[ 1 ]	Click here to navigate to the installation page. NOTE: This page is password protected. To be granted access, please email me at canislupusllc@gmail.com and summarize your project(s) for which you want to use Golden Rule.
[ 2 ]	Download the zip file. This zip contains a getting started document as well as the necessary installation files.
[ 3 ]	Unzip the downloaded zip.
[ 4 ]	Run the installer (setup.exe) and follow the prompts.
[ 5 ]	Installation requirements: Windows 7 or higher and .NET Framework 4.7.2 or higher, the latter of which will be packaged in the installer if not already installed on your computer.

Licensing

[ 1 ]	When you run the software for the first time, you will be prompted for a license.
[ 2 ]	Select “Request License” and follow the instructions.
[ 3 ]	After you have requested a license, you will receive a unique license key file via email.
[ 4 ]	Save the license key file locally and again run the software, this time selecting “Load License” when prompted.
[ 5 ]	If you are already licensed but want an upgraded license (e.g., more features included), you will go to file menu HELP à Product License and then follow the same process of requesting and loading an updated license.

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PROKNOW INTEGRATION

Set Up ProKnow Connection

[ 1 ]	Download API key from ProKnow and store in a secure location.
[ 2 ]	In Golden Rule, go to SETTINGS à Settings and Preferences.
[ 3 ]	Go to the ProKnow tab.
[ 4 ]	Enter your ProKnow domain’s unique URL.
[ 5 ]	Specify the location of your API key.
[ 6 ]	Enter a local storage directory in which your downloads and log files will be stored.
[ 7 ]	Test your connection.
[ 8 ]	Save.

The ProKnow Patient Data Selector

[ 1 ]	There are two ways to launch Golden Rule’s ProKnow patient data selector tool: (1) FILE à ProKnow Patient Data from the main file menu and (2) the PROKNOW button on the Patient Data tab, under the DICOM DATA heading.
[ 2 ]	The leftmost navigation pane will show parent data nodes that can be organized to view patients by Workspace or by Collection. To change the mode, select the VIEW file menu item and specify your preference. The default is View by Workspace.
[ 3 ]	Expand a folder on the left (i.e., expand the workspace or collection folder) to show all patients in that group in the left navigation pane.
[ 4 ]	Select a folder on the left (i.e., select a workspace or collection) to show all patients in that group in the right navigation pane.
[ 5 ]	To see all DICOM data objects and documents for any particular patient, expand the folder on the left to see a patient list, then select one of those patients.

Load ProKnow Data in Golden Rule

[ 1 ]	If a single patient dataset is selected (a patient node or a subset of the patient’s data objects) in the ProKnow patient data selector, the LOAD button will be enabled.
[ 2 ]	Once you select LOAD, the data will be downloaded and unencrypted and stored in native form (e.g., DICOM, DICOM RT, documents) in the download directory you configured with your ProKnow connection. This will happen automatically.
[ 3 ]	Once downloaded, the Golden Rule DICOM data loader will be launched with the newly downloaded data shown in the window and ready to be loaded into the user interface.

NOTE: Load ProKnow data to Golden Rule GUI is demonstrated in the prior video under the heading “The ProKnow Patient Data Selector.”

Batch Download Patient Data from ProKnow

[ 1 ]	If one or more patient datasets are selected in the ProKnow patient data selector, the DOWNLOAD button will be enabled.
[ 2 ]	Once you select DOWNLOAD, the selected data will be downloaded and unencrypted into their native form (e.g., DICOM, DICOM RT, documents).
[ 3 ]	Patient data will be organized in an intuitive nested format matching the cascading associations defined in ProKnow’s patient viewer’s “Browse” tab. Non-DICOM documents will be stored in a dedicated Documents folder.
[ 4 ]	You can then load the downloaded data into Golden Rule or any other application that can read the applicable file types.

NOTE: Batch download is demonstrated in the prior video under the heading “The ProKnow Patient Data Selector.”

View and Edit Patients’ Custom Metrics

[ 1 ]	Using the ProKnow Patient Data Selector, select one or more patients.
[ 2 ]	Select the CUSTOM METRICS menu item.
[ 3 ]	Any/all custom metrics found for the selected patients will appear in a datagrid.
[ 4 ]	If there are many items in the data grid, you can filter down using search strings for the patient (filters by ID or name) and/or the metrics (filters by metric name).
[ 5 ]	If you edit any metric values, you can select SAVE to update those values in your ProKnow domain.

