A method registers a deformable image to a fixed image by first acquiring the deformable image and the fixed image. Multi-resolution multi-level image pyramids are generated for the deformable and fixed images. Levels of the multi-resolution multi-level image pyramids are processed in a coarse to fine order, and for each deformable and fixed image at each level partitioning the deformable and fixed image into overlapping blocks, and labeling each block with a label by solving, iteratively and in parallel, until a termination condition is reached, a binary maximum flow problem, within α-expansion, for each block and performing boundary fusion for the blocks, and then registering each block according to the labels to form the fixed image.