Getting "fMRIPrep finished successfully!" message but a non-zero exit code

[michellewang]

What happened?

Hi, I am running fMRIPrep 23.1.3 and getting seemingly successful runs (no error messages, no crashfiles in the participant's log directory, fMRIPrep finished successfully! printed in the logs) but the return/exit code is 1 instead of 0.

From what I can see in the source code, if we get the fMRIPrep finished successfully! log message, the return code should be 0 except if there were failures in report generation, but there were no error messages about this and I am not sure how to debug/troubleshoot otherwise (the participant's HTML report seems fine to me).

What command did you use?

/opt/conda/envs/fmriprep/bin/fmriprep \
    /lustre06/project/6061841/mwang8/data/.ppmi/bids \
    /lustre06/project/6018311/datasets/.ppmi_derivatives/fmriprep/23.1.3/output \
    participant \
    --skip_bids_validation \
    --participant-label 100990 \
    --bids-database-dir /lustre07/scratch/mwang8/ppmi/scratch/pybids_db/fmriprep-23.1.3-100990-BL \
    --nprocs 8 \
    --omp-nthreads 4 \
    --mem 4G \
    --anat-only \
    --output-spaces anat fsnative MNI152NLin2009cSym:res-1 MNI152NLin6Sym:res-1 MNI152NLin2009cAsym:res-2 \
    --bold2t1w-init register \
    --bold2t1w-dof 6 \
    --me-t2s-fit-method curvefit \
    --output-layout bids \
    --return-all-components \
    --fd-spike-threshold 0.5 \
    --dvars-spike-threshold 1.5 \
    --skull-strip-template OASIS30ANTs \
    --skull-strip-t1w force \
    --fs-license-file /lustre06/project/6061841/mwang8/data/.ppmi/code/freesurfer_license.txt \
    --fs-subjects-dir /lustre06/project/6061841/mwang8/data/.ppmi/derivatives/freesurfer/7.3.2/output/ses-BL \
    --country-code CAN \
    -vvv \
    -w /scratch/mwang8/work/fmriprep-23.1.3-100990-BL \
    --write-graph \
    --notrack

What version of fMRIPrep are you running?

23.1.3

How are you running fMRIPrep?

Singularity

Is your data BIDS valid?

Yes

Are you reusing any previously computed results?

No

Please copy and paste any relevant log output.

Last 20 lines of the log file (with -vvv verbosity)

250205-09:16:52,938 nipype.workflow INFO:
         [Node] Finished "ds_std_dseg", elapsed time 1.4795099999999999s.
250205-09:16:52,941 nipype.workflow DEBUG:
         Needed files: /lustre06/project/6018311/datasets/.ppmi_derivatives/fmriprep/23.1.3/output/sub-100990/ses-BL/anat/sub-100990_ses-BL_acq-sag3D_run-01_space-MNI152NLin6Sym_res-1_dseg.nii.gz;/lustre06/project/6018311/datasets/.ppmi_derivatives/fmriprep/23.1.3/output/sub-100990/ses-BL/anat/sub-100990_ses-BL_acq-sag3D_run-01_space-MNI152NLin6Sym_res-1_dseg.json;/scratch/mwang8/work/fmriprep-23.1.3-100990-BL/fmriprep_23_1_wf/single_subject_100990_wf/anat_preproc_wf/anat_derivatives_wf/_in_tuple_MNI152NLin6Sym.res1/ds_std_dseg/_0xbf507564b56c28002ece8086c7b751a4_unfinished.json;/scratch/mwang8/work/fmriprep-23.1.3-100990-BL/fmriprep_23_1_wf/single_subject_100990_wf/anat_preproc_wf/anat_derivatives_wf/_in_tuple_MNI152NLin6Sym.res1/ds_std_dseg/_inputs.pklz;/scratch/mwang8/work/fmriprep-23.1.3-100990-BL/fmriprep_23_1_wf/single_subject_100990_wf/anat_preproc_wf/anat_derivatives_wf/_in_tuple_MNI152NLin6Sym.res1/ds_std_dseg/_node.pklz
250205-09:16:52,941 nipype.workflow DEBUG:
         Needed dirs: /scratch/mwang8/work/fmriprep-23.1.3-100990-BL/fmriprep_23_1_wf/single_subject_100990_wf/anat_preproc_wf/anat_derivatives_wf/_in_tuple_MNI152NLin6Sym.res1/ds_std_dseg/_report
250205-09:16:52,941 nipype.workflow DEBUG:
         Removing files: 
250205-09:16:52,941 nipype.workflow DEBUG:
         Saving results file: '/scratch/mwang8/work/fmriprep-23.1.3-100990-BL/fmriprep_23_1_wf/single_subject_100990_wf/anat_preproc_wf/anat_derivatives_wf/_in_tuple_MNI152NLin6Sym.res1/ds_std_dseg/result_ds_std_dseg.pklz'
250205-09:16:52,945 nipype.workflow DEBUG:
         [Node] Writing post-exec report to "/scratch/mwang8/work/fmriprep-23.1.3-100990-BL/fmriprep_23_1_wf/single_subject_100990_wf/anat_preproc_wf/anat_derivatives_wf/_in_tuple_MNI152NLin6Sym.res1/ds_std_dseg/_report/report.rst"
250205-09:16:52,984 nipype.workflow INFO:
         [Job 209] Completed (fmriprep_23_1_wf.single_subject_100990_wf.anat_preproc_wf.anat_derivatives_wf.ds_std_dseg).
250205-09:16:53,110 nipype.workflow IMPORTANT:
         fMRIPrep finished successfully!
250205-09:16:53,145 nipype.workflow IMPORTANT:
         Works derived from this fMRIPrep execution should include the boilerplate text found in <OUTPUT_PATH>/logs/CITATION.md.
250205-09:16:56,562 nipype.utils DEBUG:
         /lustre06/project/6018311/datasets/.ppmi_derivatives/fmriprep/23.1.3/output/desc-aseg_dseg.tsv

Additional information / screenshots

No response

[effigies]

Do you still see this in the latest release? 23.1 is over a year out of date, and we won't be making more releases in that series.

[michellewang]

@effigies I tried with 24.1.1 and it didn't have this problem anymore, so will close the issue