Load / Download ProKnow Scorecard(s) in Golden Rule

[ 1 ]	With or without a patient dataset open in Golden Rule, you can download and convert a patient scorecard.
[ 2 ]	Go to the PLAN METRICS tab and select ProKnow icon.
[ 3 ]	Select one or more scorecard templates in the data grid.
[ 4 ]	To select multiple scorecards at once, use these techniques: (1) hold the control key down as you left-mouse click multiple scorecards or (2) to select a contiguous range of rows, left-mouse click the top row then hold the shift key down and click the last row.
[ 5 ]	Select to LOAD and then wait for the scorecard(s) to be loaded to Golden Rule. NOTE 1: If you select more than one scorecard and select LOAD, they will all be merged into a union of all metrics and objectives. NOTE 2: Golden Rule does not read ProKnow custom metrics, only computed metrics derived from plan, structure sets, dose, DVH, etc.
[ 6 ]	If you click DOWNLOAD, then the selected ProKnow scorecard(s) will be rendered as JSON files and stored to the local ProKnow storage folder that you configured in the setup.

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PROKNOW WORKSHOP PREP

Preparing for multi-user contouring or planning workshops requires several general steps.

[ 1 ]	First, you will prepare template dataset(s) that you will distribute to each workshop participant.
[ 2 ]	Next, you will copy and rename the dataset(s) so that each participant will have their own, unique copy.
[ 3 ]	Finally, you will assign each participant access to their specific copies of the workshop data.

For instance, a typical contouring study might involve first deciding on the right imageset (or if multi-modality, two or more imagesets and spatial registration objects that fuse them into the same frame of reference) and a structure set template, i.e., names and colors, of anatomical structures to be contoured.

A typical planning study would distribute copies of the necessary imageset(s) as well as a structure set of pre-defined targets and OARs, unless contouring is also part of the exercise.

Instructions can also be provided and distributed via either ProKnow Notes or Documents in the template patient record.

Make One Copy of a Patient Dataset

[ 1 ]	Open the ProKnow Patient Data Selector.
[ 2 ]	Select a single patient dataset either by selecting it under its parent workspace or collection folder (left pane), or by selecting it from a patient list (right pane) for an activated workspace or collection.
[ 3 ]	See that the COPY PATIENT menu item is enabled. NOTE: This feature is intended to copy a whole patient and its objects and documents. If you select a subset of the objects for copying, the menu items will become disabled. Likewise, if you select more than one patient, the menu items will also be disabled.
[ 4 ]	Select menu item COPY PATIENT –> Copy Selected Patient – Make One Copy
[ 5 ]	Select the destination Workspace from the pulldown list of workspaces.
[ 6 ]	The default Patient ID (MRN) and Patient Name will be those of the dataset to be copied. If you wish to change these values, edit them here. NOTE: If you are going to copy the patient to the same workspace as the source patient, you must enter a new and unique Patient ID (MRN).
[ 7 ]	Select OK to create the copy.

Batch Copy a Patient Dataset

[ 1 ]	Open the ProKnow Patient Data Selector.
[ 2 ]	Select a single patient dataset either by selecting it under its parent workspace or collection folder (left pane), or by selecting it from a patient list (right pane) for an activated workspace or collection.
[ 3 ]	See that the COPY PATIENT menu item is enabled. NOTE: This feature is intended to copy a whole patient and its objects and documents. If you select a subset of the objects for copying, the menu items will become disabled. Likewise, if you select more than one patient, the menu items will also be disabled.
[ 4 ]	For a reminder about the format of the input file to drive the batch copy, select the COPY PATIENT à Instructions for Batch Copy menu item.
[ 5 ]	To do a batch copy, select menu item COPY PATIENT –> Copy Selected Patient – Make Multiple Copies (Batch).
[ 6 ]	Select the delimited spreadsheet that governs this batch copy. NOTE: This spreadsheet can be created and edited in a spreadsheet program (e.g., Excel) but should be stored as a comma-delimited file (*.csv). The contents of this spreadsheet will be a data table with at least three columns defined in this order: (1) Workspace Name, (2) Patient ID (MRN), and (3) Patient Name. The first row should be the column labels and the following rows containing the data for the new patients to be created as copies.
[ 7 ]	Select OK to create the copies.
[ 8 ]	After the process is finished, you will receive a summary of results. The results will also be added to a log file that you can find in the ProKnow storage directory defined in your configuration.

Please click here to download some template *.csv files for batch analyses, including batch copying a patient to make multiple copies in specified workspaces and with specified Patient IDs and Names.

Assign Patient-Specific Access to Users

[ 1 ]	Open the ProKnow Patient Data Selector.
[ 2 ]	Select one or more patients.
[ 3 ]	From the main menu, select USER PERMISSIONS –> Assign User Permissions to Selected Patient(s).
[ 4 ]	Select the defined permission set (called a ‘Role’ in ProKnow) and the user to whom you wish to assign the permission set.
[ 5 ]	Select OK.
[ 6 ]	You will be shown results (success, failure, or error messages) for each attempted assignment.

