Thanks Doug, Where can I find the surface annotation for the fsaverage (or any other template) data? I will need to import the data into matlab eventually, so I'm thinking that the surface annotation file should be readable using load_mgh.m (and writable using save_mgh.m). I'm very new to FreeSurfer so I'd really appreciate if you can describe each step for me.
Thank you. Joon On Fri, Feb 19, 2010 at 11:47 AM, Douglas N Greve <gr...@nmr.mgh.harvard.edu> wrote: > 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
