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:
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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