hello Bruce, I have another question, what's the function of -first_wm_peak in mris_make_surfaces? I know it helps "settle WM surface at first peak in intensity profile insted of highest". what does this mean and do I need to specify a value for it. Thanks. Best, Paul

On Mon, Jan 9, 2017 at 4:19 PM, miracle ozzoude miracooloz@gmail.com wrote:

Thanks a lot Antonin.I will try it out. I am trying to figure out how to use mris_make_surfaces to extend my pial surface with T2 argument included and also, play around with -first_wm_peak and -nsigmas

On Mon, Jan 9, 2017 at 4:06 PM, Antonin Skoch ansk@ikem.cz wrote:

...

Dear Paul,

you can also try to play with "reposition surface" tool in freeview, where you (apart from other options) can directly edit coordinates of the surface vertices. However, this tool is not well documented and I myself would like to know the significance of some of the parameters - see my unanswered post from 4th january 2017:

http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg50759.html

And, I am not sure how this works in 5.3 version of freeview, I have used it only in V6beta (dev) version.

Regards,

Antonin

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

---

Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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.

Thanks for your response bruce. Do you think I can use it for 3T scans and do i need to specify a specific starting value?

Best, Paul

On Mon, Jan 9, 2017 at 5:00 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:

Hi Paul

it's to help with cortex where the deep layers are heavily myelinated and the gray/white boundary isn't as big a jump in contrast as infragranular/supragranular. It usually is only needed for hires data

cheers Bruce

On Mon, 9 Jan 2017, miracle ozzoude wrote:

hello Bruce, I have another question, what's the function of -first_wm_peak

...

in mris_make_surfaces? I know it helps "settle WM surface at first peak in intensity profile insted of highest". what does this mean and do I need to specify a value for it. Thanks. Best, Paul

On Mon, Jan 9, 2017 at 4:19 PM, miracle ozzoude miracooloz@gmail.com wrote: Thanks a lot Antonin.I will try it out. I am trying to figure out how to use mris_make_surfaces to extend my pial surface with T2 argument included and also, play around with -first_wm_peak and -nsigmas

On Mon, Jan 9, 2017 at 4:06 PM, Antonin Skoch ansk@ikem.cz wrote:

Dear Paul, you can also try to play with "reposition surface" tool in freeview, where y ou (apart from other options) can directly edit coordinates of the surface v ertices. However, this tool is not well documented and I myself would like to know th e significance of some of the parameters - see my unanswered post from 4th j anuary 2017: http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg50759.html And, I am not sure how this works in 5.3 version of freeview, I have used it only in V6beta (dev) version. Regards, Antonin 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 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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.

---

Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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.

yes, and you shouldn't need a starting value (not sure what that even means) On Mon, 9 Jan 2017, miracle ozzoude wrote:

Thanks for your response bruce. Do you think I can use it for 3T scans and do i need to specify a specific starting value?  Best,  Paul

On Mon, Jan 9, 2017 at 5:00 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: Hi Paul

  it's to help with cortex where the deep layers are heavily
  myelinated and the gray/white boundary isn't as big a jump in
  contrast as infragranular/supragranular. It usually is only
  needed for hires data

  cheers
  Bruce

  On Mon, 9 Jan 2017, miracle ozzoude wrote:

        hello Bruce, I have another question, what's the
        function of -first_wm_peak
        in mris_make_surfaces? I know it helps "settle WM
        surface at first peak in
        intensity profile insted of highest". what does this
        mean and do I need to
        specify a value for it. Thanks. 
        Best, 
        Paul

        On Mon, Jan 9, 2017 at 4:19 PM, miracle ozzoude
        <miracooloz@gmail.com>
        wrote:
              Thanks a lot Antonin.I will try it out. I am
        trying to figure
              out how to use mris_make_surfaces to extend my
        pial surface with
              T2 argument included and also, play around
        with -first_wm_peak
               and -nsigmas

        On Mon, Jan 9, 2017 at 4:06 PM, Antonin Skoch
        <ansk@ikem.cz> wrote:

        Dear Paul,
        you can also try to play with "reposition surface"
        tool in freeview, where y
        ou (apart from other options) can directly edit
        coordinates of the surface v
        ertices.
        However, this tool is not well documented and I
        myself would like to know th
        e significance of some of the parameters - see my
        unanswered post from 4th j
        anuary 2017:
        http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg50759.html
        And, I am not sure how this works in 5.3 version of
        freeview, I have used it
         only in V6beta (dev) version.
        Regards,
        Antonin
        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
        _______________________________________________
        Freesurfer mailing list
        Freesurfer@nmr.mgh.harvard.edu
        https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


        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.

---

Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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.