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If you’ve got a stat-tracking script (for example, from Google Analytics), Thesis makes it easy for you to add the necessary code to your site’s pages, with its Stats Software/Scripts section, available from the Site Options subpanel:
Paste your code in the Tracking scripts field
Note that anything you add here will be served after the HTML (i.e., just before the closing <body> tag) on every page of your site. This is the preferred position because it prevents the script(s) from interrupting the page load.
If you only wish to add your tracking script code to certain pages, you would use a custom function, one or more WordPress conditional tags, and thesis_hook_after_html (via your custom_functions.php file).