I'd been considering doing something like this:
mkdir func func-brain
fsl4.1-fslsplit func.nii.gz run/func- -t
for FILE in func/*; do fsl4.1-bet "${FILE}" "run-brain/${FILE##*/}"; done
fsl4.1-fslmerge -t func-brain.nii.gz func-brain/*
fsl4.1-mcflirt -in func-brain.nii.gz -out func-brain-mcf.nii.gz
However it's been mentioned twice before on this mailing list (by Steve Smith) that one should not perform brain extraction before invoking mcflirt.
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=FSL;1f232570.05
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=FSL;9b7f3193.0906
On the other hand, the FAQ recommends doing brain extraction on both volumes before running flirt.
http://www.fmrib.ox.ac.uk/fslfaq/#title_flirt
Given that flirt and mcflirt are ostensibly both doing linear registration, why is brain extraction helpful to one but harmful to the other?
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