A perfusion analysis system includes a perfusion modeller and a user interface. The perfusion modeller generates a patient specific perfusion model based on medical imaging perfusion data for the patient, a general perfusion model, and a quantification of one or more identified pathologies of the patient that affect perfusion in the patient. The user interface accepts an input indicative of a modification to the quantification of the one or more identified pathologies. In response, the perfusion modeller updates the patient specific perfusion model based on the medical imaging perfusion data for the patient, the general perfusion model, and the quantification of the one or more identified pathologies of the patient, including the modification thereto.