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 <[email protected]> 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
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