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

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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I think this problem is fixed in 6.0 (if and when we get it out) On Mon, 9 Jan 2017, miracle ozzoude wrote:

Thanks bruce for your response. I accidentally listed number 3 twice instead of 4. Here's my 4th question: 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? Please see attached screenshot. I came across a post with similar error in the forum and you diagnosed but it wasn'tfix https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2016-April/045097 .html  Best,  Paul

On Mon, Jan 9, 2017 at 2:55 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: 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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        The information in this e-mail is intended only for
        the person to whom it is
        addressed. If you believe this e-mail was sent to
        you in error and the e-mail
        contains patient information, please contact the
        Partners Compliance HelpLine at
        http://www.partners.org/complianceline . If the
        e-mail was sent to you in error
        but does not contain patient information, please
        contact the sender and properly
        dispose of the e-mail.

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The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.