High intensity focused ultrasound (HIFU) is registered with imaging. The effects of transmission from a HIFU transducer, such as a rise in temperature, are detected by a separate imaging system. By using multiple transmissions, a plurality of locations of the transmissions from the HIFU transducer are determined within the imaging system coordinates. A transform relating the imaging system coordinates to the HIFU transducer coordinates is determined from the detected effects. The transform may be used to relate locations indicated in images of the imaging system with coordinates of the HIFU transducer for application of HIFU. The imaging system may not have to scan the HIFU transducer or fiducials and a fixed relationship may not be needed.
