Hi Paul

Have you tried using the wmseg?

Cheers

Bruce

From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of miracle ozzoude
Sent: Wednesday, December 2, 2020 1:35 PM
To: Douglas N Greve <freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] Fwd: extracting mask for basal ganglia, deep grey, and centrum semiovale

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Any help with this will be greatly appreciated. 

Thanks.

---------- Forwarded message ---------
From: miracle ozzoude <miracooloz@gmail.com>
Date: Fri, Nov 27, 2020 at 9:28 AM
Subject: extracting mask for basal ganglia, deep grey, and centrum semiovale
To: Douglas N Greve <freesurfer@nmr.mgh.harvard.edu>

Hello Experts, 

I did like to create a mask for basal ganglia, deep grey matter, and centrum semiovale. I know how to extract the mask for the first 2 (using aseg.mgz) however, how do I extract the last one. What mask should I use to extract the centrum semiovale? I don't want to include the cerebellar white matter. 

Thanks. 

Best, 

Paul