If you've already run qcache, then it will be in the subject/surf folder with a name like lh.thickness.fsaverage.fwhm10.mgz



On 2/6/18 11:22 PM, 박경일 wrote:
Thanks, Bruce.
From that, I got thickness data (vertex#, location x/y/z, thickness value). But, amount and location of vertex are different among subjects. As far as i understand, it is the subject space, not common space. is that right? If so, how can i get the thickness values in common space to compare the vertex data between subjects?

(I'd already run recon-all and qcache process.)

Kyung


2018-02-03 0:33 GMT+09:00 Bruce Fischl <fis...@nmr.mgh.harvard.edu <mailto:fis...@nmr.mgh.harvard.edu>>:

    Hi Kyung

    you should look at the mris_convert help. It has an example of how
    to convert a scalar overlay like a curv file to ascii:


    Convert a scalar overlay file to ascii:
      mris_convert -c lh.thickness lh.white lh.thickness.asc


    it needs the surface as an input to do the conversion properly.

    cheers
    Bruce


    On Fri, 2 Feb 2018, 박경일 wrote:

        Hi Bruce
        I found a directory having a file with ".curv", open terminal
        and run following command.

        [root@localhost surf]# mris_convert rh.curv rh.curv.asc
        nquads=4587523,  nvertices=476
        ERROR: MRISread: file 'rh.curv' has many more faces than vertices!
        Probably trying to use a scalar data file as a surface!
        No such file or directory

        what is wrong?

        Thanks as always.

        Kyung

        2018-01-31 0:04 GMT+09:00 Bruce Fischl
        <fis...@nmr.mgh.harvard.edu <mailto:fis...@nmr.mgh.harvard.edu>>:
              Hi Kyung

              the thickness values are stored as "curvature" file
        format that you can load into matlab
              with read_curv.m. Alternatively, you can convert them to
        ascii with mris_convert and do
              what you want with them. For each index, you can look up
        its location on the white or
              pial (or whatever surface). That is, for the 2nd
        thickness value (index 1), you would go
              find vertex #1 on the other surface and read its
        location that way

              cheers
              Bruce
              On Tue, 30 Jan 2018, 박경일 wrote:

                    Hi Bruce, I am very new for FS, so did not
        understand you comments
                    completely. sorry..

                    For cortical thickness from each vertex in one
        subject, which scripts should
                    follow "mris_convert"?
                    And another question is how to recognize the
        location of each vertex in
                    brain finally.

                    thank you so much

                    Kyung


                    2017-11-13 10:06 GMT+09:00 Bruce Fischl
        <fis...@nmr.mgh.harvard.edu <mailto:fis...@nmr.mgh.harvard.edu>>:
                          p.s. if you want the vertices to correspond,
        first run recon-all
                    -qcache for each
                          subject. That will generate a set of
        thickness maps in fsaverage space
                    at predefined
                          smoothing levels (so that the vertex numbers
        correspond across
                    subjects)

                          On Mon, 13 Nov 2017, 박경일 wrote:

                                Hi Bruce,What I want is the values of
        cortical thickness in each
                    vertex in
                                each subject. Is that
                                possible?
                                Thanks so much.

                                Kyung



                                2017-11-13 0:43 GMT+09:00 Bruce Fischl
                    <fis...@nmr.mgh.harvard.edu
        <mailto:fis...@nmr.mgh.harvard.edu>>:
                                      Hi Kyung

                                      you can load them into matlab or
        convert them to ascii if
                    you want
                                      Bruce
                                      On Sun, 12 Nov 2017, 박경일 wrote:

                                            Dear FS experts,
                                            I could get QDEC image
        comparing two groups.
                                            However, is there a way to
        get numerical values of
                    cortical
                                thickness in
                                            each vertex?

                                            Thank you

                                            Best,
                                            Kyung




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




                                --

                                Kyung-Il Park, MD, PhD.

                                Professor,

                                Department of Neurology, Seoul
        National University
                    Hospital; Seoul National
                                University Hospital
                                Healthcare System Gangnam Center.

                                Office: 82-2-2112-5756 / Fax:
        82-2-2112-5635

                                Email: kip...@snuh.org
        <mailto:kip...@snuh.org> / ideo...@gmail.com
        <mailto:ideo...@gmail.com>



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




                    --

                    Kyung-Il Park, MD, PhD.

                    Professor,

                    Department of Neurology, Seoul National University
        Hospital; Seoul National
                    University Hospital
                    Healthcare System Gangnam Center.

                    Office: 82-2-2112-5756 / Fax: 82-2-2112-5635

                    Email: kip...@snuh.org <mailto:kip...@snuh.org> /
        ideo...@gmail.com <mailto:ideo...@gmail.com>



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




        --

        Kyung-Il Park, MD, PhD.

        Professor,

        Department of Neurology, Seoul National University
        Hospital; Seoul National University Hospital
        Healthcare System Gangnam Center.

        Office: 82-2-2112-5756 / Fax: 82-2-2112-5635

        Email: kip...@snuh.org <mailto:kip...@snuh.org> /
        ideo...@gmail.com <mailto:ideo...@gmail.com>



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




--

Kyung-Il Park, MD, PhD.

Professor,

Department of Neurology, Seoul National University Hospital; Seoul National University Hospital Healthcare System Gangnam Center.

Office: 82-2-2112-5756 / Fax: 82-2-2112-5635

Email: kip...@snuh.org <mailto:kip...@snuh.org> / ideo...@gmail.com <mailto:ideo...@gmail.com>



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

_______________________________________________
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.

Reply via email to