CT has some advantages over MRI regarding skullstripping. If your data is in standard Hounsfeld units, you can remove skull by intensity. To get brain only, you can then use something like 3dSkullStrip.
# take data only between intensities of 830-1300
3dcalc -a CT+orig'<830..1300>' -expr a -prefix CT_noskull
# get brain only
3dSkullStrip -prefix test_CT_ns -orig_vol -input CTnoskull3+orig.
If there has been surgery done, then that can be more complicated, and you may need to try some options like the "push_to_edge" or smoothing operations.
