1. A method for performing coordinate transformation in navigation-guided procedures between an imaging diagnostic tool with at least one reference structure having a known surface geometry and orientation relative to the imaging diagnostic tool, and a position-determining system, comprising: positioning the at least one reference structure adjacent to the imaging diagnostic tool, said at least one reference structure comprising a plurality of truncated pyramid-shaped recesses; tracing the at least one reference structure by contacting the at least one reference structure with the tip of a pointer at three or more contact points forming a non-isosceles triangle, wherein the tip of the pointer has markers that can be detected by the position-determining system, determining the coordinates of the contacted points by the position-determining system in a coordinate system of this position-determining system and are transmitted to an evaluation computer of the imaging diagnostic tool, wherein the imaging diagnostic tool assumes an orientation that is substantially insensitive to the effect of mechanical forces during the tracing of the reference structure, and adjustment axes of the imaging diagnostic tool are locked such that the kinematics of the imaging diagnostic tool are predicted as a function of the ordered series of measurement values of position sensors located on the imaging diagnostic tool, and recursively transforming the coordinate systems of the position-determining system and the imaging diagnostic tool one into the other with a transformation matrix, wherein the transformation matrix is calculated from the coordinates of the contacted points in the coordinate system of the position-determining system, and from the known surface geometry of the reference structure in a coordinate system of the imaging diagnostic tool, by a computer program in the evaluation computer.