BOLD signal brain mask not including parts of frontal grey matter

[dameder]

What happened?

When running fmriprep on my slab EPI images, the BOLD mask (red contour) does not include the most anterior part of prefrontal cortex. This happens in all participants.

I have browsed the forum and fmriprep documentation, but have not been succesful in a) understanding where the issue might arise (found some old posts where the BOLD mask went wrong due to erroneous n4 bias field correction, but there it seemed to have gone completely wrong). nor b) understanding the implications of this error. Does this "only" affect the compCorr generation, or does it also have other consequences down the line?

Any help appreciated,

David

What command did you use?

Commandline: singularity run --cleanenv --contain -B /mnt/projects/OPD/bids/rawdata:/projectFolder -B /mnt/scratch/projects/OPD/bids/derivatives/fmriprep.product.1027-1327:/product -B /mnt/scratch/projects/OPD/bids/derivatives/nobackup/scratch/templateflow2:/templateflow -B /mnt/scratch/projects/OPD/bids/derivatives/fmriprep:/work /mnt/projects/OPD/bids/rawdata/code/singularity/fmriprep-25.2.3.sif --participant-label 009 -w /work --bids-filter-file /projectFolder/filter_file.json --output-spaces MNI152NLin2009cAsym:res-2 --fs-no-reconall --fs-license-file /projectFolder/code/singularity/license.txt /projectFolder /product participant

What version of fMRIPrep are you running?

25.2.3 - but get same error with previous versions

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.

fmriprep finishes otherwise succesfully without error

Additional information / screenshots

No response

[effigies]

My first guess would be an issue with the masking process interacting with a limited field-of-view scan. If you send me an example subject (just one bold run) that reproduces this reliably, I can try to track it down.

[dameder]

My first guess would be an issue with the masking process interacting with a limited field-of-view scan. If you send me an example subject (just one bold run) that reproduces this reliably, I can try to track it down.

Yes, I have a scan of my own brain where that happens, happy to share it. How do I best do so? Thanks already for the offer!