Described embodiments include a processor that receives signals from a probe, as the probe is placed at respective locations on a body of a subject, and derives, from the signals, a set of points that correspond to the respective locations. The processor then registers the set of points with a three-dimensional image of the body, by identifying, for each of the points, one or more voxels of the image whose respective surface normals are oriented within a given angle of an orientation at which the probe was held at the location to which the point corresponds, and computing a transformation that aligns each of the points with a selected one of the voxels that were identified for the point. The processor then tracks, based on the registering, a location of an intrabody tool, in a coordinate system of an imaging device that was used to acquire the image.