you can try mris_volmask or mri_surf2vol. volmask is the better choice if it works for your data. Look in recon-all to see how to call it. This is what creates the ribbon.mgz file, which sounds like what you need
On 11/20/2015 12:28 PM, Sherihane Bensemmane wrote:
Hi, I am using freesurfer for non_human primate. I did the segmentation in freesurfer , at the end i have the wm.mgz but not grey matter since the command to get it during segmentation doesn't work in monkey brain. in the forlder /surf/ i have all files such as lh/rh.pial, curv, sulc, white. Since I am also using SPM and some toolbox to conduct my connectivity data i need good segmentation, so i wanted to use the files in surf, the pial and white to get the grey matter information and then convert it to a volume file. I've been looking for solutions, but didn't find anything, can you help? how shall i proceed to get my grey matter mask from my segmentation, in the native space.
Thank you,
Best regards, Sherihane KUL
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