Hi all, I have to implement a Difference element method on a volume extracted from a mri. Using freesurfer I am able to extract the volume file for the brain (ie. $h.ribbon), but I need also the volume files for the skull and for the skin. I have seen that the flag -surf exits in the watershed command to extract only the superficial meshes of these. I have also tried to use the flag -LABEL; according to the manual the option -LABEL adds a label for each voxel according to the region in which it is located: 0 -> exterior 1 -> scalp 2 -> skull 3 -> csf 4 -> gray 5 -> white 6 -> fat tissue
but the results are completely wrong, for example I have a label 3 also for regions external to the scalp! Could someone please help me explaining how to use the watershed command using the -LABEL option?