It can be done, but there are some limitations with your 6601 board.
You'll need to configure two counter tasks to perform hardware-clocked sampling using 'DAQmx Timing.vi'. You'll probably want to generate the sample clock yourself using another counter. Finally, at least one of your position measurement counter tasks will need to be configured for interrupt-based data transfer because your board only supports 1 channel of DMA-based data transfer.
There are some examples posted by fredni late in this thread that ought to illustrate how to configure interrupts vs. DMA on a 6601. You can expect sampling rate limitations somewhere in the kHz realm.
-Kevin P.
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