Re: [Freesurfer] Skull-stripped brain for non-T1 image

2020-03-20 Thread Douglas N. Greve 

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:


External Email - Use Caution

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 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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[Freesurfer] Skull-stripped brain for non-T1 image

2020-03-20 Thread Xiaojiang Yang 
External Email - Use Caution

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 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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