Embodiments include a system for determining cardiovascular information for a patient which may include at least one computer system configured to receive patient-specific data regarding a geometry of an anatomical structure of a patient; create a model representing at least a portion of the anatomical structure; create a physics-based model relating to a blood flow characteristic within the anatomical structure; determine a first blood flow rate at at least one point of interest in the model; modify the model; determine a second blood flow rate at a point in the modified model corresponding to the at least one point of interest in the model; and determine a fractional flow reserve value as a ratio of the second blood flow rate to the first blood flow rate.