You probably can't do that with the limited-capability counter on a USB-6009, which only supports simple edge counting. (Higher-spec devices have counters that can natively perform "two edge separation measurement".)
With a 6009, you'll probably need to capture the two signals using an AI task with a sample rate well above 1 kHz and then do some software post-processing to find the time difference you're interested in.
-Kevin P
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