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This page describes the training steps utilized by the TCGA Renal Phenotype Research Group to develop and test their Renal 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 | vsurabhi |
KI-01-0001 | In Progress | 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 | In Progress |
KI-01-0003 | In Progress | 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 | In Progress |
KI-02-0001 | In Progress | In Progress | In Progress | In Progress | In Progress | In Progress | In Progress | In Progress | In Progress |
KI-02-0002 | In Progress | In Progress | In Progress | In Progress | In Progress | In Progress | In Progress | In Progress | In Progress |
KI-02-0003 | In Progress | In Progress | In Progress | In Progress | In Progress | In Progress | In Progress | In Progress | In Progress |
KI-02-0004 | In Progress | In Progress | In Progress | In Progress | In Progress | In Progress | In Progress | In Progress | In Progress |
Getting the data
To sign up for access please do the following:
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- Download the AIM template
- Round 1: tcga-renal-aim-05-14-12-v1.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 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.
- Set up the AIM Data Service
- 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 - once per case), mass features (MASS - once per mass identified), and enhancement features (ENHANCEMENT - once per enhancement phase per anatomic entity)
- 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 - once per case), mass features (MASS - once per mass identified), and enhancement features (ENHANCEMENT - once per enhancement phase per anatomic entity)
ClearCanvas sign-on
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Name
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User 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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Performing
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1
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Srinivasa Prasad
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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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Performing
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3
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Matthew Heller
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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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Performing
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5
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Hebert Vargas
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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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Performing
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7
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Venkata Katabathina
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vkatabathina
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Performing
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8
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Venkateswar Surabhi
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vsurabhi
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Performing
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