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

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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