In methods and an apparatus for registering two medical images of a subject, a first image is compared with a first anatomical atlas and a second image with a second anatomical atlas, to generate labels for anatomical features in each image. The first anatomical atlas has at least two anatomical features in common with the second, and each label includes a suggested location of the anatomical feature to which it relates. A number of labels are identified for each image, and a value of a similarity function between labels of the respective images is calculated. The two images are registered based on the value of the similarity function.