Greetings,
A PFI line is a Programmable Function Input. Counter gates have default PFI lines. Most E-Series DAQ devices use PFI9 for CTR0 and PFI4 for CTR1, but you should verify the correct lines with the manual for your particular device. You can use any PFI line for the gate of a counter. If you would like to use a line that is not the default, you will need to use "Counter Set Attribute.vi" with the "attribute ID" input set to "gate selection", the "attribute value type" input set to "PFI n", and the "attribute value number" input set to your desired PFI line number.
Good luck with your application.
Spencer S.