Another option to consider is to pair your counter/timer board with one of the 653x high-speed digital devices, such as the PCI-DIO-32HS. The digital board can be set up in "change detection" mode which will save the digital pattern only when one of the bits changes.
The digital board can further fire a pulse over RTSI with each bit change. Your counter board can then be programmed to buffer the instantaneous encoder position with each pulse.
At your change rate of ~80 Hz or less, you could also program a second counter to track cumulative time of the pulses. (With your 6601, you will need to program the "data transfer mode" to be "interrupts" using "Set DAQ Device Information.vi" because you only have one DMA channel available for buffered c
ounting operations.)
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