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Launching the Query Tool

You will be unable to launch the Query without CDAS approval; please click to the link below for obtaining approved credentials:

https://biometry.nci.nih.gov/cdas/nlst/


PART I: Log in, search and filter, upload a list.

To download the images, you’ll need to have a text (.txt) file containing a column of PID (participant ID) values for your selected participants. 

You'll also need to have java installed. You can check your version and/or download for free at https://java.com

Let’s call the file “pids.txt” for the remainder of this email.  Your file should contain only a list of PIDs (i.e. 6-digit numbers), nothing else.

It may be wise for you to break up the download into several chunks of about 1000 rows each, in case the download is interrupted for some reason. 


  1. Launch the Query Tool. To do so…
    1. If you normally use IMS login service credentials to log into CDAS, Log in via the IMS Login Service.

      1. Navigate to https://cdas.cancer.gov/login/?next=/projects/  and, If you normally use IMS login service credentials to log into CDAS, Log in via the IMS Login Service.
      2. You should then see the "Welcome" message and the blue button "Browse NLST Images" should appear under that message. If you are using Linux or Windows, this should still work for you. Click that blue button.
      3. Your authentication should carry directly into the NLST Web Query Tool interface. If you are prompted to log in again here, please review the instructions on this page for what to do next.
          
    2. If you normally use TCIA login service credentials to work with NLST data,

      1. if you have a TCIA username & password that you have used for other datasets within TCIA, you can try to use that credential with NLST Query Tool after NLST authorization is granted.
      2. start with the National Lung Screening Trial wiki page.
      3. Scroll down and then click the orange "Search" button to navigate to https://queries.cancerimagingarchive.net/NLSTQueryTool/faces/main.xhtml and type in your TCIA username and password.
      4. NOTE: You will be prompted for your TCIA login and password again.
  2. Log into CDAS when prompted.
  3. The Query Tool should now appear on a separate tab in your web browser.
  4. Click on the "File" button and then click “Read PID List”.
  5.  Then click "Choose" to open a directory popup window.Follow the instructions to upload the file pids.txt (NOTE: the text file pids.txt that you create should contain no headers and only one patient ID per row).
  6. When you see your file and a progress bar, click "Upload".
  7. You’ll then receive a success message:
  8. In "Select Returned Values" tab, Select Demographics.pid
  9. In "Add Constraints" tab, you should see some values are present in the second column. These two small steps ensure you won't have an empty set in a moment when you try to download.

Part II – (CDAS) Downloading with main.xhtml.jnlp

  1. Next, click the “Run Query / View Results” tab. Select the “Download Associated CT Images (CDAS)” button.
  2. You’ll then be prompted to open the NBIA Download Manager by opening a file named xhtml, (which is a Java Net Launch Protocol file) with Java Web Start Launcher.  If you use the Firefox web browser, this is fairly automatic; just click OK.  I recommend you save the JNLP file (filename: main.xhtml.jnlp ) that the Query Tool generates. It may be useful for later troubleshooting if the download software crashes (or your computer crashes / re-starts, etc.).  Screenshots also help us to troubleshoot.
    you may see either popup   
  3. If you did not see Java as an option but you know java is installed on your machine, you can click “Other Programs” and navigate in your computer to the java executable (javaws.exe, for example) which should associate our file with the program correctly.
  4. Next, the Download Manager will launch.  If this is the first time you’ve run the Download Manager, you may see this screen; click “Run” to proceed.
  5. You’ll have to choose where you want to save the images. Once you’ve chosen the location, you can start the download. 
  6. Progress bars will indicate the % complete for each image series. This is often a multithreaded process.

Please contact help@cancerimagingarchive.net if you have any questions regarding the query tool.



Part IIB –  (TCIA) Downloading with the NBIA Data Retriever App

  1. This option may work best for those who have previously encountered java problems and are using Mac or Linux to work with the Web Query tool. This workaround will require you to also have contacted TCIA and established yourself an account here.
  2. Ensure you can login to TCIA here (click Login at right) https://nbia.cancerimagingarchive.net/nbia-search/
  3. Download an NBIA Data Retriever app for your Operating system from the Apple store or from here: Downloading TCIA Images
  4. Extract and install the NBIA Data Retriever for your Operating system (follow the extract and run/execute prompts). You will not run this application directly.

  5. Return to the web Query Tool interface:
  6. When you have selected your search filters, click the “Run Query / View Results” tab.
  7. Select the “Download Associated CT Images (TCIA)” button.
  8. A small manifest file (*.tcia) will be downloaded to your default location, like the Downloads folder, or your main Desktop.
  9. This manifest file should be “opened with” the NBIA Data Retriever app that you get through the Apple store or through https://wiki.cancerimagingarchive.net . It may be useful for later troubleshooting if the download software crashes (or your computer crashes / re-starts, etc.) to save the files and document your progress.  Screenshots also help us to troubleshoot.
  10. Next, the Download Manager will launch.  If this is the first time you’ve run the Download Manager, you may see this screen; click “Run” to proceed.
  11. You will see a big gray login screen because you are working with access-limited datasets. USE YOUR TCIA credential to log in here.
  12. You’ll have the option to choose where you want to save the images.  Once you’ve chosen the location, you can start the download. 
  13. Progress bars will indicate the % complete for each image series.


Please contact help@cancerimagingarchive.net if you have any questions regarding the query tool.

If you do not have a TCIA account

  1. Start here: https://public.cancerimagingarchive.net/ncia/legalRules.jsf and follow the several screens to get yourself started.
  2. Test your login here: https://nbia.cancerimagingarchive.net/nbia-search/ NOTE: NLST CT data is not available in this place. You will have to come back t the NLST Web Query Tool.
  3.  If you believe you should be able to use TCIA credentials to work with NLST data and it's not working, create a helpdesk ticket including your TCIA username and your approved NLST- project number. The TCIA helpdesk can associate the account with the necessary permissions.
  4. Go to Part IIB

NLST Query Tool


 






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