In our most recent version of HDIP, 1.3.0, there is a new tool to perform internal standardization. This tool streamlines the process of performing internal standardization, by providing a wizard which allows the user to step-by-step go over the process. The tool is part of our efforts to provide an easier workflow for processing a large amount of bulk analysis scans with HDIP.
Here's a screenshot of how one of the pages of the tool will look like.
More information can be found in the manual of version 1.3+.