Tutorial: Build a Contouring Library Using ProKnow DS

Overview

ProKnow DS is an excellent tool to help an organization build a standardized contouring accuracy library that can be used to measure the accuracy and quantify the variation of anatomy contouring across a population of users and/or autosegmentation methods. The goal can be to either build a private contouring accuracy library (available to your organization only) or create public contouring datasets (available to the international user base for research and/or in conjunction with scientific meetings) that will be deployed using ProKnow's quality system for anatomy contouring.

This article will help you get started by describing the basic steps of how to build a contouring library using ProKnow DS:

Note Regarding Your ProKnow DS Domain

If you are a ProKnow DS customer, you will already have a secure, private domain.

If you are not yet a ProKnow DS customer but you are building out contours for a sanctioned workshop, meeting, or study, then you will be provided details about (and access to) a ProKnow-hosted sub-domain dedicated for your specific project.

In order to upload patient data, create and edit patient anatomical contours, you will need to (1) be defined as a user for a ProKnow DS domain and (2) have a base level of permissions necessary to upload DICOM data and create and edit patient data. If you are not yet a user of a domain, or if you find that your permissions are not sufficient, then contact your ProKnow administrator and have him/her configure your user account and set adequate permissions.

Preparation

There are some necessary preparatory steps that you will need to do only once (or at least rarely) before you begin building your contouring library.

  1. VERIFY YOUR LOG IN

    Navigate your supported browser to your assigned ProKnow DS domain and log in. See Tutorial: Logging In for the First Time and Beyond for help.

  2. CREATE (OR BE ASSIGNED) A PROKNOW DS WORKSPACE

    If you are a ProKnow DS customer with a secure, private domain that you use for other clinical and research purposes, then you may wish to create a dedicated workspace (or multiple workspaces, i.e., one per body site) that will house the images and contours that you are considering for your contouring accuracy library. This allows you to better organize data, but also to control who has permissions to access, upload, review, and edit patient data in the workspace(s).

    If you are not a ProKnow DS customer and you have been given access to a ProKnow-hosted domain, then the dedicated workspace will already be created for you.

  3. PRIORITIZE BODY SITES

    It is a good idea to organize your contouring library into body sites and/or contouring protocols. Think about which body sites you eventually wish to cover, then prioritize them to determine the order in which you will build them.

  4. PLAN IMPORTANT STRUCTURES PER BODY SITE

    Develop a list of important anatomical structures per body site or protocol category. Think about high-priority organs-at-risk (OARs) and target volumes for which contouring accuracy is critical.

    You should also formulate a list of standard contour names and syntax, as contouring accuracy studies are a great way to enforce standard naming conventions.

  5. ASSIGN EXPERTS

    To create (and/or, review) the contours you will be putting forth as standards, you will need to assign appropriate experts from within your group. Without the time and effort of these experts, you may find it difficult to develop your contouring accuracy library.

  6. COLLECT PATIENT IMAGES

    Start collecting representative and appropriate image sets to cover the body sites and structures you have prioritized.

    Image sets can be computed tomography (CT) or magnetic resonance (MR) as long as it is an axial series. Oblique planes (e.g., MR) can also be used, but they will be resampled to form axial planes, which in some cases may degrade image quality.

    After you collect each image set (and, potentially, RT structure set per image set), it is a good idea to anonymize all DICOM files to remove sensitive information and to assign generic and descriptive patient names.

  7. (OPTIONAL) COLLECT SUPPLEMENTARY EDUCATIONAL MATERIALS & INSTRUCTIONS

    The contouring accuracy library allows for educational materials (documents, movies, etc.) to be accessed for each structure. Some materials can be accessed by the user before (and while) they contour. Other materials can be set to be available only after the user has made one attempt at contouring the full structure.

    These supplementary materials are not required, but they certainly enhance the efficiency and impact of contouring exercises.

Create Standard (Expert) Contours

The following steps describe how to start building standard contours.

