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Help creating a software/hardware design

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Binome

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Hi,
I need help for my project:
I use a DE0-nano board from Altera to record the timeline of 4 external signals (one of them is an external clock). I can use all the hardware parts of the board and make a NIOS ii processor on the Cyclone IV FPGA to execute code (by the way, how do you prononciate NIOS?). I don't know how to do that exactly. Do you think I need a CPU? And what part do you think it should execute?
Thanks for your help.
 

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