A method for mapping a target image to a reference image includes receiving a target image; receiving a reference image that overlaps the target image; preprocessing the target image, wherein the preprocessing includes: rejecting a target image with a shadow region above a shadow threshold while keeping a target image with a shadow region below a shadow threshold; providing an uncertainty in a location of the kept target image relative to the reference image; transforming the kept target image to an atlas projection to match the reference image; partitioning the transformed kept target image into a sub-region; and determining a matching statistic for each sub-region to determine a location for each sub-region relative to the reference image.