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