VASARI Reader Instructions

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 TCIA
2. Click "Search Shared List" from the left side bar
3. Enter "Round 3" without the quotes for the Shared List Name and hit Submit
4. Click the "TCGA Glioma Group Round 3 - Baseline + scans <1 month" link that appears in the search results (this loads only the new cases to your Data Basket)
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. When completed all progress bars will indicate 100% and a message will appear in the window notifying you the download is finished.

Installing the required software

1. If you have a different version of ClearCanvas, uninstall it from your computer and reboot before beginning the rest of the steps
2. Download ClearCanvas at: http://gforge.nci.nih.gov/frs/download.php/9244/AIM_TCGA_CC_3.0.2.rar
   1. Extract the .RAR file (If you don't have software for unzipping .RAR files you can use install 7zip for free)
   2. Once extracted, run the installation, hit "next" several times until completion
   3. Restart your computer
3. Download the AIM template at: VASARI Template-6-17.xml (Right click and choose "Save as" or else it may just display the XML file in your browser)
4. 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)
   3. Verify your AIM settings
      1. From the menus at the top, choose Tools > Options
      2. Verify that all 4 check boxes are checked (Send New Annotations to caGrid, Store New Annotations Locally, Require User Information, and Require Graphic Markup in Annotation)
   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://ivi02.cci.emory.edu:9090/wsrf/services/cagrid/AIM3DataService
   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)
5. Test out the Google Form
   1. The table is here: https://wiki.cancerimagingarchive.net/display/Public/VASARI+Reading+assignments
   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