The NI 5401 is a Function Generator; this is significant in that it is made to make periodic waveforms such as Sine, Square, and even a user defined periodic waveform that a user can download (the 16K buffer). The board can be triggered to start generation, and with a software call, abort generation. But there is no hardware that can specify how many cycles of a waveform has been generated to control the number of cycles at the output.
Depending on the rate of the pulses you need, it may be possible to do something. A pulse train is essentially a square wave with a certain duty cycle. Set up the device for a certain frequency that matches the rate of your pulses, and program it to start with a Software trigger. The best output to use is the Sync output which w
ill give you a TTL pulse.
After the software trigger is called in your code, use the Wait VI to wait a certain amount of time that corresponds to the number of cycles/pulses for the signal that you need, and then after the wait, immediately call NI-FGEN Abort to stop the output generation.
If you are unable to control the number of pulses through software, the NI 5401 really isn't made for this operation. The NI 5411 Arbitrary Waveform Generator is the device made to do this, create the pulse waveform you need, select how many times you want it to "loop", and then generate a waveform of zero volts. The NI 5411 has the hardware to count number of loops, and trigger, etc.
I hope this helps.