Issue w/ generating anatomical brain mask from pre-skull stripped T1w


The fMRIprep brain extraction for my data did not work well for several subjects. Outside of fMRIprep, I skull stripped using FSL BET. In my fmriprep command I 1) used the bids filter file to select the brain extracted T1w and 2) added the skip skull stripping flag.

It still looks like the creation of the brain mask from the anatomical data is failing. I’ve attached a picture below. Is there an alternate way to increase the anatomical accuracy of the brain mask using this method?

Thank you,

command (v21.0.2)


–participant-label $subject \

–ignore fieldmaps slicetiming \

–bids-filter-file /data/sen_be.json \

–fs-license-file /data/derivatives/license.txt \

–skull-strip-t1w skip \

–nthreads 8 –omp-nthreads 8 \

–work-dir /work \

–write-graph --notrack -v \

/data/nifti /data/derivatives/FMRI_Sentences participant"