dgg,
1. Under DAQmx, you can configure a "Pause Trigger" so that your counter only counts when an external signal is logic high (or alternately, only when logic low).
2. I'm not near my Data Acq PC now to check this out for sure. I don't think you can use a software call to reset the count value of a counter while its task is in a run state. I think you would have to set an initial value when it's not running.
3. There *is* a way to reset the count value using hardware which should work for your M-series board. It's kinda complicated though, especially if you haven't done much with counters before. If you give me a couple days, I can probably whip up an example. The basic outline is to configure for measuring position of a 2-pulse encoder in units of ticks rather than counting edges. Then you'd also enable z-indexing. Finally you'd run a wire from either a digital output bit or your other counter to act as this z-index signal. Oh yeah, you'd probably also need to wire a particular counter input to logic low.
I tend to lose threads in the general LabVIEW forum because of all the traffic. If you don't hear back from me, perhaps you could post in the Hardware-->Counter Timer forum?
-Kevin P.
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