fMRIPrep 25.2.5 reports 'finished successfully' but produces no desc-preproc_bold or confounds files

Software Support
1

Summary of what happened:

Running fMRIPrep 25.2.5 via Singularity with --level full (the default, not explicitly set at first, then confirmed explicitly). The run completes with “fMRIPrep finished successfully!” printed in the log and a 0-looking exit, but the func/ output directory only contains early registration/motion-correction files – no *_desc-preproc_bold.nii.gz, no *_desc-confounds_timeseries.tsv, for any task or participant. Reproduced identically across 2 of 9 participants so far (others still running).

What the resolved config (fmriprep.toml) confirms:

level = "full"
spaces = "T1w MNI152NLin2009cAsym"
output_layout = "bids"

What actually exists in func/ output (for each of 2 tasks per participant):

  • *_desc-brain_mask.nii.gz / .json
  • *_desc-coreg_boldref.nii.gz / .json
  • *_desc-hmc_boldref.nii.gz / .json
  • *_from-orig_to-boldref_mode-image_desc-hmc_xfm.txt / .json

What’s missing: any final resampled BOLD (desc-preproc_bold, any space), any confounds file, any carpet plot.

Has anyone seen this specific “fit-only, no apply/derivatives” behavior with 25.2.5? Is there an additional flag needed in this version to trigger the resampling/confounds stage within a single invocation, given the fit/derivatives workflow split introduced in 23.2? Happy to provide the full .out log or fmriprep.toml if useful.

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

singularity run --cleanenv \
    -B ${STUDY}:/data \
    -B ${WORK}:/scratch_work \
    -B /work/afslab:/work/afslab \
    fmriprep_25.2.5.sif \
    /data/rawdata /data/derivatives/fmriprep participant \
    --participant-label ${SUBJECT} \
    --fs-license-file /work/afslab/freesurfer/license.txt \
    --work-dir /scratch_work \
    --output-spaces T1w \
    --nprocs 8

Version:

25.2.5

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

Singularity

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):

What the generated CITATION.md boilerplate says (seemingly describing full processing, which doesn’t match the actual output):

“For each of the 2 BOLD runs found per subject… All resamplings can be performed with a single interpolation step by composing all the pertinent transformations… Gridded (volumetric) resamplings were performed using nitransforms, configured with cubic B-spline interpolation.”

Screenshots / relevant information:

  • BIDS layout summary in the config log reads Subjects: 1 | Sessions: 0 | Runs: 0 for this participant (our filenames don’t use a run- BIDS entity since each task occurs once per session – not sure if this is related)
  • No errors or warnings in the .err log beyond two benign ones (SINGULARITYENV_TEMPLATEFLOW_HOME/APPTAINERENV preference notice, and a Node.js “closing directory handle on garbage collection” warning)
  • Container is GACRC’s (Georgia Advanced Computing Resource Center) centrally-installed image at /apps/singularity-images/fmriprep_25.2.5.sif
  • FreeSurfer license and TemplateFlow cache both confirmed present and correctly bind-mounted
2

Hi @Ashley_Sanders and welcome to neurostars!

May you please add in the portion of the post that asks for the BIDS validator report? Those outputs definitely seem like the --level minimal output set, which is odd. Just to be sure, have you tried rerunning with a fresh working directory? And if you do try, can you try to add these flags:

--level full \
--write-graph \
-vvv \

I am curious if the workflow graph that is produced actually has all the full processing steps plotted out.

Best,
Steven