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I copied the iso off Avatar the last airbender, now I go to run iso file and it starts off with the screen saying I need to cusmize it, so I do, but then it tells me I need to insert a PS or PS2 disc. I thought with an ISO you didn't have to do that.

If I have to insert my disc how do I link it up with my computers cd/dvd drive?

set the CDVD ROM drive to Linusz ISO CD 0.9.0. if you're not. if you are, then it might be a bad rip and/or disc.

which method are you using to make the ISO?
If you are not using this method, i would recommend it
http://forums.pcsx2.net/Thread-Dump-PS2-...#pid162688
it creates a byte by byte copy of the disc which has some areas of data that conventional copying could miss.