Extract smoothed cortical thickness whole-brain vertex-wise

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Nicolette Schwarz

7 Jul 2017 7 Jul '17

7:15 p.m.

Hello everyone,

I'm pretty new to FS and can't seem to find the solution for my problem.

I am trying to write whole-brain vertex-wise cortical thickness (CT) data from each participant into ascii files. In my original analysis, each participant's average CT in clusters derived from a whole-brain GLM were extracted and used in a second analysis. I'd like to extract CT vertex-wise to perform a whole-brain version of this second analysis. I need the smoothed and "fsaveraged" (to get the same # of vertices across participants in a template space) CT values to match the cluster data and that seems to be tricky.

This works: mris_convert -c lh.thickness lh.sphere.reg test1.thickness.asc

This doesn't work: mris_convert -c lh.thickness.fwhm10.fsaverage.mgh lh.sphere.reg test2.lh.thickness.asc # ERROR: number of vertices in lh.thickness.fwhm10.fsaverage.mgh does not match surface (163842,124874)

I presume the issue is that ?h.thickness.fwhm10.fsaverage.mgh is a volume file while ?h.sphere.reg is a surface file. So I've tried to convert volume to surface (created a folder test1/surf and copied both fsaverage/surf/lh.sphere.reg and sub/surf/lh.thickness.fwhm10.fsaverage.mgh there) using different combinations of mri_vol2surf, e.g.:

mri_vol2surf --srcsubject test1 --src lh.thickness.fwhm10.fsaverage.mgh --trgsubject test1 --surfreg lh.sphere.reg --regheader test1 --hemi lh --o test.surf

This doesn't work as it wants me to specify a type but I have no clue what the type for the surface is (or better, it doesn't seem to be an option going by mris_convert). Other combinations asked for --reg files and I played with tkmedit2 but none of this is working out.

Also, is ?h.sphere.reg an appropriate choice and would it have to be smoothed to FWHM=10 prior to mris_convert?

Trying to solve this has me going in all kinds of circles and I'm unsure about this approach anyway. Hence, I would truly appreciate any help.

Thank you very much in advance,

Nic

-- Nicolette Schwarz, Ph.D. Postdoctoral Research Fellow http://heartbrain.hms.harvard.edu

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Bruce Fischl

8 Jul 8 Jul

11:10 a.m.

New subject: Extract smoothed cortical thickness whole-brain vertex-wise

Hi Nic

the problem isn't a surface/volume one, it's that the file lh.thickness.fwhm10.fsaverage.mgh is on the fsaverage surface not on the individual subject one. If you run that command using the sphere.reg from fsaverage (or any other surface from the lh fsaverage) it should work

cheers Bruce

On Fri, 7 Jul 2017, Nicolette Schwarz wrote:

...

Hello everyone,

I'm pretty new to FS and can't seem to find the solution for my problem.

I am trying to write whole-brain vertex-wise cortical thickness (CT) data from each participant into ascii files. In my original analysis, each participant's average CT in clusters derived from a whole-brain GLM were extracted and used in a second analysis. I'd like to extract CT vertex-wise to perform a whole-brain version of this second analysis. I need the smoothed and "fsaveraged" (to get the same # of vertices across participants in a template space) CT values to match the cluster data and that seems to be tricky.

This works: mris_convert -c lh.thickness lh.sphere.reg test1.thickness.asc

This doesn't work: mris_convert -c lh.thickness.fwhm10.fsaverage.mgh lh.sphere.reg test2.lh.thickness.asc # ERROR: number of vertices in lh.thickness.fwhm10.fsaverage.mgh does not match surface (163842,124874)

I presume the issue is that ?h.thickness.fwhm10.fsaverage.mgh is a volume file while ?h.sphere.reg is a surface file. So I've tried to convert volume to surface (created a folder test1/surf and copied both fsaverage/surf/lh.sphere.reg and sub/surf/lh.thickness.fwhm10.fsaverage.mgh there) using different combinations of mri_vol2surf, e.g.:

mri_vol2surf --srcsubject test1 --src lh.thickness.fwhm10.fsaverage.mgh --trgsubject test1 --surfreg lh.sphere.reg --regheader test1 --hemi lh --o test.surf

This doesn't work as it wants me to specify a type but I have no clue what the type for the surface is (or better, it doesn't seem to be an option going by mris_convert). Other combinations asked for --reg files and I played with tkmedit2 but none of this is working out.

