Functional single photon emission computed tomography (SPECT) images of brain activation are based on a comparison of base line and activation images. The correctness of the functional images depends, among other factors, on the accurate spatial registration (alignment) of the base line and activation image data. The relationship between the registration errors and the errors of the resulting functional images is studied. It is shown that misregistration errors as small as a shift by 1/8 pixel or rotation by 1 degree result in 5%-10% errors of the pixel values of functional SPECT images of regional blood flow (the ratio and the relative difference images).