Pulmonary functions play an important role in diagnosis of pulmonary diseases. One method for functional lung MRI is Fourier Decomposition technique, which obtains ventilation and perfusion weighted images from dynamic free-breathing acquisitions. Although this method is validated against well-established methods, its robustness depends on scan parameters and temporal resolution. In this work, we have investigated the effects of common scan parameters on image quality. In vivo results are presented to demonstrate the performance differences in protocols.