Ventilation-perfusion (V/Q) scan plays an important role in the assessment of lung function. Currently, Fourier Decomposition (FD), a method for simultaneous ventilation and perfusion measurement, uses fractional ventilation (FV) as a semi-quantitative measurement of lung ventilation. Just recently, a multi-echo spoiled gradient echo sequence method for regional alveolar ventilation (AV) measurement with FD was presented. This study demonstrates that both methods suffer from an artificial proton amount change during registration, which affects quantification. Correction factors are derived for both methods and used to compare AV and FV measurement. Additionally, the regional influence of T2* correction is assessed.