A technique for producing a three-dimensional segmented image of blood vessels and automatically labeling the blood vessels. A scanned image of the head is obtained and an algorithm is used to segment the blood vessel image data from the image data of other tissues in the image. An algorithm is used to partition the blood vessel image data into sub-volumes that are then used to designate the root ends and the endpoints of major arteries. An algorithm is used to identify a seed-point voxel in one of the blood vessels within one of the sub-volume of the partition. Other voxels are then coded based on their geodesic distance from the seed-point voxel. An algorithm is used to identify endpoints of the arteries. This algorithm may also be used in the other sub-volumes to locate the starting points and endpoints of other blood vessels. One sub-volume is further sub-divided into left and right, anterior, medial, and posterior zones. Based on their location in one of these zones, the voxels corresponding to the endpoints of the blood vessels are labeled. Starting from these endpoints, the artery segments are tracked back to their starting points using an algorithm that simultaneously labels all of the blood vessel voxels along the path with a corresponding anatomical label identifying the blood vessel to which it belongs.