The fixed pattern noise, which is due to the nonuniform amplifier gains and scintillator sensitivities, should be alleviated in radiography imaging and should have less influence on measuring the noise power spectrum (NPS) of the radiography detector. In order to reduce the influence, background trend removing methods, which are based on low-pass filtering, polynomial fitting, and subtracting the average image of the uniform exposure images, are traditionally employed in the literature. In terms of removing the fixed pattern noise, the subtraction method shows a good performance. However, the number of images to be averaged is practically finite and thus the noise contained in the average image contaminates the image difference and inflates the NPS curve. In this paper, an image formation model considering the nonuniform gain is constructed and two measuring methods, which are based on the subtraction and gain correction, respectively, are considered. In order to accurately measure a normalized NPS (NNPS) in the measuring methods, the number of images to be averaged is considered for NNPS compensations. For several flat-panel radiography detectors, the NNPS measurements are conducted and compared with conventional approaches, which have no compensation stages. Through experiments it is shown that the compensation can provide accurate NNPS measurements less influenced by the fixed pattern noise.