A method and system for retrospective image combination for free-breathing magnetic resonance (MR) images is disclose. A free-breathing cardiac MR image acquisition including a plurality of frames is received. A key frame is selected of the plurality of frames. A deformation field for each frame to register each frame with the key frame. A weight is determined for each pixel in each frame based on the deformation field for each frame under a minimum total deformation constraint. A combination image is then generated as a weighted average of the frames using the weight determined for each pixel in each frame.