run it with -autorecon2 and -autorecon3
On 5/25/2021 1:47 PM, Camargo, Aldo wrote:
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Hi Bruce,
I was wondering if there is way to continue the process to recon-all
once I have done the recon-all with the option -autorecon1.
Thanks a lot,
Aldo
------------------------------------------------------------------------
*From:* freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Fischl, Bruce
<bfis...@mgh.harvard.edu>
*Sent:* Monday, May 24, 2021 10:17 AM
*To:* Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
*Subject:* Re: [Freesurfer] How to extract the GM and WM
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-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@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
* External Email - Use Caution *
* External Email - Use Caution *
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
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