A computer system for determining one or more patient-specific blood flow characteristics, the system comprising: a data storage device storing instructions for evaluating a patient with vascular disease; and a processor configured to execute the instructions to perform a method including: receiving a coronary artery model associated with either the patient or with a plurality of individuals receiving a myocardium tissue model of the patient; receiving (321, 341) observed perfusion values, or observed wall motion values; registering the myocardium tissue model to image(s) from which the perfusion values were observed, or associating the observed wall motion values with the wall motion values in the myocardium tissue model; systematically deforming (325, 345) the coronary model to represent pathologies at one or more different locations and, for each of the deformations, applying computational fluid dynamics and determining a set of resulting myocardial perfusion values; selecting (325, 345) a coronary model that results in a minimum of the maximum perfusion difference, or of the maximum wall motion difference, between the observed and computed myocardium models; and estimating (327, 347) one or more blood flow characteristics of the patient from the selected coronary model. a data storage device storing instructions for evaluating a patient with vascular disease; and a processor configured to execute the instructions to perform a method including: receiving a coronary artery model associated with either the patient or with a plurality of individuals receiving a myocardium tissue model of the patient; receiving (321, 341) observed perfusion values, or observed wall motion values; registering the myocardium tissue model to image(s) from which the perfusion values were observed, or associating the observed wall motion values with the wall motion values in the myocardium tissue model; systematically deforming (325, 345) the coronary model to represent pathologies at one or more different locations and, for each of the deformations, applying computational fluid dynamics and determining a set of resulting myocardial perfusion values; selecting (325, 345) a coronary model that results in a minimum of the maximum perfusion difference, or of the maximum wall motion difference, between the observed and computed myocardium models; and estimating (327, 347) one or more blood flow characteristics of the patient from the selected coronary model. receiving a coronary artery model associated with either the patient or with a plurality of individuals receiving a myocardium tissue model of the patient; receiving (321, 341) observed perfusion values, or observed wall motion values; registering the myocardium tissue model to image(s) from which the perfusion values were observed, or associating the observed wall motion values with the wall motion values in the myocardium tissue model; systematically deforming (325, 345) the coronary model to represent pathologies at one or more different locations and, for each of the deformations, applying computational fluid dynamics and determining a set of resulting myocardial perfusion values; selecting (325, 345) a coronary model that results in a minimum of the maximum perfusion difference, or of the maximum wall motion difference, between the observed and computed myocardium models; and estimating (327, 347) one or more blood flow characteristics of the patient from the selected coronary model.