If your emulator crashes, freezes on a black screen, or complains about missing files, the solution is simple:
Download and run C-Xbox Tool.
sudo apt-get install extract-xiso extract-xiso -r input.iso output.xiso No GUI required. The command line is identical across all platforms. If you have 50 ISO files to convert, doing them one by one is painful. Save this script as convert.bat on Windows: Convert Iso To Xiso