hmmm, you had 3 numbered questions below, which is what my response referred to
On Mon, 9 Jan 2017, miracle ozzoude wrote:
Thanks bruce for your response. Please, which of my questions did you answer since I listed 4. Best, Miracle
On Mon, Jan 9, 2017 at 2:46 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: 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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