Abstract: Brain images are processed and analyzed with the aid of a computer for stroke diagnosis or therapeutic decision making, where multiple stroke-related images are superimposed. The superimposed images include brain images that have infarct and penumbra regions, and patient-specific brain atlas images. The infarct and penumbra regions are determined and delineated on the superimposed images. Each patient-specific brain atlas image may be formed by mapping a pre-existing brain atlas to a co-ordinate system in which the brain images are co-registered. A brain atlas may depict brain structures such as anatomy structures, blood supply territories (BST), or cerebral vasculature. The superimposed images may be used to determine any overlap between a particular brain structure and the infarct and penumbra regions.