A method for determining a mapping between coordinates relative to a body and corresponding coordinates in a three-dimensional image of the body in stereotactic surgery. The method includes attaching an instrumented pointing device to the body, for example, attaching the pointing device directly to a skull. The pointing device includes an arm and an instrumented joint for coupling the arm to the body and for generating a position signal encoding a position of the arm relative to the joint. The method includes positioning the arm at each of a plurality of known points on the body, each of the known points corresponding to a known location in the three-dimensional image, and generating the position signal when the arm is positioned at each of the known points. The method then includes determining from the position signals and the known locations of the points in the three-dimensional image a mapping between a coordinate system that is fixed relative to the anchor and a coordinate system of the three-dimensional image.