Embodiments include a system for planning treatment for a patient. The system may include at least one computer system configured to receive patient-specific data regarding a geometry of an anatomical structure of the patient, create a three-dimensional model representing at least a portion of the anatomical structure of the patient based on the patient-specific data, and determine a first fractional flow reserve within the anatomical structure of the patient based on the three-dimensional model and a physics-based model relating to the anatomical structure of the patient. The at least one computer system may be further configured to modify the three-dimensional model, and determine a second fractional flow reserve within the anatomical structure of the patient based on the modified three-dimensional model.
