Dear Freesurfer users,
I have been using the function mri_watershed with options -LABEL and -atlas to segment into csf, scalp and skull. This option also gives a segmentation of the gm and wm. All voxels of the head are assigned to one of the labels.
Nevertheless, the segmentation obtained in the file aseg.mgz of the cortical ribbon is of much better quality the fast mri_watershed -LABEL one. The problem is now if I use the csf obtained with mri_watershed -LABEL together with the aseg.mgz gm segmentation, some voxels in the border between cortical ribbon and csf are unassigned.
My question is then : how could I generate a csf map like the one obtained with mri_watershed -LABEL, but that is complementary of the segmentation present in aseg.mgz of the cortical ribbon ?
Thanks a lot in advance,
Best,