Mercurial > hg > orthanc-book
changeset 760:e9da78572539
documentation of tcia
author | Sebastien Jodogne <s.jodogne@gmail.com> |
---|---|
date | Sun, 29 Aug 2021 13:31:57 +0200 |
parents | 94f5fc38b927 |
children | 525d59a7c198 |
files | Sphinx/source/images/tcia-interface.png Sphinx/source/images/tcia-nbia-export.png Sphinx/source/plugins/tcia.rst |
diffstat | 3 files changed, 107 insertions(+), 1 deletions(-) [+] |
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--- a/Sphinx/source/plugins/tcia.rst Sat Aug 28 10:21:27 2021 +0200 +++ b/Sphinx/source/plugins/tcia.rst Sun Aug 29 13:31:57 2021 +0200 @@ -6,4 +6,110 @@ .. contents:: -Soon available. +This **official** plugin extends Orthanc with a Web interface that can +be used to import open-data medical images from `The Cancer Imaging +Archive (TCIA) <https://www.cancerimagingarchive.net/>`__, and serve +them immediately using Orthanc. + +The plugin can be used to import so-called "cart spreadsheet" +generated by the `NBIA Search Client +<https://nbia.cancerimagingarchive.net/nbia-search/>`__, or to browse +the image collections of TCIA thanks to its `REST API +<https://wiki.cancerimagingarchive.net/display/Public/TCIA+REST+API+Guide>`__. + + +Compilation +----------- + +.. highlight:: bash + +The procedure to compile this plugin is similar of that for the +:ref:`core of Orthanc <binaries>`. The following commands should work +for most UNIX-like distribution (including GNU/Linux):: + + $ mkdir Build + $ cd Build + $ cmake .. -DSTATIC_BUILD=ON -DCMAKE_BUILD_TYPE=Release + $ make + +The compilation will produce a shared library ``OrthancTcia`` +that contains the TCIA plugin for Orthanc. + +Pre-compiled Linux Standard Base (LSB) binaries `can be downloaded +<https://lsb.orthanc-server.com/plugin-tcia/>`__. + +Pre-compiled binaries for Microsoft Windows and macOS `are also +available +<https://www.orthanc-server.com/browse.php?path=/plugin-tcia>`__. + +Furthermore, the :ref:`Docker images <docker>` +``jodogne/orthanc-plugins`` also contain the plugin. + + +Configuration +------------- + +You of course first have to :ref:`install Orthanc <compiling>`. Once +Orthanc is installed, you must change the :ref:`configuration file +<configuration>` to tell Orthanc where it can find the plugin: This is +done by properly modifying the ``Plugins`` option. + +You then have to set the two following options: + +* The setting ``Enable`` in section ``Tcia`` must be set to ``true`` + to enable the TCIA plugin. + +* The setting ``HttpsCACertificates`` must contain a path to a file + containing a list of `trusted Certificate Authorities (CA) + <https://curl.haxx.se/docs/sslcerts.html>`__. Depending on your + operating system, this file can be found as follows: + + - On Debian-based system, the standard file + ``/etc/ssl/certs/ca-certificates.crt`` can be used. + - On other systems (including Microsoft Windows), the cURL project + provides `CA certificates + <https://curl.haxx.se/docs/caextract.html>`__ that are extracted + from Mozilla. + +.. highlight:: json + +On Ubuntu, you could for instance use the following minimalist +configuration file:: + + { + "HttpsCACertificates" : "/etc/ssl/certs/ca-certificates.crt", + "Plugins" : [ + "/home/user/OrthancTcia/Build/libOrthancTcia.so" + ], + "Tcia" : { + "Enable" : true + } + } + +.. highlight:: text + +Orthanc must of course be restarted after the modification of its +configuration file. + + +Usage +----- + +Once Orthanc Explorer is opened, a button entitled "The Cancer Imaging +Archive" will show up at the bottom of the page. Clicking on this +button will open the TCIA interface for Orthanc: + +.. image:: ../images/tcia-interface.png + :align: center + :width: 640 + +As can be seen, this Web application allows to both import a cart from +the NBIA Search Client, and to browse the various collections of +medical images from TCIA. + +The following screenshot illustrates how to export a cart using the +NBIA Search Client, that can then be imported using this plugin: + +.. image:: ../images/tcia-nbia-export.png + :align: center + :width: 640