Re: [Freesurfer] Extract smoothed cortical thickness whole-brain vertex-wise

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