Disclosed are systems for and methods of creating a synthetic image by registering a reference or atlas image to a clinical image using both rigid and deformable image registration algorithms. In some embodiments, a synthetic computed tomography (CT) image may be created by registering an atlas CT image to a clinical image such as an MR scan. Rigid registration in some embodiments may be followed by a smoothing B-spline transform algorithm with a mutual information similarity metric and an optimizer； followed then by an image signal intensity algorithm with displacement vectors at each voxel and diffeomorphic transformations.
