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Summary

This page describes the training steps utilized by the TCGA Breast Phenotype Research Group to develop and test their Imaging Feature Scoring.

Training Progress

This is the latest progress on training cases. See instructions for obtaining the data and setting up the software below.

Completed - Reader has finished reading the case and submitted their AIM characterizations to the AIM data service
In Progress - Reader has been instructed to review this case, but has not yet completed it
Unassigned - Reader has not yet been asked to review this case

Round 2

Case

Anatomic Site Location Descriptor

emorris

mzuley

gwhitman

ebonaccio

vking

bdogan

TCGA-AR-A1AN

Right Upper Outer Quadrant

In Progress

In Progress

In Progress

In Progress

Completed

Missing CRF

TCGA-AR-A1AQ

Right Upper Inner Quadrant,
Right Upper Outer Quadrant

In Progress

In Progress

In Progress

In Progress

Completed

Missing CRF

TCGA-AR-A1AX

Left Upper Inner Quadrant,
Left Upper Outer Quadrant

In Progress

Missing Mass

In Progress

In Progress

Completed

Missing CRF

Round 1

Case

emorris

mzuley

gwhitman

ebonaccio

BreastDX-01-0065

Completed

Completed

Completed

Completed

BreastDX-01-0073

Completed

Completed

Completed

Completed

BreastDX-01-0086

Completed

Completed

Completed

In Progress

Getting the data

To sign up for access please do the following:

  1. Go to http://cancerimagingarchive.net
  2. Click the "Log in to the Cancer Imaging Archive" box next to the rotating banner.
  3. Click "Register now" underneath the login section (this is not the same account as the old NBIA site). During normal business hours you should receive confirmation that your account is ready within an hour.

Downloading the data:

  1. Log in to the site
  2. Click "Search Shared List" from the left side bar
  3. Enter the appropriate Shared List name and hit Submit
    1. For Round 1 readers should enter: TCGA Breast Reader Training (completed)
    2. For Round 2 readers should enter: TCGA Breast Reader Training Round 2
  4. Click the corresponding link that appears in the search results
  5. Click "Download Manager" button
  6. Once the Download Manager has opened just select the directory where you'd like to save your images and start the download

Installing the required software

Note: If you have an old version of ClearCanvas, uninstall it from your computer and reboot before beginning these steps

  1. Download ClearCanvas w/ AIM at: https://gforge.nci.nih.gov/frs/download.php/9329/AIM_TCGA_WS_3.0.3.rar
  2. Extract the .RAR file (If you don't have software for unzipping .RAR files you can install 7zip for free)
  3. Once extracted, run the "TCGAClearCanvasSetup_x86.msi", hit "next" several times until completion
  4. Restart your computer
  5. Verify the installation was successful by taking these steps:
    1. Go the the Start Menu and/or desktop icon and start ClearCanvas
    2. Enter your login information (see "ClearCanvas sign-on" table below for your user name)
    3. Click on the "My computer" tab near the top left corner of the program
    4. Browse to where you've downloaded your DICOM data from TCIA
    5. Right click the folder which holds the data and choose either "Open" or "Import"
      1. "open" will just load the data one time
      2. "import" will store the study under the "DICOM" tab so that you don't have to repeat these steps again later (they will now show up in the "My studies" window under the DICOM tab)

Testing the AIM Template

  1. Download the AIM template (Right click and choose "Save as" or else it may just display the XML file in your browser)
    1. Round 1: BRCA-12-21-11.xml (completed)
    2. Round 2: BRCA 04-18-12.xml
  2. Run ClearCanvas and load a test case
    1. Double click the ClearCanvas icon on your desktop or open it from your Start menu
    2. Enter your login information (see "ClearCanvas sign-on" table below for your user name) if you haven't already
    3. Verify your AIM settings
      1. From the menus at the top, choose Tools > Options
      2. Verify that the following 3 check boxes are checked (Send New Annotations to caGrid, Store New Annotations Locally, Require User Information) and that Require Graphic Markup in Annotation is not checked.
    4. Set up the AIM Data Service
      1. From the menus at the top, choose Tools > caGrid Tools > AIM Data Service Settings
      2. Enter this URL in the box that appears: http://aime01.cci.emory.edu:9090/wsrf/services/cagrid/AIM3DataService (if you want to test the process before you review the real data change 9090 to 8080 in this URL)
    5. Click on the "My computer" tab near the top left corner of the program
    6. Browse to where you've downloaded your DICOM data
    7. Right click the folder which holds the data and choose either "Open" or "Import"
      1. "open" will just load the data one time
      2. "import" will store the study under the "DICOM" tab so that you don't have to repeat these steps again later (they will now show up in the "My studies" window under the DICOM tab)
    8. Open a study
    9. Click the "AIM Annotation" button – note there are several buttons that mention AIM, you want the one that just says "AIM" in the icon.
    10. Now click the AIM Template button in the new side bar that appeared, and point it to the XML file you downloaded in step 3 (you only have to do this once, and it will automatically use this template on all cases from now on unless you choose a new one)
  3. Begin reading cases assigned to you (see table below)
    1. For each case use the appropriate form to score generic features (CRF - once per case), mass features (MASS - once per mass identified), and nonmass features (NONMASS - once per nonmass identified)
    2. Please notify John/Justin when you are done scoring your first case so we can verify your results were properly received before you put time into additional cases.
    3. If you plan to be a reader and have not had any cases assigned to you please contact Justin (kirbyju @ mail dot nih dot gov)

ClearCanvas sign-on

Name

User name

Login name

Role In Clinical Trial

Number within role in clinical trial

Elizabeth Morris

emorris

emorris

Performing

1

Margarita Zuley

mzuley

mzuley

Performing

2

Gary Whitman

gwhitman

gwhitman

Performing

3

Ermelinda Bonaccio

ebonaccio

ebonaccio

Performing

4

Valencia King

vking

vking

Performing

5

Basak Dogan

bdogan

bdogan

Performing

6

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