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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