Sorry for any confusion, I meant that you would include the T2 flag to the end of your current recon-all command. So you could have a command that would look something like

 

recon-all -subject subjectname -i /path/to/input_volume -T2 /path/to/T2_volume -T2pial -all

 

 

So you are inputting both T1 and T2 images. For your command in your first message, I think you should just add -T2 /path/to/T2_volume -T2pial.

 

Hope this helps,

Bill Ammon

 

From: <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Rosalia Dacosta Aguayo <rdacostaa@gmail.com>
Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Date: Wednesday, March 3, 2021 at 1:18 PM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Include T2 in recon-all command

 

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Hi William,

 

I wanted to use both T1 and T2 to do the recon -all -all.

 

Could it be: 

 

• recon-all -subject subjectname -i invol1 <-i invol2> -all

 

 

El mié., 3 mar. 2021 17:16, Ammon, William <WAMMON@mgh.harvard.edu> escribió:

Hi Rosalia,

 

You can include T2 images by adding the flags  -T2 /path/to/volume (to point to the T2 images) and -T2pial -all (to generate new pial surfaces using T2 images).

You can read more about this here on our wiki.

 

Bill Ammon

 

From: <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Rosalia Dacosta Aguayo <rdacostaa@gmail.com>
Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Date: Wednesday, March 3, 2021 at 7:36 AM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] Include T2 in recon-all command

 

        External Email - Use Caution        

Dear Freesurfer community,

 

I would like to include the T2 image in the recon-all command to improve segmentation.

 

Any idea how I should do this in the following command?

 

recon-all -s Artico1 -i subj01_anat.nii.gz -all -qcache -3T

 

Regards,

Rosalia

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