NECK MATTERS - remove neck with robustfov first

BET (FSL)

BET does not automatically remove bias field! You must use -B

bet sub-7_ses-01_T1w.nii.gz T1w_bet_B_R -B -f 0.3

Synthstrip (freesurfer)

mri_synthstrip -i sub-7_ses-01_T1w.nii.gz -o T1_synthstrip_b0.nii.gz -b 0

ANTS

download OASIS template; use different template in case of specific age groups

./antsBrainExtraction.sh -d 3 -a sub-7_ses-01_desc-rfov.nii.gz -e OASIS/MICCAI2012-Multi-Atlas-Challenge-Data/T_template0.nii.gz -m OASIS/MICCAI2012-Multi-Atlas-Challenge-Data/T_template0_BrainCerebellumProbabilityMask.nii.gz -o ants_rfov

fmriprep - removes neck and bias field automatically (last chance)

fmriprep --anat-only --fs-license-file ~/repo/license.txt --fs-no-reconall ./MJRIS/ ./ participant