Hi Ran,
There are a few examples of either counting digital pulses on your quadrature encoder, or measuring the revolution frequency (frequency measurement). Depending on your application you will need to connect your device to your E series card to either the gate (frequency, period and time measurements) or the source (simple event counting) of the counters. These are decribed clearly in the E Series Help File. http://digital.ni.com/manuals.nsf/websearch/0E0DFDBB7706687A86256F6300560584?OpenDocument&node=10968_US
In addition, we have a few examples and tutorials on this website. You can simply make quick searches with the few key words i have just mentionned.
You also have to make sure that the signal coming out of your encoder is in the appropriate format (5V digital). In some cases, you would need a voltage divider.
As for the second question, I would need some clarification. You can definately process the information you have acquired in any way you want. You can search for our VIs by selecting the search button in the function pallette. Most data processing VIs are for analog signals.
Best regards,
Nathan Yang
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Applications Engineer
National Instruments