An apparatus, comprising: a handheld registration tool, comprising: an ultrasound transducer, which is configured, when the registration tool is attached sequentially to multiple respective predefined locations on a patient head, to acquire respective US measurements of bone tissue at the predefined locations; and a position sensor of a position-tracking system, which is configured to acquire respective position measurements of the registration tool at the predefined locations, wherein the position sensor is coupled to the US transducer and the position sensor is concentrically disposed around the US transducer; and a processor, which is configured to: receive the multiple US measurements and the respective position measurements acquired by the registration tool; calculate first positions of the bone tissue at the multiple predefined locations, based on the position measurements and the US measurements; identify second positions of the bone tissue at the multiple predefined locations, in an anatomical image of the patient head; and register the anatomical image with a coordinate system of the position-tracking system, by correlating the first positions and the second positions, so as to enable tracking a medical instrument, which is inserted into the patient head and comprises another position sensor of the position-tracking system, using the anatomical image registered with the position-tracking system. a handheld registration tool, comprising: an ultrasound transducer, which is configured, when the registration tool is attached sequentially to multiple respective predefined locations on a patient head, to acquire respective US measurements of bone tissue at the predefined locations; and a position sensor of a position-tracking system, which is configured to acquire respective position measurements of the registration tool at the predefined locations, wherein the position sensor is coupled to the US transducer and the position sensor is concentrically disposed around the US transducer; and an ultrasound transducer, which is configured, when the registration tool is attached sequentially to multiple respective predefined locations on a patient head, to acquire respective US measurements of bone tissue at the predefined locations; and a position sensor of a position-tracking system, which is configured to acquire respective position measurements of the registration tool at the predefined locations, wherein the position sensor is coupled to the US transducer and the position sensor is concentrically disposed around the US transducer; and a processor, which is configured to: receive the multiple US measurements and the respective position measurements acquired by the registration tool; calculate first positions of the bone tissue at the multiple predefined locations, based on the position measurements and the US measurements; identify second positions of the bone tissue at the multiple predefined locations, in an anatomical image of the patient head; and register the anatomical image with a coordinate system of the position-tracking system, by correlating the first positions and the second positions, so as to enable tracking a medical instrument, which is inserted into the patient head and comprises another position sensor of the position-tracking system, using the anatomical image registered with the position-tracking system. receive the multiple US measurements and the respective position measurements acquired by the registration tool; calculate first positions of the bone tissue at the multiple predefined locations, based on the position measurements and the US measurements; identify second positions of the bone tissue at the multiple predefined locations, in an anatomical image of the patient head; and register the anatomical image with a coordinate system of the position-tracking system, by correlating the first positions and the second positions, so as to enable tracking a medical instrument, which is inserted into the patient head and comprises another position sensor of the position-tracking system, using the anatomical image registered with the position-tracking system.