What are you planning on measuring with?
I've done it two ways.
Use a DC output LVDT, wire the output to one of the ADC inputs on the Galil card. Scan the part and record the measurements. ( @AN[n] function )
If one axis is perpendicular to the plane to be checked wire a touch probe or touch switch to one of the latch inputs (inputs 1 and 2) and latch the encoder position while probing with the axis. (commands AL.. and RL.. )
Bob
PS: The 18x2 card (a two axis would be a 1822 card) is the econo series and doesn't support auxiliary encoders.
Both above methods will work on this card though.