Functional brain mask issues (a lot of non-brain included)

[clarawa]

Summary of what happened:

Hello, we ran fmriprep on 49 subjects and for some of them the functional brain masks contain a significant amount of non-brain tissue, but the anatomical brain masks look fine. I am not sure why this happens, I have read it can be due to noisy background for example, but I don’t know if this is the case. Is there anything I can do in fmriprep, or outside and then feed it to fmriprep, to improve the bold brain mask generation?

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

singularity run --cleanenv \
    -B ${DATA_DIR}:/data \
    -B ${OUT_DIR}/:/out \
    -B ${SCRATCH_DIR}:/wd \
    -B ${LICENSE}:/license \
    /fmriprep_singularity/fmriprep_25.1.3.simg \
    --skip_bids_validation \
    --participant-label ${SUBJECT} \
    --omp-nthreads 5 --nthreads 5 --mem_mb 30000 \
    --output-spaces MNI152NLin2009cAsym fsaverage\
    --dummy-scans 5 \
    --fs-license-file /license \
    --work-dir /wd \
    --cifti-output 91k \
    /data /out/ participant

Version:

fMRIprep version 25.1.3

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

Singularity

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

BIDS 

Relevant log outputs (up to 20 lines):

NA

Screenshots / relevant information:

Example screenshot of the functional brain mask.

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