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Thanks a lot Bruce,

Have a nice day,

Aldo

From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Fischl, Bruce 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-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto: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.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: [Freesurfer] How to extract the GM and WM

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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

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

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*From:* freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Fischl, Bruce BFISCHL@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-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

*        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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