Hello Tristan,
If your stepper motor is TTL compatible you should be able to control it with one of the two counters on the board. Keep in mind that the stepper will ask for a certain amount of power so before attaching it track down how much power it consumes and take a look at the
Specifications of the PCI-6111 to be sure that the counters on the board can deliver that amount. If the stepper takes to much power you have to use some kind of power drive which can be controlled with digital (TTL) signals or Analog signals between -10V and +10V.
Hope this helps.
Best regards
RikP
Application Engineering
National Instruments
Rik Prins, CLA, CLED
Software Development Engineer