The present invention provides a motion analysis system for measuring the relative function of one anatomical structure to another based on optical fiducial markers tracked in a series of images and in turn data, where the components of hard and soft tissue are used in analysis and where the image data can be compared in a time series such that probabilities of involvement with various tissues can be correlated to the image data.The system measures displacement at various positions and can relate the data to various muscle and other soft tissue variations within the constraints of the anatomy and physiology including motion in three dimensional space, including rotations and translations and functions including velocity and acceleration.
