Re: [Freesurfer] Fwd: mris_make_surfaces scripts and how and when to use

Hi Paul

for 1 and 2, these are run internally to recon-all and don't need to be run again afterwards. 3. looks right to me

cheers Bruce On Mon, 9 Jan 2017, miracle ozzoude wrote:

---------- Forwarded message ---------- From: miracle ozzoude miracooloz@gmail.com Date: Mon, Jan 9, 2017 at 11:06 AM Subject: mris_make_surfaces scripts and how and when to use To: Douglas N Greve freesurfer@nmr.mgh.harvard.edu

Hello Freesurfer, I was going to the ReconAllDevTable (https://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllDevTable) and i came across 3 different mris_make_surfaces scripts.

1. When do I use any of the 3 mris_make_surfaces scripts after running recon-all -all?
2. Is there a default/standard nsigma above/below the mean to use when running the third mris_make_surfaces?
3. Which of the mris_make_surfaces can I use to correct the pial surface when it does cross the white matter and also, which is helpful with white matter surface

extension? 3) Is this the correct recon-all script to use after wm edits with T2pial option? "recon-all -autorecon-wm -autorecon3 -T2 /T2_volume T2pial -s"

Thanks

Paul