There are two options that you can use to accomplish this application setup. The best one would be to use an external clock to control the transfer. For example, when doing pattern I/O you will want to provide an external REQ signal. You will want the external clock to fire off X number of pulses each time is receives a trigger. One of the best ways to accomplish this is to use two counters (on 6601, 6602, or an Eseries board). You can use one counter as a retriggerable pulse and the another as pulse train generation. The pulse train will be gated by the retriggerable pulse, hence evertime you send a trigger it will generate X number of pulses in the pulse train.
The other solution if the triggers are far apart (maybe ~0.5sec or more) from each other is to se
t the board for triggered operation and after the trigger has completed reconfigure the board for another triggered operation for the next chuck of data.