A method and system for multi-atlas segmentation brain structures and vessel territories in a brain computed tomography (CT) image is disclosed. Each of a plurality of atlas images is individually registered to an input brain CT image, resulting in a plurality of warped atlas images. A region of interest is defined based on labeled brain structures in each of the plurality of warped atlas images. For each atlas image, a respective sum of squared difference (SSD) value is calculated between the corresponding warped atlas image and the brain CT image within the region of interest defined for the corresponding warped atlas image. A number of the atlas images are selected based on the SSD values calculated for the atlas images. The brain structures and vessel territories are segmented in the brain CT image using only the selected atlas images.