A PFI is a programmable function input for an E-series board. They
are initially set to input, and have a specific function they are
wired for unless otherwise routed via the Route.VI.
If you want to use a PFI for a gate (like a counter), look up the pin
definitions of your PFI pins for your particular board. There is
probably a PFI pin designated for the gate, and all you have to do is
wire it up.
Mark