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 <fis...@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 <fis...@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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