Simple methods are described using correlation analysis to rotate functional brain images to a standard vertical orientation, identify the antero-posterior centerline, and align multiple images from the same brain level. Image rotation and centering are performed by determining the angle of rotation and centerline coordinate that result in maximal left-right correlation. Testing of this method on sets of multiple images acquired simultaneously through different brain levels suggests that the optimal rotation can be determined within 1 degree and the centerline within 0.3 mm. Spatial alignment of two or more images from the same brain level of a single subject is accomplished by finding the translation and rotation that yield the highest correlation between the images. Testing of the alignment method on sets of simultaneously acquired images at multiple brain levels suggests that the optimal translation can be determined within 0.45-0.69 mm and the optimal rotation within 0.8 degrees. These methods are completely objective and can easily be automated.