Hi Aldo

Usually we just run recon-all with -all instead of the individual -autorecon options. This will give you pretty much everything, including GM and WM

Cheers

Bruce

From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Camargo, Aldo
Sent: Sunday, May 23, 2021 11:25 PM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] How to extract the GM and WM

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Hi Freesurfer experts:

I want to extract the White Matter and the Gray Matter from a T1 image. I have extracted the brain by using the command:

recon-all with the option -autorecon1

Thanks a lot and have a nic day,

Aldo