A method is disclosed for resolving misregistration errors resulting from dual energy double-shot projection radiographic image acquisition. The method involves an iterative multi-scale, multi-resolution registration process that corrects misregistration errors progressively at scales ranging from bulk anatomical drift down to smaller scale motion such as that of fine pulmonary vasculature. The method may be incorporated as part of a dual energy image processing chain to create dual energy images with improved image quality and diagnostic performance.