".
201231-10:42:54,306 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 /scratch/fmriprep_wf/single_subject_04_wf/anat_preproc_wf/split_seg/aseg_label-GM_mask.nii.gz --interpolation Gaussian --output aseg_label-GM_mask_trans.nii.gz --reference-image /home/fmriprep/.cache/templateflow/tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_res-01_T1w.nii.gz --transform /scratch/fmriprep_wf/single_subject_04_wf/anat_preproc_wf/anat_norm_wf/_template_MNI152NLin2009cAsym/registration/ants_t1_to_mniComposite.h5
201231-10:43:24,236 nipype.workflow INFO:
     [Node] Finished "_std_tpms0".
201231-10:43:25,932 nipype.workflow INFO:
     [Node] Setting-up "_std_tpms1" in "/scratch/fmriprep_wf/single_subject_04_wf/anat_preproc_wf/anat_norm_wf/_template_MNI152NLin2009cAsym/std_tpms/mapflow/_std_tpms1".
201231-10:43:26,36 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 /scratch/fmriprep_wf/single_subject_04_wf/anat_preproc_wf/split_seg/aseg_label-WM_mask.nii.gz --interpolation Gaussian --output aseg_label-WM_mask_trans.nii.gz --reference-image /home/fmriprep/.cache/templateflow/tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_res-01_T1w.nii.gz --transform /scratch/fmriprep_wf/single_subject_04_wf/anat_preproc_wf/anat_norm_wf/_template_MNI152NLin2009cAsym/registration/ants_t1_to_mniComposite.h5
201231-10:43:43,969 nipype.workflow INFO:
     [Node] Finished "fmriprep_wf.single_subject_04_wf.anat_preproc_wf.anat_norm_wf.tpl_moving".
201231-10:43:46,113 nipype.workflow INFO:
     [Node] Setting-up "_std_tpms2" in "/scratch/fmriprep_wf/single_subject_04_wf/anat_preproc_wf/anat_norm_wf/_template_MNI152NLin2009cAsym/std_tpms/mapflow/_std_tpms2".
201231-10:43:46,326 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 /scratch/fmriprep_wf/single_subject_04_wf/anat_preproc_wf/split_seg/aseg_label-CSF_mask.nii.gz --interpolation Gaussian --output aseg_label-CSF_mask_trans.nii.gz --reference-image /home/fmriprep/.cache/templateflow/tpl-MNI152NLin2009cAsym/tpl-MNI152NLin2009cAsym_res-01_T1w.nii.gz --transform /scratch/fmriprep_wf/single_subject_04_wf/anat_preproc_wf/anat_norm_wf/_template_MNI152NLin2009cAsym/registration/ants_t1_to_mniComposite.h5
201231-10:43:53,5 nipype.workflow INFO:
     [Node] Finished "_std_tpms1".
201231-10:44:12,59 nipype.workflow INFO:
     [Node] Finished "_std_tpms2".
201231-10:44:16,156 nipype.workflow INFO:
     [Node] Setting-up "fmriprep_wf.single_subject_04_wf.anat_preproc_wf.anat_norm_wf.std_tpms" in "/scratch/fmriprep_wf/single_subject_04_wf/anat_preproc_wf/anat_norm_wf/_template_MNI152NLin2009cAsym/std_tpms".
201231-10:44:16,302 nipype.workflow INFO:
     [Node] Setting-up "_std_tpms0" in "/scratch/fmriprep_wf/single_subject_04_wf/anat_preproc_wf/anat_norm_wf/_template_MNI152NLin2009cAsym/std_tpms/mapflow/_std_tpms0".
201231-10:44:16,354 nipype.workflow INFO:
     [Node] Cached "_std_tpms0" - collecting precomputed outputs
201231-10:44:16,355 nipype.workflow INFO:
     [Node] "_std_tpms0" found cached.
201231-10:44:16,374 nipype.workflow INFO:
     [Node] Setting-up "_std_tpms1" in "/scratch/fmriprep_wf/single_subject_04_wf/anat_preproc_wf/anat_norm_wf/_template_MNI152NLin2009cAsym/std_tpms/mapflow/_std_tpms1".
201231-10:44:16,421 nipype.workflow INFO:
     [Node] Cached "_std_tpms1" - collecting precomputed outputs
201231-10:44:16,421 nipype.workflow INFO:
     [Node] "_std_tpms1" found cached.
201231-10:44:16,439 nipype.workflow INFO:
     [Node] Setting-up "_std_tpms2" in "/scratch/fmriprep_wf/single_subject_04_wf/anat_preproc_wf/anat_norm_wf/_template_MNI152NLin2009cAsym/std_tpms/mapflow/_std_tpms2".
201231-10:44:16,487 nipype.workflow INFO:
     [Node] Cached "_std_tpms2" - collecting precomputed outputs
201231-10:44:16,488 nipype.workflow INFO:
     [Node] "_std_tpms2" found cached.
201231-10:44:16,532 nipype.workflow INFO:
     [Node] Finished "fmriprep_wf.single_subject_04_wf.anat_preproc_wf.anat_norm_wf.std_tpms".

It seems that the program is unfrozen and get back to work again. The 5 latest modified files in the output dir were:

2020-12-31 18:44:20.2156337000 ./sub-04/ses-movie/anat/sub-04_ses-movie_hemi-L_inflated.surf.gii
2020-12-31 18:44:20.8657378000 ./sub-04/ses-movie/anat/sub-04_ses-movie_hemi-R_inflated.surf.gii
2020-12-31 18:44:21.4567880000 ./sub-04/ses-movie/anat/sub-04_ses-movie_hemi-L_midthickness.surf.gii
2020-12-31 18:44:22.0308171000 ./sub-04/ses-movie/anat/sub-04_ses-movie_hemi-R_midthickness.surf.gii
2020-12-31 18:45:34.0161692000 ./sub-04/figures/sub-04_ses-movie_space-MNI152NLin2009cAsym_T1w.svg

I think I should probably just wait for the results. Or do you have any other suggestions?

thanks!

xingyu-liu commented 3 years ago

Hey,

new update. The programm finished succesually on 2020.12.31-23:42:11,72.

To summarize, 12.17-12.21: ran smoothly 12.21-12.31: paused 12.31-12.31: restarted and finished successfully

I'm not sure whether it was my own problem. Please close this issue if you think there is nothing to be worried.

Happy new year! Xingyu

julfou81 commented 3 years ago

Hi I think you are not alone. It is something I encounter regularly on a personal computer with fmriprep-docker. I will have to look more in details but it seems that is related to some ressource issue, even though I am using an iMac with 32Go of RAM with 24Go allocated to Docker. You may have to fine tune the ressources you allocate to the docker image and not be to greedy when launching fmriprep-docker. Fortunately for me, I have access to a cluster with much more ressources where I can run the singularity image with no such issue and I don't have to worry too much on fmriprep-docker, only for testing some patches.