fMRIPrep 23.0.2 hangs during anatomical normalization with multiple sessions

Software Support
1

Summary of what happened:

I am running fMRIPrep v23.0.2 (Docker) and encountering a problem during the anatomical normalization step:

fmriprep_23_0_wf.single_subject_<subject_id>_wf.anat_preproc_wf.anat_norm_wf.registration

When the input dataset contains multiple sessions for a subject, the workflow consistently gets stuck at this step. The process does not crash, but appears to hang indefinitely.

Observed behavior:

  • CPU usage drops to < 1 core

  • Memory usage remains stable (~12 GB)

  • No further progress is made, even after several days

  • No explicit error messages are produced

Control test:

  • When I run the exact same subject but include only a single session in the input data, the workflow completes successfully without any issues.

Additional notes:

  • The issue appears specifically tied to multi-session datasets

  • The hang occurs reproducibly at the same anatomical normalization/registration step

Questions:

  1. Is this a known issue with multi-session processing in fMRIPrep 23.0.2?

  2. Are there recommended workarounds (e.g., flags, session-wise processing)?

Thank you for your help!

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

runai submit --name fmriprep-times \
-i registry.rcp.epfl.ch/rcp-runai-uphummel-hudry/fmriprep_caas:23.0.2 \
--existing-pvc claimname=uphummel-scratch,path=/data \
--run-as-gid 82789 --run-as-uid 312106 – \
/data/gbaron/TiMeS \
/data/gbaron/TiMeS/derivatives/fmriprep \
participant \
--participant-label TiMeSWP11001 \
--fs-license-file /data/gbaron/ReverseStroke/fmristroke_utils/license_freesurfer_antonin.txt \
--fs-subjects-dir 
/data/gbaron/TiMeS/derivatives/fmriprep/sourcedata/freesurfer_TiMeSWP11001 \
--work-dir /data/gbaron/TiMeSWP11001_work \
--output-layout bids \
--write-graph \
--return-all-components \
--force-no-bbr \
--bids-database-dir tmp/process_01 \
--output-spaces MNI152NLin2009cAsym anat func \
--verbose \
--skip_bids_validation

Version:

23.0.2

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):

PASTE LOG OUTPUT HERE

Screenshots / relevant information:

2

Hi @Giorgia_Baron,

Does the error persist on the newest fmriprep version? How much memory are you letting Docker access? Also, runai submit is not the typical way of running Docker jobs; is it possible this is limiting your resources?

Best,

Steven

3

Hello @Steven

Thank you for your reply.

Unfortunately, I am not able to test the newest fMRIPrep version, as the denoising tool I plan to use (fmristroke: https://github.com/alixlam/fmristroke) is currently built specifically on fMRIPrep 23.0.2.

Regarding resources, I am not explicitly limiting memory allocation. The job is being executed on my institution’s research computing cluster using runai submit, which is the standard workflow provided there. I will follow up with our IT team to confirm whether any resource limits might be affecting the job.

I will update you as soon as I have more information, thank you!

Giorgia