I tried this, but something is going wrong. Here's what I did: 1. I ran $ mri_binarize --i subjid/mri/aparc+asec.mgz --match xx --match yy --o lobe.mgz - this produces a nice binary mask of, say, the left frontal lobe. 2. Then I ran $ mri_surf2vol --mkmask --surf pial --hemi lh --template lobe.mgz --identity subjid --o lobe_surface.mgz - this produces a nice binary image of the pial surface, but it contains the whole surface, not only the intersection with lobe.mgz. What am I doing wrong?
Thanks, Martin Douglas N Greve wrote: > Use mri_surf2vol to create volumes. You can binarize aparc+aseg.mgz to > give a mask of an area (use --match), then take the intersection of the > mask with the surface-in-volume. > > doug > > Martin Ystad wrote: > >> Hi, >> I'm working on a fractal dimension analysis of the pial- and >> white-matter surface. The matlab script that calculates the fractal >> dimension needs binary nifti-files as input. Since FreeSurfer creates >> the surfaces I need, here's what I want to do: >> I'd like to convert the pial and white-matter surfaces (separately) to >> .nii-volumes (e.g. 256x256) where the voxels intersected by the >> respective surfaces are white, and everything else is black. >> Furthermore, I'd like to do this for individual subregions of each >> surface; for example only the precentral gyrus or the whole frontal >> lobe, so that only the voxels intersected by the surface belonging to >> the specific label I choose appear white, and everything else is black. >> How do I get this output from FreeSurfer? >> >> Thanks, >> Martin Ystad >> PhD-candidate, >> University of Bergen, Norway >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> >> > > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
