Difference between revisions of "Documentation/Nightly/Extensions/TCIABrowser"

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* '''Step 2: Browse the collections'''
 
* '''Step 2: Browse the collections'''
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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 [[Image:Report-icon-tcia.png|thumb|20px|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.
+
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 [[Image:Report-icon-tcia.png|thumb|20px|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.
  
 
|[[Image:TCIA-New02.png|thumb|820px|Module GUI]]
 
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* '''Step 3: Access Clinical Data from TCGA'''
 
* '''Step 3: Access Clinical Data from TCGA'''
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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.
 
|[[Image:TCIA-New03.png|thumb|600px|Module GUI]]
 
|[[Image:TCIA-New03.png|thumb|600px|Module GUI]]
 
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* '''Step 4: Download a Series'''
 
* '''Step 4: Download a Series'''
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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.[[Image:DownloadAndIndex.png|thumb|20px|Clinical Data Icon]][[Image:DownloadAndLoad.png|thumb|20px|Clinical Data Icon]]
 
|[[Image:TCIA-New05.png|thumb|720px|Module GUI]]
 
|[[Image:TCIA-New05.png|thumb|720px|Module GUI]]
 
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Revision as of 18:42, 15 February 2014

Home < Documentation < Nightly < Extensions < TCIABrowser


For the latest Slicer documentation, visit the read-the-docs.


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 Reasearch (QIICR) (U24 CA180918) (PIs Kikinis and Fedorov).
Authors: Alireza Mehrtash(SPL), Andrey Fedorov (SPL)
Contact: Alireza Mehrtash, mehrtash at bwh dot harvard dot edu

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.

  • TCIA public collections-collections.png
  • TCIA public collections-modalities.png
  • TCIA public collections-body parts.png
  • TCIA public collections-manufacturers.png


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: 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.
Clinical Data Icon
Clinical Data Icon
Module GUI


Similar Modules

References

Information for Developers

Work in progress
 Section under construction.
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