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| − | <noinclude>{{documentation/versioncheck}}</noinclude> | + | <noinclude>{{documentation/versioncheck}} |
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| − | {{documentation/{{documentation/version}}/module-header}}
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| − | {{documentation/{{documentation/version}}/module-section|Introduction and Acknowledgements}}
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| − | {{documentation/{{documentation/version}}/module-introduction-start|{{documentation/modulename}}}}
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| − | {{documentation/{{documentation/version}}/module-introduction-row}}
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| − | Extension: [[Documentation/{{documentation/version}}/Extensions/TCIABrowser|TCIABrowser]]<br>
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| − | Acknowledgments:
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| − | This work is funded by the National Institutes of Health, National Cancer Institute through the Grant [http://qiicr.org Quantitative Image Informatics for Cancer Reasearch (QIICR)] (U24 CA180918) (PIs Kikinis and Fedorov).<br>
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| − | Authors: Alireza Mehrtash({{collaborator|name|spl}}), Andrey Fedorov ({{collaborator|name|spl}})<br>
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| − | Contact: Alireza Mehrtash, mehrtash at bwh dot harvard dot edu<br>
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| − | License: [http://www.slicer.org/pages/LicenseText Slicer License]
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| − | {{documentation/{{documentation/version}}/module-introduction-logo-gallery
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| − | |{{collaborator|logo|qiicr}}|{{collaborator|longname|qiicr}}
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| − | |{{collaborator|logo|spl}}|{{collaborator|longname|spl}}
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| − | |{{collaborator|logo|namic}}|{{collaborator|longname|namic}}
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| − | }}
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| − | {{documentation/{{documentation/version}}/module-introduction-end}}
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| − | {{documentation/{{documentation/version}}/module-section|Module Description}}
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| − | 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.
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| − | As of February 2014, the following collections of TCIA are available via public TCIA API interface (see [https://wiki.cancerimagingarchive.net/display/Public/Collections description of TCIA collections] for details):
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| − | * QIBA CT-1C
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| − | * TCGA-GBM *
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| − | * RIDER PHANTOM PET-CT
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| − | * RIDER PHANTOM MRI
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| − | * Phantom FDA
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| − | * TCGA-LGG *
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| − | * TCGA-KIRC *
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| − | * TCGA-BRCA *
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| − | * BREAST-DIAGNOSIS
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| − | * PROSTATE-DIAGNOSIS
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| − | * LIDC-IDRI
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| − | * TCGA-LUAD *
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| − | * RIDER Lung CT
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| − | * RIDER NEURO MRI
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| − | * RIDER Lung PET-CT
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| − | * CT COLONOGRAPHY
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| − | * REMBRANDT
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| − | * RIDER Breast MRI
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| − | For the collections marked with *, available clinical data is linked from [http://cancergenome.nih.gov/ The Cancer Genome Atlas].
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| − | 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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| − | <gallery widths="500px" heights="500px" perrow="2">
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| − | Image:TCIA_public_collections-collections.png
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| − | Image:TCIA_public_collections-modalities.png
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| − | Image:TCIA_public_collections-body_parts.png
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| − | Image:TCIA_public_collections-manufacturers.png
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| − | </gallery>
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| − | {{documentation/{{documentation/version}}/module-section|Tutorials}}
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| − | Not available at this time.
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| − | {{documentation/{{documentation/version}}/module-section|Panels and their use}}
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| − | | |
| − | {|
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| − | * '''Step 1: Connect to the server'''
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| − | 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.
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| − | 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.
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| − | |[[Image:Tcia-browser-1.png|thumb|360px|Module GUI]]
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| − | |}
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| − | {|
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| − | * '''Step 2: Browse the collections'''
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| − | |[[Image:Tcia-browser-4.png|thumb|820px|Module GUI]]
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| − | |}
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| − | | |
| − | {|
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| − | * '''Step 3: Download a Series'''
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| − | |[[Image:Tcia-browser-5.png|thumb|720px|Module GUI]]
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| − | |}
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| − | <!-- ---------------------------- -->
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| − | {{documentation/{{documentation/version}}/module-section|Similar Modules}}
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| − | * [[Documentation/4.3/Extensions/XNATSlicer|XNATSlicer]]
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| − | <!-- ---------------------------- -->
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| − | {{documentation/{{documentation/version}}/module-section|References}}
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| − | * [http://qiicr.org/ Quantitative Image Informatics for Cancer Research (QIICR)]
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| − | * [http://imaging.cancer.gov/programsandresources/specializedinitiatives/qin Quantitative Imaging Network (QIN)]
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| − | * [http://cancerimagingarchive.net/ TCIA Home Page]
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| − | * [https://wiki.cancerimagingarchive.net/display/Public/Collections Description of TCIA Collections]
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| − | * [https://wiki.cancerimagingarchive.net/display/Public/TCIA+Programmatic+Interface+%28REST+API%29+Usage+Guide TCIA Rest API Documentation]
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| − | * [http://www.na-mic.org/Wiki/index.php/2014_Project_Week:TCIA_Browser_Extension_in_Slicer Project page at NAMIC 2014 Project Week]
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| − | {{documentation/{{documentation/version}}/module-section|Information for Developers}}
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| − | * [https://github.com/QIICR/TCIABrowser Source Code]
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| − | {{documentation/{{documentation/version}}/module-developerinfo}}
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| − | {{documentation/{{documentation/version}}/module-footer}}
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| | [[Category:Documentation/{{documentation/version}}/Modules/Informatics]] | | [[Category:Documentation/{{documentation/version}}/Modules/Informatics]] |
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| + | '''Please see documentation of this module here: https://github.com/QIICR/TCIABrowser''' |
