1. A method of registering two medical images of a subject comprising the steps of: comparing a first image with a first anatomical atlas and comparing a second image with a second anatomical atlas, to generate labels for anatomical features in each image, wherein the first anatomical atlas has at least two anatomical features in common with the second, and wherein each label comprises a suggested location of the anatomical feature to which it relates; identifying a plurality of labels for each image; calculating a value of a similarity function between labels of the first image and labels of the second image; and registering the two images based on the value of the similarity function.