A medical apparatus includes a registration tool, which includes a position sensor, A position-tracking system is configured to acquire position coordinates of the sensor in a first frame of reference defined by the position-tracking system. A processing unit is configured to receive 3D image data with respect to the body of the patient in a second frame of reference, to generate a 2D image of the surface of the patient based on the 3D image data, to render the 2D image to a display screen, and to superimpose onto the 2D image icons indicating locations of respective landmarks. The processing unit receives the position coordinates acquired by the position-tracking system while the registration tool contacts the locations on the patient corresponding to the icons on the display, and registers the first and second frames of reference by comparing the position coordinates to the three-dimensional image data.