A system for evaluating blood flow in a vessel of a patient includes a catheter containing a first pressure sensor and a second pressure sensor and configured to simultaneously measure pressure data within a vessel on either side of a stenosis. Pressure data generated by the catheter includes a first series of pressure measurements from the first pressure sensor a second series of pressure measurements from the second pressure sensor. The system further includes an FFR calculation module executable on one or more processors and configured to calculate a stability index for each of two or more portions of the pressure data, wherein each stability index indicates at least one of heart rate stability and catheter stability for the respective portion of the pressure data. An optimal time window is identified based on the stability indexes for calculation of fractional flow reserve (FFR) based on the pressure data. An FFR value is then calculated based on the pressure data in the optimal time window.
