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 10:33 AM, Xiaojiang Yang wrote:

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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 <subjectid>/mir directory.

Now I have a non-T1 image of the same subject, say, the (T2)FLAIR series, and I want to get the corresponding skull-stripped brain image of that FLAIR series by using some kind of registration. How should I do that? Please advise. Thank you!

Xiaojiang

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