Systems and methods for characterizing spatial distortions in location data determined by an imaging system, for example as employed in imaged guided therapy. A three dimensional phantom is custom formed for a desired imaging space of a given imaging system. The phantom includes a large plurality of control points fixed rigidly in space to a high degree of known accuracy. The phantom is fixed to a stereotactic frame defining a known calibrated reference or zero and imaged. An algorithm customized for the phantom determines the spatial locations of the control points. A comparison is made between the known and the determined spatial locations for at least a subset of the control points. The comparison results in indicia for any determined spatial distortions observed. The raw image data can be manipulated to compensate for any spatial distortion. The control points can have fixed locations known to an accuracy of 100.mu. or better. The algorithm can determine an initial estimate for the detected location of a control point accurate to .+-.0.5 pixel or better.