Hi Ruthger,
I use the following command to take the binary lesion mask (native space) to
the freesurfer space:
mri_convert -rl mri/brainmask.mgz -rt nearest lesion_mask_native_space.mgz
lesion_mask_fs_space.mgz
I always overlay lesion_mask_fs_space.mgz on brainmask.mgz to check that
things look
Dear Freesurfers,
I would like that surface analyses (i.e., cortical thickness) are not
confounded by subcortical lesions in patients. Freesurfer provides a
work-around in its release notes (
http://surfer.nmr.mgh.harvard.edu/fswiki/ReleaseNotes), which is to set lesion
voxels in brainmask.mgz
