The focus of a focused ultrasound system is calibrated with respect to a frame-of-reference, such as that of a magnetic resonance system, by selectively activating only specific regions of the ultrasound transducer of the ultrasound system, thereby altering the shape of the focus. The focal shape is selectively modified in shape and positioned in successive steps of a calibration procedure, while moving the focus through successive localizers of the frame-of-reference. The parameters for operating the ultrasound system when the calibration procedure is completed are stored as parameters that accurately position the focus of the ultrasound system with respect to the frame-of-reference.
