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This page describes the training steps utilized by the the TCGA Renal Phenotype Research Group to develop and test their Renal Image Feature Key.
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 1
Case | oakin | sprasad | rvikram | mheller | aoto | hvargas | ckarlo | vkatabathina |
KI-01-0001 | In Progress | In Progress | In Progress | In Progress | In Progress | In Progress | In Progress | In Progress |
KI-01-0002 | In Progress | In Progress | In Progress | In Progress | In Progress | In Progress | In Progress | In Progress |
KI-01-0003 | In Progress | In Progress | In Progress | In Progress | In Progress | In Progress | In Progress | In Progress |
KI-01-0004 | In Progress | In Progress | In Progress | In Progress | In Progress | In Progress | In Progress | In Progress |
Scoring Project. These instructions describe the process used to setup the Amazon cloud instances. If you are an active reader on this project please refer to the TCGA Research on the Cloud page as these steps have already been completed for you.
Getting the data
To sign up for access to TCIA please do the following:
- Go to http://cancerimagingarchive.net
- Click the "Log in to the Cancer Imaging Archive" box next to the rotating banner.
- 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:
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- For Round 1 readers should enter: TBD - coming soon
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After receiving notification that your registration is complete and obtaining permission from the TCIA Helpdesk, log in to TCIA and choose the Simple Search and scroll down to the "Collection" search criteria.
Training data can be found in the Renal Training collection, however this collection is restricted at this time. If you wish to practice prior to scoring real TCGA cases using this data please notify the TCIA Helpdesk to request permission to access the 8 subjects the groups used for training.
The real data is located in the TCGA-KIRC collection. Please contact the TCIA Helpdesk if you have trouble downloading the data.
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Installing the required software
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- Download ClearCanvas w/ AIM at: http://gforge.nci.nih.gov/frs/download.php/95419706/AIM_WS_3.0.4.3.rar
- Extract the .RAR file (If you don't have software for unzipping .RAR files you can install 7zip for free)
- Once extracted, run the "TCGAClearCanvasSetup_x86.msi", hit "next" several times until completion
- Restart your computer
- Verify the installation was successful by taking these steps:
- Go the the Start Menu and/or desktop icon and start ClearCanvas
- Enter your login information (see "ClearCanvas sign-on" table below for your user namename and user name (this feature is not currently connected to TCIA authentication but we suggest you use your TCIA user name here)
- Click on the "My computer" tab near the top left corner of the program
- Browse to where you've downloaded your DICOM data from TCIA
- Right click the folder which holds the data and choose either "Open" or "Import"
- "open" will just load the data one time
- "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
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Venkata Katabathina
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vkatabathina
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vkatabathina
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Performing
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- A summary of the features is posted at: Renal Feature Key.
- Download the AIM templateRound 1: tcga-renal-aim-0509-1413-12-v1complete.xml (. Right click and choose "Save as" or else it may just display the XML file in your browser).
- Run ClearCanvas and load a test case
- Double click the ClearCanvas icon on your desktop or open it from your Start menu
- Enter your login information (see "ClearCanvas sign-on" table below for your user name) if you haven't already
- Verify your AIM settings
- From the menus at the top, choose Tools > Options
- Verify that the following 3 2 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.
- From the menus at the top, choose Tools > caGrid Tools > AIM Data Service Settings
- Enter this URL in the box that appears: TBD - coming soon (if you want to test the process before you review the real data change 9090 to 8080 in this URL)
- Click on the "My computer" tab near the top left corner of the program
- Browse to where you've downloaded your DICOM data
- Right click the folder which holds the data and choose either "Open" or "Import"
- "open" will just load the data one time
- "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)
- Open a study
- Click the "AIM Annotation" button – note there are several buttons that mention AIM, you want the one that just says "AIM" in the icon.
- 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)
- Begin reading cases assigned to you (see table below)
- For each case use the appropriate form to score metastatic features (METASTASIS evaluate available imaging (Protocol - once per case), mass tumor related features (MASS Tumor - once per mass identifiedcase for largest tumor), and enhancement features (ENHANCEMENT Enhancement - once per enhancement phase per anatomic entityenhancing entity, total of possible 12 scores)
- For the markup associated with the forms you must also submit a measurement with the Ruler or Elliptical tool. (indicated on the form)
- You can tell the markup went through with your other answers if the measurement updates with a label including a date/time stamp, e.g. "BreastDx-01-0065_user1_2012-03-21 12:09 PM". If the measurement did not go through it will only show the length without this other information.
- To ensure the markup is submitted successfully make sure that the series where you drew the markup is active on your screen before pressing the "Create Annotation" button to send your scores.
- For the markup associated with the forms you must also submit a measurement with the Ruler or Elliptical tool. (indicated on the form)
- 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.
- 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)
- For each case use the appropriate form to score metastatic features (METASTASIS evaluate available imaging (Protocol - once per case), mass tumor related features (MASS Tumor - once per mass identifiedcase for largest tumor), and enhancement features (ENHANCEMENT Enhancement - once per enhancement phase per anatomic entityenhancing entity, total of possible 12 scores)
ClearCanvas sign-on
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Name
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User name
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Login name
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Role In Clinical Trial
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Number within role in clinical trial
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Oguz Akin
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oakin
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oakin
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Performing
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1
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Srinivasa Prasad
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sprasad
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sprasad
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Performing
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2
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Raghu Vikram
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rvikram
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rvikram
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Performing
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3
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Matthew Heller
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mheller
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mheller
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Performing
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4
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Aytekin Oto
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aoto
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aoto
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Performing
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5
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Hebert Vargas
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hvargas
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hvargas
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Performing
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6
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Christoph Karlo
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ckarlo
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ckarlo
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Performing
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7
- Consult the How To Guide - Reading Renal Cases with Clearcanvas for more information on using the AIM templates to evaluate the cases