Issue with fMRIPrep brain segmentation

[ET_123456]

Summary of what happened:

Fmriprep failed segmentation and skull stripping, it cut off a lot of the frontal lobe. Do you have any suggestions of how I can change the code to improve segementation? I was using fmriprep v 23.1.4 and freesurfer/7.2.0

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

cmd="${SINGULARITY_CMD} \
/data \
 /data/${DERIVS_DIR} \
participant \
--participant-label 6 \
-w /work/\
 -vv \
--omp-nthreads 8 --nthreads 12 --mem_mb 30000 \
--output-spaces MNI152NLin2009cAsym:res-2 anat fsnative fsaverage5 \
--use-aroma \
--fs-subjects-dir /fsdir \
--skip_bids_validation"

Version:

23.1.4

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

I used 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):

PASTE LOG OUTPUT HERE

Screenshots / relevant information:

---

[Steven]

Hi @ET_123456,

Can you highlight where the problematic areas are on your picture?

Also, AROMA functionality was removed beginning in 23.1.0. If you want to use AROMA you should use fMRIPost-AROMA. For that you will need to use the FSL MNINLin6Asym version in res-2 as an output space, as a heads up.

Have you tried pre-skull stripping your images and then skipping skull stripping in fmriprep?

Best,
Steven