A method and a system for registering multi-modal brain images includes registering two or more full volumes of brain images based on a projection based reference image. The registration is based on sharing of mass in a predetermined direction such as axial, sagittal and coronal direction. After the registration of two or more brain images, a two or more partial volumes in a region of interest is registered through a modified mutual information. The modified mutual information may be a factor of an overlap rate and a weight assigned to it.
System and method for registration of brain images