Also, is ?h.sphere.reg an appropriate choice and would it have to be smoothed to FWHM=10 prior to mris_convert?

Trying to solve this has me going in all kinds of circles and I'm unsure about this approach anyway. Hence, I would truly appreciate any help.

Thank you very much in advance,

Nic

-- Nicolette Schwarz, Ph.D. Postdoctoral Research Fellow http://heartbrain.hms.harvard.edu

Nicolette Schwarz

10 Jul 10 Jul

12:12 p.m.

Hi Bruce,

Thank you for your answer!

I have tried: mris_convert -c lh.thickness.fwhm10.fsaverage.mgh lh.sphere.reg test.asc

but get this: ERROR: number of vertices in lh.thickness.fwhm10.fsaverage.mgh does not match surface (163842,141823)

Why might that be?

Thank you in advance!

Nic

On Saturday, July 8, 2017, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:

...

Hi Nic

the problem isn't a surface/volume one, it's that the file lh.thickness.fwhm10.fsaverage.mgh is on the fsaverage surface not on the individual subject one. If you run that command using the sphere.reg from fsaverage (or any other surface from the lh fsaverage) it should work

cheers Bruce

On Fri, 7 Jul 2017, Nicolette Schwarz wrote:

Hello everyone,

...
I'm pretty new to FS and can't seem to find the solution for my problem.

I am trying to write whole-brain vertex-wise cortical thickness (CT) data from each participant into ascii files. In my original analysis, each participant's average CT in clusters derived from a whole-brain GLM were extracted and used in a second analysis. I'd like to extract CT vertex-wise to perform a whole-brain version of this second analysis. I need the smoothed and "fsaveraged" (to get the same # of vertices across participants in a template space) CT values to match the cluster data and that seems to be tricky.

This works: mris_convert -c lh.thickness lh.sphere.reg test1.thickness.asc

This doesn't work: mris_convert -c lh.thickness.fwhm10.fsaverage.mgh lh.sphere.reg test2.lh.thickness.asc # ERROR: number of vertices in lh.thickness.fwhm10.fsaverage.mgh does not match surface (163842,124874)

I presume the issue is that ?h.thickness.fwhm10.fsaverage.mgh is a volume file while ?h.sphere.reg is a surface file. So I've tried to convert volume to surface (created a folder test1/surf and copied both fsaverage/surf/lh.sphere.reg and sub/surf/lh.thickness.fwhm10.f saverage.mgh there) using different combinations of mri_vol2surf, e.g.:

mri_vol2surf --srcsubject test1 --src lh.thickness.fwhm10.fsaverage.mgh --trgsubject test1 --surfreg lh.sphere.reg --regheader test1 --hemi lh --o test.surf

This doesn't work as it wants me to specify a type but I have no clue what the type for the surface is (or better, it doesn't seem to be an option going by mris_convert). Other combinations asked for --reg files and I played with tkmedit2 but none of this is working out.

Also, is ?h.sphere.reg an appropriate choice and would it have to be smoothed to FWHM=10 prior to mris_convert?

Trying to solve this has me going in all kinds of circles and I'm unsure about this approach anyway. Hence, I would truly appreciate any help.

Thank you very much in advance,

Nic

-- Nicolette Schwarz, Ph.D. Postdoctoral Research Fellow http://heartbrain.hms.harvard.edu

-- Nicolette Schwarz, Ph.D. Postdoctoral Research Fellow http://heartbrain.hms.harvard.edu

Bruce Fischl

2:09 p.m.

