Methods and systems for targeting, accessing and diagnosing diseased lung compartments are disclosed. The method comprises introducing a diagnostic catheter with an occluding member at its distal end into a lung segment via an assisted ventilation device inflating the occluding member to isolate the lung segment and performing a diagnostic procedure with the catheter while the patient is ventilated. The proximal end of the diagnostic catheter is configured to be attached to a console. The method may also comprise introducing the diagnostic catheter into the lung segment inflating the occluding member to isolate the lung segment and monitoring blood oxygen saturation. The method may further comprise introducing the diagnostic catheter into the lung segment determining tidal flow volume in the lung segment determining total lung capacity of the patient and determining a flow rank value based on the tidal flow volume of the lung segment and the total lung capacity.
