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 herehttps://surfer.nmr.mgh.harvard.edu/fswiki/recon-all#UsingT2orFLAIRdatatoimprovepialsurfaces 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