Help- Short circuit voltage noise measurement

Hi, I have designed a simple preamplifier using 2 - AD829 in cascade. I want to measure the input short circuit voltage noise density. Essentially i want to get the plot of e_n vs frequency. The bad news is i don't have a spectrum analyzer and the good news - that i have a National instrument PXI-digitizer. I have been trying to use it to aquire one snapshot in time of the output of the amplifier while the inputs are shorted. I do that and take the FFT in matlab, and plot the magnitude versus the frequency. This sh'ld give me the spectral noise - however it seems i am making a mistake as the spectrum looks very strange (with lots of high frequency components). Is there anyway to get these plots using a digitizer (regular digital oscilloscope) and matlab? If anyone has ideas please throw in.