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