1. A system for registration of medical images, comprising: a processor adapted to detect one or more image areas in a first image, the image areas being insufficiently similar to corresponding image areas of a second image, wherein the first and second images include a same portion of a same vessel, the first image is acquired using a first imaging protocol and the second image is acquired using a second different imaging protocol, the one or more image areas and the corresponding image areas are areas within the vessel, and the areas of the first image that are insufficiently similar to the corresponding image areas of a second image are insufficiently similar in pixel intensity, wherein one or more image areas within the vessel in the second image and one or more corresponding image areas within the vessel in the first image have similar pixel intensity; the processor further adapted to create at least one exclusion mask to specify image pixels or voxels belonging to these insufficiently similar image areas; the processor further adapted to determine a centerline of the corresponding region of interest of the second image; the processor further adapted to determine a radius of the corresponding region of interest in the second image from the centerline; the processor further adapted to copy the determined centerline to the first image, wherein the processor creates that at least one exclusion mask in the first image as a region about the copied centerline having a radius less than the determined radius; the processor further adapted to identify a wall of the region of interest from the copied centerline in first image, wherein the wall is away from the copied centerline by a distance about equal to the determined radius; the processor further adapted to determine a thickness of the wall and extend at least a sub-portion of the at least one exclusion mask beyond the wall in response to the thickness of the wall exceeding a predetermined wall thickness; and the processor further adapted to perform a registration between image areas of the first image which are not included in the exclusion mask and corresponding image areas of the second image.