A method for optimizing images, the method comprising, receiving a designation of a first feature of interest, receiving a designation of a second feature of interest, receiving a target image, receiving an atlas image including labels of first and second features of interest of the target image and a first optimization parameter associated with the first feature of interest and a second optimization parameter associated with the second feature of interest, mapping the atlas image onto the target image resulting in a global mapped image, defining an area of the first feature of interest and an area of the second feature of interest, mapping the reference image onto the area of the first feature of interest on the global mapped image using the first optimization parameter, and mapping the reference image onto the area of the second feature of interest on the global mapped image using the second optimization parameter.