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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
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:
External Email - Use Caution
External Email - Use Caution
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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External Email - Use Caution
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?
Get Outlook for iOShttps://secure-web.cisco.com/1IxB-lo0pgD9udRKPPTBsnWTZLszgdXtotGk9G-Wemi4AXattXHDgManQ19Ow3Joqa0WjhNTWPLHUOZ_TKrdbNIAX7DJz7MI5qGnoE69NAqofvt-oiVuzs7b7nXggTiCCWfyVIRi3bSMha6mA1FPmBaUq8Ng0ku2yJCh-iLS-ajC6DUBcYN5fDK8T2zdGUIqB3pH7TlO6i-r7gUm-meQm8YBOhrV0vn7a6T_qQ2v6Kg5aaqNLpCTKR-HQqcTbV56zHsAWW6_cndBfA-3dQoA3YQ/https%3A%2F%2Faka.ms%2Fo0ukef ________________________________ 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:
External Email - Use Caution
External Email - Use Caution
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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freesurfer@nmr.mgh.harvard.edu
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Douglas N. Greve -
Mohanad Arafe