Registration of an image with a tracking system

A medical apparatus, comprising:

• a registration tool, which comprises a position sensor and is configured to be brought into contact with a surface of a part of a body of a patient;
• a position-tracking system, which is configured to acquire position coordinates of the position sensor in a first frame of reference defined by the position-tracking system in a vicinity of the part of the body of the patient;
• a display screen;
• and
• a processing unit configured:
• to receive three-dimensional (3D) image data with respect to at least the part of the body of the patient in a second frame of reference;
• to generate a two-dimensional (2D) image of the surface of the part of the body of the patient based on the 3D image data;
• to render the 2D image to the display screen;
• to superimpose onto the displayed 2D image a plurality of icons indicating locations of respective landmarks on the surface of the part of the body;
• to receive the position coordinates acquired by the position-tracking system while the registration tool contacts the locations on the surface of the part of the body of the patient corresponding to the icons on the display;
• and
• to register the first and second frames of reference by comparing the position coordinates to the corresponding locations in the three-dimensional image data.