Blog Templates and wpmu_create_blog

In my Network Admin, I can add a new site by navigating to Sites -> Add New.
(URL: /wp-admin/network/site-new.php)

When I use this form, the new site will successfully use the Blog Template assigned using the New Blog Template plugin: (https://premium.wpmudev.org/project/new-blog-template/).

However, if I create a new site using wpmu_create_blog (http://codex.wordpress.org/WPMU_Functions/wpmu_create_blog) the new site doesn't use the Blog Template.

So my questions is, how can I assign the Blog Template to new sites when they are created using wpmu_create_blog?

Thanks!