Re: [Freesurfer] Extracting brain volume seperately

[Douglas N. Greve]

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 --
*From: * "Douglas N. Greve";
*Date: * Wed, Feb 1, 2023 11:00 PM
*To: * "freesurfer";
*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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Re: [Freesurfer] Extracting brain volume seperately

[江一川(JIANG Yichuan)]

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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--
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Re: [Freesurfer] Extracting brain volume seperately

[Douglas N. Greve]

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

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
___
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[Freesurfer] Extracting brain volume seperately

[江一川(JIANG Yichuan)]

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Dear Experts,  
How can I extract scalp, skull, csf, gray, and white volume, seperately. 
Best wishes,Yichuan Jiang___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is 
addressed.  If you believe this e-mail was sent to you in error and the e-mail 
contains patient information, please contact the Mass General Brigham 
Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline 
 .
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
continue communication over unencrypted e-mail, please notify the sender of 
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