1. A brain disease diagnosis system for diagnosing a brain disease of an examined person, comprising: acquiring means for acquiring a brain image of the examined person so as to obtain an acquired image; region setting means for setting a plurality of regions in the acquired image acquired by the acquiring means; individual index value calculating means for calculating an individual index value based on a pixel value of the acquired image, in each of the plurality of regions set by the region setting means; whole index value calculating means for calculating a whole index value by weighting the individual index value of each of the plurality of regions calculated by the individual index value calculating means; diagnosis means for diagnosing the brain disease of the examined person based on the whole index value calculated by the whole index value calculating means; and output means for outputting information indicating a diagnosis outcome issued by the diagnosis means.