Shortcodes In header.php

Hi, I have been trying to put a shortcode for Ninja popups into the header file of a site. I have tried all the php snippets on the Ninja support and the WordPress support. None have worked. The site is a custom template based on 2011. Quite old I realize. I can get the Ninja popup to work within a regular page but not the header. The Ninja popup support have not responded to multiple emails. Any ideas would be appreciated.