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:
External Email - Use Caution
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 ------------------
*From: * "Douglas N. Greve"<dgr...@mgh.harvard.edu>;
*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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