A method and system are provided to measure cardiac motion data using a cardiovascular navigation system. The method and system position a patient reference sensor (PRS) on a patient, wherein the PRS determines a position of the patient relative to a reference point. The method and system determine a reference orientation matrix based on an orientation of the PRS relative to a reference point and determining a normalization time based on an electrical signal. The method and system obtain point specific (PS) motion data for a plurality of map points. The PS motion data indicates a three dimensional trajectory that occurs at the corresponding map point on a wall of a heart of the patient during at least one cardiac cycle. Further the method and system compensate the PS motion data based on the PRS.