fMRIPrep stuck at mris_fix_topolo

Software Support
1

Summary of what happened:

Hi!

Fmriprep doesn’t give me error, but for some subjects it consistently gets stuck for hours at the part below.

I think the command it is performing is mris_fix_topolo. I do not understand what I am missing, could you help me?

Command used (and if a helper script was used, a link to the helper script or the command generated):

fmriprep-docker \
$HOME/data/ \
$HOME/out/derivatives \
participant \
--participant-label sub-022S6716 sub-023S4115 sub-024S6033 sub-027S6327 sub-027S6640 sub-027S6788 \
--ignore fieldmaps \
--fs-license-file $HOME/license.txt \
--fs-subjects-dir $HOME/fastsurfer_dir/ \
--output-spaces T1w MNI152NLin2009cAsym \
--omp-nthreads 6 \
-w $HOME/work2/ \
--cifti-output 91k \
-u 8096

Version:

25.0.0

Environment (Docker, Singularity / Apptainer, custom installation):

Docker

Data formatted according to a validatable standard? Please provide the output of the validator:

PASTE VALIDATOR OUTPUT HERE

Relevant log outputs (up to 20 lines):


[Node] Executing "gen_cifti" <niworkflows.interfaces.cifti.GenerateCifti>
250414-20:49:57,85 nipype.workflow INFO:
         [Node] Finished "gen_cifti", elapsed time 19.958328s.
250414-20:49:59,862 nipype.workflow INFO:
         [Node] Setting-up "fmriprep_25_0_wf.sub_023S4115_wf.bold_ses_01_task_rest_wf.carpetplot_wf.conf_plot" in "/scratch/fmriprep_25_0_wf/sub_023S4115_wf/bold_ses_01_task_rest_wf/carpetplot_wf/conf_plot".
250414-20:49:59,875 nipype.workflow INFO:
         [Node] Executing "conf_plot" <fmriprep.interfaces.confounds.FMRISummary>
250414-20:50:19,76 nipype.workflow INFO:
         [Node] Finished "conf_plot", elapsed time 19.200975s.

Screenshots / relevant information:

2

Hi @cmatti,

I the future, please format your software support posts using the post template. You can see I edited in for you this time.

It is not clear from the log you provided what step is being performed, since it looks like the two steps mentioned in the log (gen_cifti and conf_plot) both started and completed okay and in reasonable times. Is there a better part of the log you can share?

How much resources are you devoting to the job, and have you checked if jobs can finish when only running a single subject?

Best,
Steven

3

mris_fix_topolo is the freesurfer process that corrects the WM defects. Sometimes this process might take a really long time to complete because there are too many WM defects—possibly be due to a bad skullstrip. If this is the case, I would suggest to skullstrip your t1w images using freesurfer’s synthstrip tool before running fMRIprep