If you're using a recent version, you have to go to Emulation -> Slot 1 and then pick "Retail with NAND Flash" for the game to boot, but be advised in-game saves don't work with it(by don't work, I mean you can save your progress, but the next time you boot the game, it'll be a clean slate; it never saves to the hard drive). You'll have to use save states to keep any sort of progress, unfortunately, which means you won't be able to carry progress over to newer versions of the emulator.