A system for registration feedback includes a segmentation module configured to segment a relevant three-dimensional structure in a first image to be registered and to segment a same relevant structure in a second image to be registered to provide three-dimensional segmentations of the first and second images. A registration module is configured to register the three-dimensional segmentations of the first and second images by applying a registration transformation to one of the three-dimensional segmentations to map one three-dimensional segmentation onto the coordinate space of the other. A display is configured to jointly display the three-dimensional segmentations of the first and second images, each of the three-dimensional segmentations having a different visual characteristic to permit identification of each of the three-dimensional segmentations in a joint display image such that registration between the three-dimensional segmentations in the joint display image provides an immediate indication of registration quality to a user.