A method of compensation for intra-operative brain shift of a living subject. In one embodiment, the method includes the steps of pro-operatively acquiring brain images of the living subject, constructing a statistical atlas of brain displacements of the living subject from the pro-operatively acquired brain images, intra-operatively measuring brain displacements of the living subject, deriving an intra-operative displacement atlas from the intra-operatively measured brain displacements and the statistical atlas, obtaining intra-operative brain shift at least from the intra-operative displacement atlas, and compensating for the intra-operative brain shift.