First register the T2/FLAIR to the anatomical
bbregister --mov T2.mgz --T2 --reg reg.T2.lta --subject subject
Then map it to the orig space
mri_vol2vol --mov T2.mgz --reg.T2.lta --fstarg --o T2-in-orig.mgz
then Apply the mask
mri_mask T2-in-orig.mgz brain.mgz T2-in-orig-masked.mgz
On 3/20/2020
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Hi everyone,
Suppose I have run Freesurfer with respect to a subject using the T1 image,
and I have gotten the skull-stripped brain image (brain.mgz) in the
/mir directory.
Now I have a non-T1 image of the same subject, say, the (T2)FLAIR series,
and
