A 4x4 affine transformation matrix describes spatial rotation, translation, scale changes and affine transformations that register referenced images to the Registration IE's homogeneous RCS. These steps are expressible in a single matrix, or as a sequence of multiple independent rotations, translations, or scaling, each expressed in a separate matrix. Normally, registrations are rigid body, involving only rotation and translation. Changes in scale or affine transformations occur in atlas registration or to correct minor mismatches.