We do not generate a scalp segmentation (but you can use samseg which generates skull and something like skin). If you want to create a binary volume with a chosen seg or tissue type = 1 and everything else = 0, you can use something like
mri_binarize --i aseg.mgz --match 4 5 14 15 43 44 --o csf.mgz
where those numbers come from $FREESURFER_HOME/FreeSurferColorLUT.txt just chose the ones you want

On 2/1/2023 12:00 PM, 江一川(JIANG Yichuan) wrote:

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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
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:

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Dear Experts, 


How can I extract scalp, skull, csf, gray, and white volume, seperately. 
Best wishes,
Yichuan Jiang

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