I've used Doctrine a number of times with CI and I love it. As I understand it there are two different ways to integrate CI with it, you can either install it as a plugin or use hooks.
Reference:
http://web.archive.org/web/20160126131627/http://www.phpandstuff.com/articles/codeigniter-doctrine-from-scratch-day-1-install-and-setup
http://docs.doctrine-project.org/en/2.0.x/cookbook/integrating-with-codeigniter.html