Michael,
Have you tried searching the ni site for help on this. There is a lot of info and examples on performing operations of the sort you are looking for. Try the CRIO developers guide, for one. This can be found here: http://decibel.ni.com/content/docs/DOC-8793
The chapter on FPGA programming has examples on creating counters.
You can use boolean logic and a shift register to capture rising/falling edges (low to high and high to low). Each time an edge is found, increment the counter and store it another shift register. Reset the counter as necessary.
Dan
