Systems and methods for co-registering medical images obtained with different imaging modalities are provided. For instance, images obtained with x-ray imaging, such as x-ray computed tomography (“CT”), can be co-registered with images obtained with magnetic resonance imaging (“MRI”). The different imaging modalities generate images that have different visualization characteristics for tissues; thus, in general, co-registration is accomplished by identifying different anatomical features in the different images and then utilizing a known spatial relationship between those anatomical features to co-register the different images.