A system and method for performing an MRI or MRS scan that is optimized for a particular target structure. A prescan is conducted during a first session in which an image that is optimized for segmentation is acquired along with an alignment scout image or a 2D or 3D navigator signal. The segmentation process is employed to locate and define the target structure. During a second session the alignment scout image or navigator signal is reacquired and the information is used to determine the position transformation needed to align images from the two sessions. The position transformation information and the segmentation information are then employed to tailor a prescribed pulse sequence to examine the target structure.