Apparatus for generating an organ timing signal relating to an inspected organ within the body of a patient, including a medical positioning system, and a processor coupled with the medical positioning system, the medical positioning system including at least one reference electromagnetic transducer placed at a reference location, at least one inner electromagnetic transducer attached to a surgical tool inserted in a blood vessel in the vicinity of the inspected organ, and a medical positioning system processor coupled with the reference electromagnetic transducer and the inner electromagnetic transducer, the medical positioning system processor determining the three-dimensional position of the inner electromagnetic transducer, by processing transmitted electromagnetic signals transmitted from one of the reference electromagnetic transducer and the inner electromagnetic transducer with detected electromagnetic signals detected by the other of the reference electromagnetic transducer and the inner electromagnetic transducer, the medical positioning system processor further generating medical positioning system data sets, each of the medical positioning system data sets including a collection of three-dimensional position coordinate readings demonstrating the motion trajectory of the surgical tool over time, the processor generating the organ timing signal from the medical positioning system data sets by detecting and identifying periodic motion frequencies in the medical positioning system data sets, and filtering the periodic motion frequencies from the medical positioning system data sets.