Medical images are collected in a plurality of cardiac and respiratory phases. The images are transformed into a series of respiratory compensated images with the plurality of cardiac phases, but all at a common respiration phase. The series of respiratory compensated images are transformed into one image at a selected cardiac phase and the common respiration phase. In some embodiments, a database of gated transform matrices is generated. The database may be based on specific patient information or on information generated from a pool of patients. The database may account for respiratory motion, cardiac contractile motion, other physiological motion, or combinations thereof. For a current image to be motion corrected, the transformation matrices collected in the database are used to estimate a current set of transformation matrices accounting for the motion in the current image, and a motion-compensated image is generated based on the current set of transform matrices.