A method and apparatus for defining a volume of interest in a physiological image based upon an anatomical image. The method and system acquires an anatomical image of a volume of interest using a first imaging modality. A physiological image is acquired using a second imaging modality different from the first imaging modality. An outline of the volume of interest is defined on the anatomical image and applied to the physiological image to define the volume of interest m the physiological image. Based upon the outline, the system and method assigns binary values to voxels within the outline to more accurately define the volume of interest.