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Hi Douglas, 

Thank you for your reply. I'm a beginner in freesurfer and my previous statement was not very clear. My purpose is to generate new .mgz files (e.g., scalp.mgz and CSF.mgz, etc.) that are not in the MRI folder. 

Bset regards, 
Yichuan Jiang


 
 
------------------ Original ------------------
Date:  Wed, Feb 1, 2023 11:00 PM
To:  "freesurfer"<freesurfer@nmr.mgh.harvard.edu>;
Subject:  Re: [Freesurfer] Extracting brain volume seperately
 
everything except skull and scalp are in the aseg.stats file. You can get skull by running samseg, eg,
cd subject/mri
samseg --i orig.mgz --o samseg
there will be a stats file in the samseg folder with skull volume in it

On 2/1/2023 5:00 AM, 江一川(JIANG Yichuan) wrote:

        External Email - Use Caution        

Dear Experts, 


How can I extract scalp, skull, csf, gray, and white volume, seperately. 

          
Best wishes,

          
Yichuan Jiang

          

          

        

      

      

      

      
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