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<https://surfer.nmr.mgh.harvard.edu/fswiki/recon-all#UsingT2orFLAIRdatatoimprovepialsurfaces> on our wiki. Bill Ammon From: <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Rosalia Dacosta Aguayo <rdacos...@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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