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Triggering analogue measurement from counter signal

I am building a small rig to test the noise levels of infra red detectors and am driving the source with a counter from my USB 6211, I need to be able to measure the peak and trough value of the measured signal on each cycle. I  need to be able to trigger a measurement at the same point of each cycle and thought I could use a second counter synced to the first to trigger when to sample/measure the analogue measured signal. Firstly how do I synchronize the signals and then use the second to trigger continuous measurements?  

I have attached a picture of the wave I need to sample/measure.

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