1. A method for characterizing spatial distortion of a medical imaging system, the method comprising: estimating a contour and dimensions of a desired target volume; determining a desired coordinate system; determining a volumetric arrangement and non-uniform spacing of a plurality of control points in a three-dimensional space, wherein the desired arrangement and spacing is matched to the contour, dimensions, and coordinate system such that the control points are interspersed within and throughout the entire target volume; providing a substantially rigid three-dimensional phantom that is matched to the determined volumetric arrangement and non-uniform spacing of the plurality of control points in the three-dimensional space and that is also configured to rigidly fix the control points in an interspersed manner throughout its substantially rigid structure; fixing the phantom with respect to a stereotactic frame such that the plurality of control points defines a corresponding plurality of first known spatial locations; imaging the phantom; determining second measured spatial locations based on the imaging; comparing at least a selected volumetric subset of the first known spatial locations with corresponding second measured spatial locations; and calculating indicia of any indicated volumetric spatial distortion between the first known spatial locations and the corresponding second measured spatial locations.