The present invention relates to compensating for brain shift in catheter trajectory planning. First brain shift information is determined from an initial brain image dataset, an initial planning dataset, a patient orientation dataset, and first burr hole dataset. The brain image dataset is updated based on the first brain shift information and a trajectory of a first catheter is updated based on the updated brain image dataset. For a subsequent catheter placement, subsequent brain shift information is determined based on the updated brain image dataset, the patient orientation dataset, and a subsequent burr hole dataset. The brain image dataset is updated again based on the subsequent brain shift information. The re-updated brain image dataset is utilized to update trajectories of the subsequent catheter as well as any preceding catheters.