[freesurfer] Extracting values of cortical thickness in each vertex.

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박경일

12 Nov 2017 12 Nov '17

1:24 a.m.

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

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Bruce Fischl

12 Nov 12 Nov

10:43 a.m.

New subject: [freesurfer] Extracting values of cortical thickness in each vertex.

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

박경일

6:17 p.m.

New subject: [freesurfer] Extracting values of cortical thickness in each vertex.

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 fischl@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 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.

-- 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: kipark@snuh.org / ideopki@gmail.com

Bruce Fischl

8:05 p.m.

New subject: [freesurfer] Extracting values of cortical thickness in each vertex.

yes. You can use mris_convert to make an ascii file, or read_curv.m to read them into matlab.

cheers Bruce 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 fischl@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 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.

--

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: kipark@snuh.org / ideopki@gmail.com

Bruce Fischl

8:06 p.m.

New subject: [freesurfer] Extracting values of cortical thickness in each vertex.

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 fischl@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 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.

--

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: kipark@snuh.org / ideopki@gmail.com

박경일

30 Jan 30 Jan

1:11 a.m.

New subject: [freesurfer] Extracting values of cortical thickness in each vertex.

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 fischl@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 fischl@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 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.

--

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: kipark@snuh.org / ideopki@gmail.com
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.

Bruce Fischl

10:04 a.m.

New subject: [freesurfer] Extracting values of cortical thickness in each vertex.

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 fischl@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 <fischl@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
        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.




        --

        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: kipark@snuh.org / ideopki@gmail.com
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.

--

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: kipark@snuh.org / ideopki@gmail.com

박경일

2 Feb 2 Feb

1:56 a.m.

New subject: [freesurfer] Extracting values of cortical thickness in each vertex.

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 fischl@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 fischl@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 <
fischl@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
        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.
        --

        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: kipark@snuh.org / ideopki@gmail.com
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.

--

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: kipark@snuh.org / ideopki@gmail.com
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.

Bruce Fischl

10:33 a.m.

New subject: [freesurfer] Extracting values of cortical thickness in each vertex.

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.

what is wrong?

Thanks as always.

Kyung

2018-01-31 0:04 GMT+09:00 Bruce Fischl fischl@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 <fischl@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
        <fischl@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
                    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.




                    --

                    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: kipark@snuh.org / ideopki@gmail.com



        _______________________________________________
        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.




        --

        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: kipark@snuh.org / ideopki@gmail.com

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.

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: kipark@snuh.org / ideopki@gmail.com

박경일

6 Feb 6 Feb

11:22 p.m.

New subject: [freesurfer] Extracting values of cortical thickness in each vertex.

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 fischl@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 fischl@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 <
fischl@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
        <fischl@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
                    https://mail.nmr.mgh.harvard.e
du/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.
                    --

                    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: kipark@snuh.org / ideopki@gmail.com



        _______________________________________________
        Freesurfer mailing list
        Freesurfer@nmr.mgh.harvard.edu
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Email: kipark@snuh.org / ideopki@gmail.com
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Douglas Greve

9 Feb 9 Feb

1:07 p.m.

New subject: [freesurfer] Extracting values of cortical thickness in each vertex.

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 <fischl@nmr.mgh.harvard.edu mailto:fischl@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
    <fischl@nmr.mgh.harvard.edu <mailto:fischl@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
    <fischl@nmr.mgh.harvard.edu <mailto:fischl@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
                <fischl@nmr.mgh.harvard.edu
    <mailto:fischl@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




                           
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                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: kipark@snuh.org <mailto:kipark@snuh.org> /
    ideopki@gmail.com <mailto:ideopki@gmail.com>



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    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: kipark@snuh.org <mailto:kipark@snuh.org> /
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Office: 82-2-2112-5756 / Fax: 82-2-2112-5635

Email: kipark@snuh.org mailto:kipark@snuh.org / ideopki@gmail.com mailto:ideopki@gmail.com

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Bruce Fischl
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박경일