Since the question has been sitting a couple days, I'll take a shot for you. Just don't consider this to be a 100% rock-solid answer.
You're proposing a concept of a start and stop trigger that are wired to physically different pins. That sort of concept is supported for analog input, but I can't think of a way to support it for pulse trains with the 2 counters your board has. The best I've come up with would require 3 counters and an external logical AND gate.
In case other hardware is available (or perhaps you can budget for a PCI-6601), here's an outline of the concept:
1. Two counters are configured for retriggerable pulse generation, with extremely long (duration of experiment) pulse widths and short delays. They will be of opposite polarity.
2. The "start trigger" causes counter A to fire a looooong high pulse after a minimal delay. (Its output will be low until the start trigger arrives.)
3. The "stop trigger" causes counter B to fire a loooong low pulse after a minimal delay. (Its output will be high until the stop trigger arrives)
4. Counter C will generate the desired pulse train with "pause triggering" set up to allow pulses when the logical AND of (output A) & (output B) is high,
suppressing them when the output is low.
Notes:A. If the "stop trigger" arrives before the "start trigger," you're hosed.
B. There's a tradeoff between the duration of the two looong pulses and the timing resolution required by them. The durations can be about 53, 214, or 42900 sec for resolutions of 12.5, 50, and 10000 nanosec respectively.
C. If you use a 6601, you can generate an intermediate frequency between 100 kHz and 20 MHz as the timebase to give you more options for the tradeoff listed above.
Alternative with more external circuitry: If you can do a little more logic circuitry, you can probably replace the functions of counters A & B above with a circuit, and require only one counter on the board you've already purchased.
Replace counters A & B with two one-shots of looong duration, and invert one of them. AND them together, and feed the result to counter C's pause trigger input.
-Kevin P.
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