Signal Conditioning

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frequency response measurement sampling time

Hi,

I want to determine a frequency response function. My system is a tube. I have an accelerometer attached to it, measuring the vibrations. This accelerometer time signal is going to be the system response. I also have an impact hammer, whose  time signal is the  stimulus. I am using the frequency response functio (mag-phase).vi and LabVIEW 6.1 and for data acquisition a software trigger.
My problem: i don´t know how long i should acquire data.
When i look at the spectra (PSD) of the two time signals i see, that the spectrum varies a lot with the acquisition time. And also, for the stimulus, the hammer impcat, the signal flattens out much faster than for the accelerometer. Do the two signals have to be of same lenght (time intervall) ?
Does anybody have any idea how to do a correct measurement of a frequency response function ?

Thanks
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