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Use the -T2 and -T2pial flags.
Matt.
From: on behalf of Steve Petersen
Reply-To: Freesurfer support list
Date: Sunday, December 4, 2022 at 10:01 AM
To: "freesurfer@nmr.mgh.harvard.edu"
Subject: [Freesurfer] Autorecon-pial with T1w and
External Email - Use Caution
Dear FreeSurfer experts,
After reviewing and manually editing the recon-all outputs in freeview, I'm
going to re-run the recon-all command with the autorecon-pial flag. My
question is, does the autorecon-pial also take into account the T2w image
or doe
