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PXIe 5673 PXIe 5663E phase locked

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Hi, everyone

I'm using the PXIe 5673E to generate a pulse to DUT, and do the arctan (I/Q) to get the phase changing versus time by PXIe 5663E. However, due to bad signal to noise, I need to do lots of average. SO what I want to do is repeating the pulse and averaging the IQ data and then I can get the phase information versus time. What I have done is that I repeat the single-shot experiment by using the for loop, but the problem is that because PXIe 5673E and PXIe 5663E are not phase-locked, every single-shot data shows different phase response. 

I'm curious that is there any way to fix the phase-locked or is there any better way to do the repeating measurement. If not, then does it mean that I cannot use them to do the measurement at bad signal to noise?

Any suggestion is appreciated!

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