New subject: Extract smoothed cortical thickness whole-brain vertex-wise

it's because you are still loading the individual subject sphere.reg. Try using $SUBJECTS_DIR/fsaverage/surf/lh.sphere.reg as the surface instead of lh.sphere.reg

cheers Bruce

On Mon, 10 Jul 2017, Nicolette Schwarz wrote:

...

Hi Bruce, Thank you for your answer!

I have tried:

but get this: ERROR: number of vertices in lh.thickness.fwhm10.fsaverage.mgh does not match surface (163842,141823)

Why might that be?

Thank you in advance!

Nic

On Saturday, July 8, 2017, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: Hi Nic

  the problem isn't a surface/volume one, it's that the file lh.thickness.fwhm10.fsaverage.mgh is on the fsaverage surface not on the individual
  subject one. If you run that command using the sphere.reg from fsaverage (or any other surface from the lh fsaverage) it should work

  cheers
  Bruce



  On Fri, 7 Jul 2017, Nicolette Schwarz wrote:

        Hello everyone,


        I'm pretty new to FS and can't seem to find the solution for my problem.


        I am trying to write whole-brain vertex-wise cortical thickness (CT) data
        from each participant into ascii files. In my original analysis, each
        participant's average CT in clusters derived from a whole-brain GLM were
        extracted and used in a second analysis. I'd like to extract CT vertex-wise
        to perform a whole-brain version of this second analysis. I need the
        smoothed and "fsaveraged" (to get the same # of vertices across participants
        in a template space) CT values to match the cluster data and that seems to
        be tricky.


        This works: mris_convert -c lh.thickness lh.sphere.reg test1.thickness.asc

        This doesn't work: mris_convert -c lh.thickness.fwhm10.fsaverage.mgh
        lh.sphere.reg test2.lh.thickness.asc # ERROR: number of vertices in
        lh.thickness.fwhm10.fsaverage.mgh does not match surface (163842,124874)


        I presume the issue is that ?h.thickness.fwhm10.fsaverage.mgh is a volume
        file while ?h.sphere.reg is a surface file. So I've tried to convert
        volume to surface (created a folder test1/surf and copied both
        fsaverage/surf/lh.sphere.reg and sub/surf/lh.thickness.fwhm10.fsaverage.mgh
        there) using different combinations of mri_vol2surf, e.g.:


        mri_vol2surf --srcsubject test1 --src lh.thickness.fwhm10.fsaverage.mgh
        --trgsubject test1 --surfreg lh.sphere.reg --regheader test1 --hemi lh --o
        test.surf


        This doesn't work as it wants me to specify a type but I have no clue what
        the type for the surface is (or better, it doesn't seem to be an option
        going by mris_convert). Other combinations asked for --reg files and I
        played with tkmedit2 but none of this is working out.


        Also, is ?h.sphere.reg an appropriate choice and would it have to be
        smoothed to FWHM=10 prior to mris_convert?


        Trying to solve this has me going in all kinds of circles and I'm unsure
        about this approach anyway. Hence, I would truly appreciate any help.


        Thank you very much in advance,


        Nic




        --
        Nicolette Schwarz, Ph.D.
        Postdoctoral Research Fellow
        http://heartbrain.hms.harvard.edu

-- Nicolette Schwarz, Ph.D. Postdoctoral Research Fellow http://heartbrain.hms.harvard.edu

Nicolette Schwarz

3:04 p.m.

Thanks so much, that works!

I did try that but didn't realize that I need to specify both $SUBJECTS_DIR/sub/surf/lh.thickness.fwhm10.fsaverage.mgh as well as $SUBJECTS_DIR/fsaverage/surf/lh.sphere.reg explicitely (wanted to print from sub/surf and so thought that I'd only need to specify the other directory).

Again, thank you!