Important Note

These instructions apply to setting up a single set of patient images and corresponding structures. You can repeat the applicable steps for each additional patient or patient image set.

  1. LOG IN

    Navigate your supported browser to your assigned ProKnow DS domain and log in. See Tutorial: Logging In for the First Time and Beyond for help.

  2. CREATE NEW PATIENT

    (Note: If the patient is already created, you can simply select it and proceed with remaining steps.)

    On the left dashboard, click Patients.

    From the workspace drop-down list in the upper left, select the applicable workspace where you store (or aim to store) the patient data standards used for your contouring library.

    Create a new patient dataset using the labels (ID, name, etc.) that you wish to use for display and organization in ProKnow DS.

    Important Anonymization Note

    The source DICOM files will retain their original DICOM tag data, so be sure to anonymize data before uploading (next step) if you will be allowing download of image data to the intended contouring library users.

    If you will not allow your contouring library users to download patient data (i.e., if you will allow contouring via online ProKnow tools only), then the DICOM data will never be exposed so the ID, name, etc. are less important, but it is good practice to always anonymize patient data that will be used in your contouring library.

  3. UPLOAD PATIENT IMAGES

    After creating the patient, you can upload the axial patient images directly to this patient. The images must be an axial series of DICOM CT or MR images. Oblique MR planes must be resampled to axial planes to use in contouring.

    Reminder

    You will control if these patient images will ultimately be available via download to those with access to your contouring library, or if contouring will be online via ProKnow only. Regardless, it's is good practice to fully anonymize the DICOM files to remove any sensitive information. Edit, but do not remove, required tags (e.g., patient ID and name). Non-essential tags (referring physician, institution, etc.) you can clear.

  4. UPLOAD OR CREATE STANDARD (EXPERT) CONTOURS

    If you have already contoured all necessary targets and critical structures using another software system (e.g., your TPS), then you can upload a DICOM RT structure set directly to this patient.

    As an alternative, you can create a new structure set for this patient and use the integrated contouring tools to define all targets and critical structures.

  5. REVIEW AND FINALIZE ANATOMY STRUCTURES

    Remember that your experts are building standard anatomical contours against which all your contouring library users will be compared and accuracy measured, so be sure to review all the anatomical structures for anatomical accuracy, as well as naming standard.

    For more information on how to edit labels, colors, and/or contours and how to save the contours as a new version of the structure set, visit the Editing Structures article.

  6. WRITE BRIEF INSTRUCTIONS, PER STRUCTURE

    Use the patient notes tool to specify concise instructions for each structure that requires special guidance or detail. Write the instructions exactly as you would like them to appear to the users. These instructions will appear for the user prior to their contouring (in addition to any supplementary education materials, as described below).

  7. (OPTIONAL) UPLOAD SUPPLEMENTARY EDUCATIONAL MATERIALS (BODY SITE- or STRUCTURE-SPECIFIC)

    If you wish to give access to specific instructions or educational materials for the body site (or for each structure), you can upload these non-DICOM documents or media to ProKnow DS to be stored with the patient data.

    PDF or other highly-compatible formats such as DOC, PPT, etc. are the ideal document types. Another mode would be movies (MP4), which can be embedded in your ProKnow contouring accuracy library. Movies are a great way to do "contouring walkthroughs" that explain how the experts came up with their contours.

Publish the Structures in the Contouring Accuracy Library

Contact ProKnow by emailing support@proknowsystems.com when you are ready to port the image sets and anatomical structures into the applicable ProKnow online contouring accuracy library.

You will need to provide the anonymized patient IDs and names for the applicable data sets, as well as the structure names you wish to add to the library.

If you are using a ProKnow-hosted sub-domain, ProKnow staff will have access to the data they need. If you are a ProKnow DS customer using your private domain, then you will need to give temporary access (to the dedicated workspace only) to a ProKnow staff member so that he/she can retrieve the data and port it to your contouring accuracy library.

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