An apparatus for generating an organ timing signal relating to at least one inspected organ within the body of a patient, said apparatus comprising: a medical positioning system including: at least one reference electromagnetic transducer placed at a reference location; at least one inner electromagnetic transducer (120 1) attached to a surgical tool inserted in a blood vessel in the vicinity of said inspected organ; and an MPS processor, coupled with said at least one reference electromagnetic transducer and with said at least one inner electromagnetic transducer (120 1), said MPS processor determining the three-dimensional position of said at least one inner electromagnetic transducer (120 1), by processing transmitted electromagnetic signals transmitted from at least one of said at least one reference electromagnetic transducer and said at least one inner electromagnetic transducer (120 1) with detected electromagnetic signals detected by at least the other of said at least one reference electromagnetic transducer and said at least one inner electromagnetic transducer (120 1), said MPS processor further generating MPS data sets, each of said MPS data sets comprising a collection of three-dimensional position coordinate readings demonstrating the motion trajectory of said surgical tool over time; and characterized by a processor coupled with said MPS, generating said organ timing signal from said MPS data sets by detecting and identifying periodic motion frequencies in said MPS data sets, and filtering said periodic motion frequencies from said MPS data sets. a medical positioning system including: at least one reference electromagnetic transducer placed at a reference location; at least one inner electromagnetic transducer (120 1) attached to a surgical tool inserted in a blood vessel in the vicinity of said inspected organ; and an MPS processor, coupled with said at least one reference electromagnetic transducer and with said at least one inner electromagnetic transducer (120 1), said MPS processor determining the three-dimensional position of said at least one inner electromagnetic transducer (120 1), by processing transmitted electromagnetic signals transmitted from at least one of said at least one reference electromagnetic transducer and said at least one inner electromagnetic transducer (120 1) with detected electromagnetic signals detected by at least the other of said at least one reference electromagnetic transducer and said at least one inner electromagnetic transducer (120 1), said MPS processor further generating MPS data sets, each of said MPS data sets comprising a collection of three-dimensional position coordinate readings demonstrating the motion trajectory of said surgical tool over time; and characterized by a processor coupled with said MPS, generating said organ timing signal from said MPS data sets by detecting and identifying periodic motion frequencies in said MPS data sets, and filtering said periodic motion frequencies from said MPS data sets. at least one reference electromagnetic transducer placed at a reference location; at least one inner electromagnetic transducer (120 1) attached to a surgical tool inserted in a blood vessel in the vicinity of said inspected organ; and an MPS processor, coupled with said at least one reference electromagnetic transducer and with said at least one inner electromagnetic transducer (120 1), said MPS processor determining the three-dimensional position of said at least one inner electromagnetic transducer (120 1), by processing transmitted electromagnetic signals transmitted from at least one of said at least one reference electromagnetic transducer and said at least one inner electromagnetic transducer (120 1) with detected electromagnetic signals detected by at least the other of said at least one reference electromagnetic transducer and said at least one inner electromagnetic transducer (120 1), said MPS processor further generating MPS data sets, each of said MPS data sets comprising a collection of three-dimensional position coordinate readings demonstrating the motion trajectory of said surgical tool over time; and characterized by a processor coupled with said MPS, generating said organ timing signal from said MPS data sets by detecting and identifying periodic motion frequencies in said MPS data sets, and filtering said periodic motion frequencies from said MPS data sets.