I just saw your other message and thought you forgot in asking the question...hehehe.
Coming to your question, what you want then is either Simple Event Counting or Gated Event Counting. The difference between them is that in Simple Event Counting the counter counts the number of pulses that occur on the SOURCE signal after the counter has been armed; on Gated Event Counting the counting is halted and resumed via a GATE signal. In both cases, the counter can be armed via a software command or upon receiving a start trigger. The start trigger can be an internal signal (any of the timebases available: 100 kHz, 20 MHz, and 80 MHz) or an external signal, any of these signals will make your control more accurate.