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Since I am using FreeSurfer v6 I do not have access to samseg. How can I compute the brain volume myself from the skull-stripped image?

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From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Douglas N. Greve <dgreve@mgh.harvard.edu>
Sent: Monday, November 8, 2021 1:40:55 PM
To: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Brain Volume Extraction
 
You could run it up to the skull stripping (-autorecon1), then compute the brain volume yourself from the skull-stripped image. You could also use samseg; samseg only takes an hour or so to run and outputs a measure of total intracranial volume, but you could also extract total brain volume from it

On 11/8/2021 11:14 AM, Mohanad Arafe wrote:

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Hello,

I am new to FreeSurfer and I have a question regarding brain volume extraction. When I run recon-all on a patient, once the entire process is done, I get the brain volume levels from aseg.stats. I would like to know if there are any ways to do so without going through the entire process of 30+ steps. I need to extract brain volumes from ROIs of 100+ patients.

Thank you

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