You're better off loading in the surface annotation directly rather than dealing with aparc+aseg. To make surf2surf output the right dimensions, add --noreshape.
doug Joonkoo Park wrote: > Dear Surfers, > > I (successfully) resampled a functional data on the surface map using > mri_vol2surf: > > >> mri_vol2surf --mov func.nii --reg register.dat --projfrac 0.5 --interp >> nearest --hemi lh --o lh.func.mgh >> > > Then, I normalized this image to a standard space (fsaverage) using > mri_surf2surf: > > >> mri_surf2surf --srcsubject sub1 --trgsubject fsaverage --sval >> sub1/lh.func.mgh --tval sub1/lh.func.norm.mgh --fwhm 5 --cortex --hemi lh >> > > The dimension of the output file, lh.func.norm.mgh, was 163842 x 1 x 1 > (identified from mri_info). This file can be opened from Matlab, and I > can successfully get access to 163842 vertices. What I want now is to > take the aparc+aseg information from the average brain (fsaverage) and > be able identify which vertex falls under which ROI label. I decided > to resample aparc+aseg.mgz in fsaverage on the surface map, hoping to > get label information at the dimension of 163842 x 1 x 1. So I ran: > > >> mri_vol2surf --mov fsaverage/mri/aparc+aseg.mgz --regheader fsaverage >> --projfrac 0.5 --interp nearest --hemi lh --o fsaverage/surf/lh.roi.mgh >> mri_vol2surf --mov fsaverage/mri/aparc+aseg.mgz --regheader fsaverage >> --projfrac 0.5 --interp nearest --hemi rh --o fsaverage/surf/rh.roi.mgh >> > > The resulting mgh files, however, had a dimension of 23406 x 1 x 7. > > 1. As I said, I wanted to get label information (roi number from the > FreeSurferColorLUT) for each vertex of the surface image in the > fsaverage space. Is this the right approach? And did I do this > correctly (I'm concerned about many options above)? > > 2. If so, why is the resulting dimension different from the other one? > I assume that it's probably a reshape issue, but how I can reshape the > dimension to match 163842 x 1 x 1? > > Thanks in advance. > > Joon > > -- > Joonkoo Park > Ph.D. Candidate, Cognition & Cognitive Neuroscience > Department of Psychology, University of Michigan > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
