Hello Lancer,
Assuming that you are going to acquire analog data from one of your channels, the solution for this application is to generate a re-triggerable pulse train using the counters on the E Series DAQ board, and use the pulse train as the scan clock for the analog input operation. In order to setup the counters to generate a finite pulse train, one counter is configured to generate a re-triggerable pulse, and the second is configured for continuous pulse generation. The second counter is then gated by the output of the first one and supplies the scan clock.
Each time you trigger your signal, you can place its data in an array and do some simple math to calculate its average. You can do the same thing each time you use your trigger.
Hope this helps!
LA