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  • How To Guide - Reading Breast Cases with Clearcanvas

Before beginning this guide you must have installed Clearcanvas with AIM. Instructions for readers who are being actively assigned cases can be found on the TCGA Research on the Cloud wiki page.  Instructions for those who wish to replicate this project independently can be found on Breast Reader Training page.

Opening the images and AIM Template

1. Double click ClearCanvas from the desktop to begin scoring cases. You will be presented with a login screen. We have already filled this in for you so that all you need to do is click "Login".

2. The list of assigned cases will appear in the "My Studies" list. Double click one from the list to open it for review.

3. The case will be loaded with 4 series visible. You can adjust the panel layout to show different views or numbers of image series using the "Layout Manager" icon.

4. Use the Annotation menu at the top and choose "Create Annotation" to open the AIM Plugin.

5. The AIM Template menu will pop up on the right side of the screen.

Completing the templates

6. The Mass template is the first AIM Template, and is used for evaluating the features of any masses you find. Fill out the form (all answers must be filled in). Then right click and select the Ruler tool. Use the Ruler tool to measure the tumor and then click "Create Annotation". 

Note: You can confirm that your markup was sent successfully with your form by the appearance of some additional labels on the screen.

Before submission

After submission

7. After creating the Mass annotations and markup, use the drop down box at the top again to select the Nonmass template. Repeat the same process, answering the questions and then measuring the Nonmass. Then click "Create Annotation" to submit the Nonmass scores. Note: If there are not any Nonmasses for the subject simply skip this step.

8. Use the drop box again to select the CRF form. Again, fill out the answers to all of the question and click "Create Annotation". Note: There is no markup/measurement required for this form.

Validating your submissions (This section only applicable to readers being assigned cases on Breast Image Feature Scoring Project)

9. Open Firefox by double clicking the icon on your desktop.

10. Firefox will prompt you for a user name and password. Use your TCIA credentials. If you need login or account help contact TCIA Support.

11. Allow the browser to save your user name and password so you don't have to enter this again in the future.

12. Once this is done you will see 2 tabs open in Firefox. The active tab will likely be the 2nd one which required your TCIA credentials. This tab shows you the scores you have already submitted to the server.

Note: The TCGA-BRCA CRF is the only type of form that should be missing a Size entry. Below you can see the Mass entry (1st row) is missing a Size entry and some CRF rows (2nd row) have size entries. This means that the markup did not get properly recorded. If this occurs to you, please try filling out the form and re-drawing the markup again. Then notify Justin/John to delete the errant score.

13. The first tab in the browser shows the reader assignments. We will periodically update it to reflect which cases have been completed by each reader to keep the group informed about everyone's progress.

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