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I'm not sure this is the evidence that you were looking for, and it is certainly not all-encompassing, but through studies with monkeys, we can alter their perceptions of "reality." Let me explain...

If you can find, through single cell recording, a brain cell  in a monkey that responds particularly well to faces, and then to show that monkey a picture of static (i.e. there's not really anything there but random black and white pixels) while simulatneously exciting that cell, the monkey is more likely to respond that they see a face.

There are more examples of a change in brain activity causing a change in perception/thought, though I don't have a list. And, no, this doesn't "prove" that ideas don't cause neurons to fire (instead of the other way around) but I think that there is much more evidence showing that the brain is indeed the seat of the mind than there is for the mind being elsewhere and somehow effecting the brain/body. 

~Laura