A system to analyze the geometry of a radiation treatment apparatus, software, and methods are provided. The system includes an apparatus having a rotating assembly and a trackable body or plurality of trackable bodies, to mark a location of a preselected portion of the rotating assembly. The system also includes a trackable reference fixture and can include a constant orientation trackable body. A determiner determines the position and/or orientation of the trackable bodies, the trackable reference fixture, and constant orientation trackable body. The determiner then determines the geometry of the treatment apparatus to analyze a coordinate system used by an operator. The determiner can have a memory and geometry analyzing software stored in the memory to analyze the treatment apparatus geometry.