Getting Nios to talk to on chip logic

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Total newbie question but what is the best way to get Nios to talk to custom on chip logic ? I'm setting up a special counter in logic that I'd like to have Nios control and read. Do I need to set up a custom connection in Qsys and use the Avalon interface or is there a more direct method ?

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Thanks Bob & DSL for the great advice. As a newcomer I'm finding the capabilities of these FPGAs incredible but sifting through the documentation and getting up to speed is kinda like drinking from a fire hose. I'll try your suggestions over the next few days. (Altera: a good tutorial here would go a long way)