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
CAUTION! New LabVIEW adopters -- it's too late for me, but you *can* save yourself. The new subscription policy for LabVIEW puts NI's hand in your wallet for the rest of your working life. Are you sure you're *that* dedicated to LabVIEW? (Summary of my reasons in this post, part of a voluminous thread of mostly complaints starting here).
