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 information regarding a physiological condition of the patient. The at least one computer system may be further configured to receive input from a user regarding a plan of treatment, modify the physiological condition of the patient based on the received input, and determine a second fractional flow reserve within the anatomical structure of the patient based on the modified physiological condition of the patient.
