Once surgery actually begins, the jig guarantees the patient's head is still positioned exactly inside the jig in the same position as when the scans were made, so precise surgical procedures are possible. Jigs are unwieldy and difficult to apply. Simply positioning a patient's head inside a jig is only about as difficult as positioning snow chains around a tire. The real difficulty is positioning and tightening a relatively small number of screws to guarantee the jig stays rigidly in place and never moves once applied. Jigs are painful.
Jigs apply large amounts of pressure to a small number of points on the patient.
Jig adjustment screws often additionally injure the patient. Patients are often required to wear jigs for very long periods of time. Young children can't cope with jigs at all. Jig positioning is hard to duplicate. If a jig is removed, it's very difficult to reapply the jig in the exact same position, because it's necessary to precisely adjust multiple screws to their exact previous settings and locations.