Documentation/Nightly/Extensions/TCIABrowser

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Introduction and Acknowledgements

Extension: TCIABrowser Acknowledgments: This work is funded by the National Institutes of Health, National Cancer Institute through the Grant Quantitative Image Informatics for Cancer Research (QIICR) (U24 CA180918) (PIs Kikinis and Fedorov). Authors: Alireza Mehrtash(SPL), Andrey Fedorov (SPL) Contact: Alireza Mehrtash, <email>mehrtash@bwh.harvard.edu</email> License: Slicer License Quantitative Image Informatics for Cancer Research   Surgical Planning Laboratory (SPL)   National Alliance for Medical Image Computing (NA-MIC)

Module Description

The Cancer Imaging Archive (TCIA) hosts a large collection of Cancer medical imaging data which is available to public through a programmatic interface (REST API). TCIA Browser is a Slicer module by which the user can connect to the TCIA archive, browse different collections, patients, studies and series, download the images and visualize them in 3D Slicer.

As of February 2014, the following collections of TCIA are available via public TCIA API interface (see description of TCIA collections for details):

• QIBA CT-1C
• TCGA-GBM *
• RIDER PHANTOM PET-CT
• RIDER PHANTOM MRI
• Phantom FDA
• TCGA-LGG *
• TCGA-KIRC *
• TCGA-BRCA *
• BREAST-DIAGNOSIS
• PROSTATE-DIAGNOSIS
• LIDC-IDRI
• TCGA-LUAD *
• RIDER Lung CT
• RIDER NEURO MRI
• RIDER Lung PET-CT
• CT COLONOGRAPHY
• REMBRANDT
• RIDER Breast MRI

For the collections marked with *, available clinical data is linked from The Cancer Genome Atlas.

TCIABrowser gives you access to 18 collections, which contain a total of over 23,000 image series from a variety of manufacturers and of different modalities and organs. Some of the summary statistics of the data available from the public collections listed is provided below.

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Tutorials

Not available at this time.

Panels and their use

• Step 1: Connect to the server

Press connect button to connect to TCIA archive with 3D Slicer unique API-KEY. TCIA will provide a list of available collections and the browser will pop up automatically. If you have your own unique API and want to use that you can add your own API using the "+" button and then select it using the combo box.

Module GUI

• Step 2: Browse the collections

In the browser window from the combo box select a collection. The browser will get the patient data from the TCIA server and will populate the Patients table. In patient table, the clinical data icon besides the patient ID

Clinical Data Icon

means that the clinical data for that specific patient is available in TCGA. The use Cache check box will cache the query results on your hard drive which makes the next selections much faster. If you want to do the query (connect to TCIA Server) you can uncheck this box. Above the Patients table you can see the last access time. The process is the same for studies and series tables, selecting a patient will populate the study table for the selected one and selecting a study will update the series table.

Module GUI

• Step 3: Access Clinical Data from TCGA

You can open the context menu with right click on the specific patient ID for patients which have the TCGA clinical data available. Clicking on "Get Clinical Data" will send a request to cBioPortal server and get the available clinical data for the specific patient. Again here like TCIA queries the results will be saved on your local hard drive. You can update the cache by pressing "Update Cache" button.

Module GUI

Module GUI

• Step 4: A-Download a Series

In the final step when you select a series the download icons will become activated. Pressing the "Download and Index" button will download the images from TCIA to your computer and index the DICOM files inside 3D Slicer DICOM database. So you can review them, check the meta-data and load into the scene later with Slicer DICOM module. Pressing the "Download and Load" button will download the images and load them into the Slicer scene.

Download and Index Button

Download and Load Button

Module GUI

• Step 4: B- Download multiple patients, studies and series

You can select multiple items from all of the tables. By holding the Ctrl key and clicking on different patients, the studies for all the selected ones will be added to the studies table. You can select all the studies by pressing 'Select All' button or make a specific selection by Ctrl+Click and all the available series for download will be added to the series table. At the final step you will select series for download from the series table. The total number of images for the selected series is indicated at the bottom right corner of series table. After pressing the download button you can check the download status of each series at the 'Download Status' collapsible button at the module's widget. While the download is in progress you can still browse and add other series to the download queue or view the downloaded images in the 3D Slicer Scene.

Multiple Selections

Download Status

Similar Modules

• XNATSlicer
• DICOM

References

• Quantitative Image Informatics for Cancer Research (QIICR)
• Quantitative Imaging Network (QIN)
• TCIA Home Page
• cBioPortal for Cancer Genomics Web Interface
• Description of TCIA Collections
• TCIA Rest API Documentation
• Project page at NAMIC 2014 Project Week
• Mashape page for testing TCIA API endpoint

Information for Developers

• Source Code

Tip: The REST API can be checked by REST Console Google Chrome extension.