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