On Monday, July 10, 2017, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:

...

it's because you are still loading the individual subject sphere.reg. Try using $SUBJECTS_DIR/fsaverage/surf/lh.sphere.reg as the surface instead of lh.sphere.reg

cheers Bruce

On Mon, 10 Jul 2017, Nicolette Schwarz wrote:

Hi Bruce,

...
Thank you for your answer!

I have tried: but get this: ERROR: number of vertices in lh.thickness.fwhm10.fsaverage.mgh does not match surface (163842,141823)

Why might that be?

Thank you in advance!

Nic

On Saturday, July 8, 2017, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: Hi Nic
  the problem isn't a surface/volume one, it's that the file
lh.thickness.fwhm10.fsaverage.mgh is on the fsaverage surface not on the individual subject one. If you run that command using the sphere.reg from fsaverage (or any other surface from the lh fsaverage) it should work
  cheers
  Bruce



  On Fri, 7 Jul 2017, Nicolette Schwarz wrote:

        Hello everyone,


        I'm pretty new to FS and can't seem to find the solution for
my problem.
        I am trying to write whole-brain vertex-wise cortical
thickness (CT) data from each participant into ascii files. In my original analysis, each participant's average CT in clusters derived from a whole-brain GLM were extracted and used in a second analysis. I'd like to extract CT vertex-wise to perform a whole-brain version of this second analysis. I need the smoothed and "fsaveraged" (to get the same # of vertices across participants in a template space) CT values to match the cluster data and that seems to be tricky.
        This works: mris_convert -c lh.thickness lh.sphere.reg
test1.thickness.asc
        This doesn't work: mris_convert -c
lh.thickness.fwhm10.fsaverage.mgh lh.sphere.reg test2.lh.thickness.asc # ERROR: number of vertices in lh.thickness.fwhm10.fsaverage.mgh does not match surface (163842,124874)
        I presume the issue is that ?h.thickness.fwhm10.fsaverage.mgh
is a volume file while ?h.sphere.reg is a surface file. So I've tried to convert volume to surface (created a folder test1/surf and copied both fsaverage/surf/lh.sphere.reg and sub/surf/lh.thickness.fwhm10.fsaverage.mgh there) using different combinations of mri_vol2surf, e.g.:
        mri_vol2surf --srcsubject test1 --src
lh.thickness.fwhm10.fsaverage.mgh --trgsubject test1 --surfreg lh.sphere.reg --regheader test1 --hemi lh --o test.surf
        This doesn't work as it wants me to specify a type but I have
no clue what the type for the surface is (or better, it doesn't seem to be an option going by mris_convert). Other combinations asked for --reg files and I played with tkmedit2 but none of this is working out.
        Also, is ?h.sphere.reg an appropriate choice and would it
have to be smoothed to FWHM=10 prior to mris_convert?
        Trying to solve this has me going in all kinds of circles and
I'm unsure about this approach anyway. Hence, I would truly appreciate any help.
        Thank you very much in advance,


        Nic




        --
        Nicolette Schwarz, Ph.D.
        Postdoctoral Research Fellow
        http://heartbrain.hms.harvard.edu
-- Nicolette Schwarz, Ph.D. Postdoctoral Research Fellow http://heartbrain.hms.harvard.edu

-- Nicolette Schwarz, Ph.D. Postdoctoral Research Fellow http://heartbrain.hms.harvard.edu

Bruce Fischl

3:45 p.m.

New subject: Extract smoothed cortical thickness whole-brain vertex-wise

glad it worked out Bruce On Mon, 10 Jul 2017, Nicolette Schwarz wrote:

...

Thanks so much, that works! I did try that but didn't realize that I need to specify both $SUBJECTS_DIR/sub/surf/lh.thickness.fwhm10.fsaverage.mgh as well as $SUBJECTS_DIR/fsaverage/surf/lh.sphere.reg explicitely (wanted to print from sub/surf and so thought that I'd only need to specify the other directory).

