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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