A method for improving the alignment accuracy between different medical images may be disclosed. A warped or non-warped previous image and a warped or non-warped current image may include a plurality of respective previous and current basic units, for example, pixels in a 2-dimensional image or voxels in a 3-dimensional image. To ensure accurate registration between the previous and current images, a first basic unit from the previous image may be replaced by a second basic unit from the current image if the value of the first and second basic units are identical or nearly identical. The first and second basic units may be selected from a nearly-identical region or "kernel" within the previous and current images.