Again, thank you!

On Monday, July 10, 2017, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: it's because you are still loading the individual subject sphere.reg. Try using $SUBJECTS_DIR/fsaverage/surf/lh.sphere.reg as the surface instead of lh.sphere.reg

  cheers
  Bruce






  On Mon, 10 Jul 2017, Nicolette Schwarz wrote:

        Hi Bruce,
        Thank you for your answer!

        I have tried:
        but get this: ERROR: number of vertices in
        lh.thickness.fwhm10.fsaverage.mgh does not match
        surface (163842,141823)

        Why might that be?

        Thank you in advance!

        Nic

        On Saturday, July 8, 2017, Bruce Fischl
        <fischl@nmr.mgh.harvard.edu> wrote:
              Hi Nic

              the problem isn't a surface/volume one, it's
        that the file lh.thickness.fwhm10.fsaverage.mgh is
        on the fsaverage surface not on the individual
              subject one. If you run that command using the
        sphere.reg from fsaverage (or any other surface from
        the lh fsaverage) it should work

              cheers
              Bruce



              On Fri, 7 Jul 2017, Nicolette Schwarz wrote:

                    Hello everyone,


                    I'm pretty new to FS and can't seem to
        find the solution for my problem.


                    I am trying to write whole-brain
        vertex-wise cortical thickness (CT) data
                    from each participant into ascii files.
        In my original analysis, each
                    participant's average CT in clusters
        derived from a whole-brain GLM were
                    extracted and used in a second analysis.
        I'd like to extract CT vertex-wise
                    to perform a whole-brain version of this
        second analysis. I need the
                    smoothed and "fsaveraged" (to get the
        same # of vertices across participants
                    in a template space) CT values to match
        the cluster data and that seems to
                    be tricky.


                    This works: mris_convert -c lh.thickness
        lh.sphere.reg test1.thickness.asc

                    This doesn't work: mris_convert -c
        lh.thickness.fwhm10.fsaverage.mgh
                    lh.sphere.reg test2.lh.thickness.asc #
        ERROR: number of vertices in
                    lh.thickness.fwhm10.fsaverage.mgh does
        not match surface (163842,124874)


                    I presume the issue is that
        ?h.thickness.fwhm10.fsaverage.mgh is a volume
                    file while ?h.sphere.reg is a surface
        file. So I've tried to convert
                    volume to surface (created a folder
        test1/surf and copied both
                    fsaverage/surf/lh.sphere.reg and
        sub/surf/lh.thickness.fwhm10.fsaverage.mgh
                    there) using different combinations of
        mri_vol2surf, e.g.:


                    mri_vol2surf --srcsubject test1 --src
        lh.thickness.fwhm10.fsaverage.mgh
                    --trgsubject test1 --surfreg
        lh.sphere.reg --regheader test1 --hemi lh --o
                    test.surf


                    This doesn't work as it wants me to
        specify a type but I have no clue what
                    the type for the surface is (or better,
        it doesn't seem to be an option
                    going by mris_convert). Other
        combinations asked for --reg files and I
                    played with tkmedit2 but none of this is
        working out.


                    Also, is ?h.sphere.reg an appropriate
        choice and would it have to be
                    smoothed to FWHM=10 prior to
        mris_convert?


                    Trying to solve this has me going in all
        kinds of circles and I'm unsure
                    about this approach anyway. Hence, I
        would truly appreciate any help.


                    Thank you very much in advance,


                    Nic




                    --
                    Nicolette Schwarz, Ph.D.
                    Postdoctoral Research Fellow
                    http://heartbrain.hms.harvard.edu




        --
        Nicolette Schwarz, Ph.D.
        Postdoctoral Research Fellow
        http://heartbrain.hms.harvard.edu

-- Nicolette Schwarz, Ph.D. Postdoctoral Research Fellow http://heartbrain.hms.harvard.edu

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Bruce Fischl
Nicolette Schwarz