Batch Assign Patient-Specific Access to Users

[ 1 ]	Open the ProKnow Patient Data Selector.
[ 2 ]	For a review summary of the format of the input file that governs the batch assignment, select USER PERMISSIONS –> Instructions for Batch Assignment of User Permissions from the main menu.
[ 3 ]	To do a batch assignment of specified permissions (‘Roles’) across multiple patients, select USER PERMISSIONS –> Batch Assign Users Permissions to Patient(s).
[ 4 ]	Select the delimited spreadsheet that governs this batch assignment. NOTE: To do a batch assignment of collaborators to existing patients, you will create a spreadsheet and save it as a comma-delimited file (*.csv). This spreadsheet must be a data table with at least four columns defined in this order: (1) Workspace Name, (2) Patient ID (MRN), (3) Patient Name, (4) Permission Set Name (called a ‘Role’ in ProKnow), and (5) Collaborator Email(s). Include a header row. Then for each subsequent row, the specified workspace, patient ID, and name (i.e., the first three columns) will define the patient that will be assigned to the collaborator(s). The fourth column will specify the ProKnow ‘Role’ that holds the specific permission set you wish to assign to the user(s). The fifth column’s data will define the user(s) who will be granted access to the patient defined in this row. A user should be defined by a unique email address. If multiple users are defined, separate the emails by a space, comma, or semicolon.
[ 5 ]	Select OK to start the batch copy.
[ 6 ]	The progress bar will show you the status during the assignments.
[ 7 ]	After the process is finished, you will receive a summary of results. The results will also be added to a log file that you can find in the ProKnow storage directory defined in your configuration.

Please click here to download some template *.csv files for batch analyses, including batch assignment of user access to individual patients.

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ANATOMICAL STRUCTURE ANALYSIS

Calculation Methods

This is a background of how structure comparison calculations are done.

Compare Two Structures (from the Same or Different Structure Sets)

This shows how to do a drill-down comparison of a single structure vs. another, either from the same structure set or two different ones.

Compare Two Structure Sets

Do you want to quickly compare one structure set to another? Here’s a simple way to do that.

Build 3D Consensus Grids from Multiple Structure Sets and Batch Compare to One Reference Structure Set

For multi-observer studies on the same base imageset, this module will be very valuable to you, allow you to perform the following analyses:

[ 1 ]	Load a collection of different structure sets (from existing DICOM files or from ProKnow) all based on the same imageset.
[ 2 ]	Generate quick population statistics such as distribution of absolute volumes or distances from another ROI.
[ 3 ]	Generate a 3D “consensus grid” that captures iso-agreement lines across the multiple observers, then save as an RT Dose file for import and analysis in other systems.
[ 4 ]	Do a batch comparison of all structure sets vs. a reference structure set.

Please click here to download some template *.csv files for batch analyses, including batch loading multiple structure sets into the special Structure Analysis module.

Batch Compare Multiple Structure Set Pairs

Watch the video below for a demonstration of how to perform a batch comparison of multiple structure set pairs using a simple spreadsheet as input.

Also, please click here to download some template *.csv files for batch analyses, including batch analysis of multiple structure set pairs.

Limit Comparison to Specific Axial Slice(s) or Slice Range(s)

Golden Rule structure analysis allows you to compare structures on a limited number of axial slices or slice ranges, if desired. The usefulness of this might be if you are doing a contouring workshop or assessment but do not want the participants to contour the whole structure.

The way you do this is to identify the axial slice locations or ranges. You can do this either through the user interface when using the special structure analysis module or by configuring the input spreadsheet when doing batch analyses of multiple structure set pairs.

From the User Interface

You can do this when prompted in the GUI for analysis parameters using the field that allows you to enter axial slice ranges. In that field, the syntax is “###.# to ###.#” for a range of slice locations and just “###.#” for a single slice. Combinations can be delimited with a semicolon (“;”). See below example:

-320.0 to -250.0		This would analyze only slices with locations between -320 and -250 mm, inclusive.
110.0		This would analyze only slice location 110 mm.
-50.0 to 50.0; 100.0 to 150.0; 200.0		This would analyze slice locations between -50 and 50 mm, between 100 and 150 mm, and exactly at 200 mm.

Batch Analysis of Structure Set Pairs

In the columns following the specifications of the structure set pairs, you can specify per-structure limited slice ranges for analysis. Leaving these columns blank means the whole structure volumes will be analyzed.

If you wish to limit analysis for particular structures to specified axial slice positions, then add in a new cell (column) of text for each applicable structure. The syntax is “YRANGE-STRUCTURENAME: ###.# to ###.#; etc.” where the details following the colon are the same as described above for the manual entry in the GUI.

For example, extra columns might look like this:

YRANGE-BRAINSTEM: -100.0 to 0.0

YRANGE-CHIASM: 112.5

YRANGE-OPTIC_NERVE_L: 120.o to 130.0

Please click here to download some template *.csv files for batch analyses, including batch analysis of multiple structure set pairs but analyzing over limited axial slice locations for user-defined structures.

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