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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