A scanner (10) is used to provide images for automated diagnoses of neurodegenerative diseases, such as Alzheimers disease. The images are registered (90) to a template (78). The aligned image is analyzed (60) in relation to reference image data (76, 80) which has been registered to the template which is contained in a knowledge maintenance engine (70) for similar patterns of hypo-intensity that would indicate (in the case of an FDG tracer) reduced glucose uptake in the brain. The most appropriate reference images for the analysis of the present study are chosen by a filter (74). The present study is then given a dementia score (84) as a diagnostic feature vector that indicates to a clinician the type and severity of the ailment based on the analysis. The scanner (10) can produce PET or other metabolic and MR images for diagnosis. The MR can be used to measure blood flow rate into the brain. From the blood flow rate and the metabolic image, tracer, e.g. FDG, uptake maps can be generated for use in the automated diagnoses.