Systems and methods are provided that automatically determine whether a prospective surgical trajectory will collide with a patient's skull using a 3D representation of the patient's cranial region (including the patient's scalp, skull, and brain) adapted from imaging data of the patient's cranial region (e.g., MRI data or CT data). Taking a particular patient's varied skull thickness into account, examples can determine bone collision during a trajectory planning stage before or after a stereotactic frame is mounted to the patient. Accordingly, examples may preemptively alert a clinician to a potential bone collision before the prospective surgical trajectory is underway/has been executed, thereby reducing the risk of bone collision during the surgical procedure.