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

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