A system and method are provided for guiding surgery using MR images and radioactive markers. The method comprises reconstructing the surface of an anatomical structure and a gamma probe orientated to optimize a radioactivity reading from a radioactive seed placed at a target location in the anatomic structure for each of one or more positions of the gamma probe. The position and orientation of the gamma probe is detected in each reconstructed surface to estimate a position of the radioactive seed relative to the reconstructed surface.
