This invention relates to MRI-based methods and systems useful for diagnosing and clinically assessing the presence, location, and size of cardiovascular disease-associated stationary targets, e.g., thrombi and atherosclerotic lesions, within the vascular system. Methods and systems of the invention allow for improved anatomical information to be obtained from MRI images and allow the clinician to develop more effective treatment plans. In one aspect, the invention provides a method of determining the presence or absence of a stationary target within the vascular system of a mammal wherein two MRI data sets representing images of the vascular system and the stationary target are acquired after administration of a targeted MRI contrast agent. In another embodiment, both a targeted MRI contrast agent and a vascular MRI contrast agent are administered to a mammal, and both a vascular MRI and a targeted MRI data set are acquired.