1. A system for planning treatment for a patient, the system comprising: 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; 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; 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.