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author Alain Mazy <am@orthanc.team>
date Mon, 28 Oct 2024 09:23:08 +0100
parents 89bb195dfbc0
children
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1 .. _tcia:
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4 TCIA plugin
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5 ===========
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6
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7 .. contents::
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8
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9 This **official** plugin by the `ICTEAM institute of UCLouvain
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10 <https://orthanc.uclouvain.be/>`__ extends Orthanc with a Web
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11 interface that can be used to import open-data medical images from
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12 `The Cancer Imaging Archive (TCIA)
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13 <https://www.cancerimagingarchive.net/>`__, and serve them immediately
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14 using Orthanc.
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15
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16 The plugin can be used to import so-called "cart spreadsheet"
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17 generated by the `NBIA Search Client
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18 <https://nbia.cancerimagingarchive.net/nbia-search/>`__, or to browse
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19 the image collections of TCIA thanks to its `REST API
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20 <https://wiki.cancerimagingarchive.net/display/Public/TCIA+REST+API+Guide>`__.
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21
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22 **For researchers**: `Please cite this paper
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23 <https://dial.uclouvain.be/pr/boreal/object/boreal:257256>`__.
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26 Compilation
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27 -----------
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28
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29 .. highlight:: bash
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30
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31 Official releases can be `downloaded from the Orthanc homepage
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32 <https://orthanc.uclouvain.be/downloads/sources/orthanc-tcia/index.html>`__. As
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33 an alternative, the `repository containing the source code
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34 <https://orthanc.uclouvain.be/hg/orthanc-tcia/>`__ can be accessed using
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35 Mercurial.
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36
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37 The procedure to compile this plugin is similar of that for the
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38 :ref:`core of Orthanc <binaries>`. The following commands should work
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39 for most UNIX-like distribution (including GNU/Linux)::
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40
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41 $ mkdir Build
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42 $ cd Build
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43 $ cmake .. -DSTATIC_BUILD=ON -DCMAKE_BUILD_TYPE=Release
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44 $ make
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45
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46 The compilation will produce a shared library ``OrthancTcia``
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47 that contains the TCIA plugin for Orthanc.
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48
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49 Pre-compiled Linux Standard Base (LSB) binaries `can be downloaded
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50 <https://orthanc.uclouvain.be/downloads/linux-standard-base/orthanc-tcia/index.html>`__.
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51
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52 Pre-compiled binaries for `Microsoft Windows <https://orthanc.uclouvain.be/downloads/windows-32/orthanc-tcia/index.html>`__
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53 and `macOS <https://orthanc.uclouvain.be/downloads/macos/orthanc-tcia/index.html>`__ are available as well.
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54
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55 Furthermore, the ``jodogne/orthanc-plugins`` :ref:`Docker images
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56 <docker>` and ``orthancteam/orthanc`` :ref:`Docker images <docker-orthancteam>`
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57 also contain the plugin.
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58
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59
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60 Configuration
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61 -------------
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62
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63 You of course first have to :ref:`install Orthanc <compiling>`. Once
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64 Orthanc is installed, you must change the :ref:`configuration file
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65 <configuration>` to tell Orthanc where it can find the plugin: This is
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66 done by properly modifying the ``Plugins`` option.
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67
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68 You then have to set the two following options:
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69
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70 * The setting ``Enable`` in section ``Tcia`` must be set to ``true``
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71 to enable the TCIA plugin.
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72
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73 * The setting ``HttpsCACertificates`` must contain a path to a file
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74 containing a list of `trusted Certificate Authorities (CA)
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75 <https://curl.haxx.se/docs/sslcerts.html>`__. Depending on your
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76 operating system, this file can be found as follows:
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77
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78 - On Debian-based system, the standard file
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79 ``/etc/ssl/certs/ca-certificates.crt`` can be used.
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80 - On other systems (including Microsoft Windows), the cURL project
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81 provides `CA certificates
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82 <https://curl.haxx.se/docs/caextract.html>`__ that are extracted
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83 from Mozilla.
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84
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85 .. highlight:: json
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86
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87 On Ubuntu, you could for instance use the following minimalist
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88 configuration file::
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89
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90 {
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91 "HttpsCACertificates" : "/etc/ssl/certs/ca-certificates.crt",
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92 "Plugins" : [
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93 "/home/user/OrthancTcia/Build/libOrthancTcia.so"
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94 ],
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95 "Tcia" : {
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96 "Enable" : true
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97 }
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98 }
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99
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100 .. highlight:: text
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101
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102 Orthanc must of course be restarted after the modification of its
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103 configuration file.
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104
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105
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106 Usage
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107 -----
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108
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109 Once Orthanc Explorer is opened, a button entitled "The Cancer Imaging
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110 Archive" will show up at the bottom of the page. Clicking on this
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111 button will open the TCIA interface for Orthanc:
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112
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113 .. image:: ../images/tcia-interface.png
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114 :align: center
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115 :width: 640
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116
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117 As can be seen, this Web application allows to both import a cart from
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118 the NBIA Search Client, and to browse the various collections of
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119 medical images from TCIA.
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120
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121 The following screenshot illustrates how to export a cart using the
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122 NBIA Search Client, that can then be imported using this plugin:
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123
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124 .. image:: ../images/tcia-nbia-export.png
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125 :align: center
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126 :width: 640
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127
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128 The TCIA plugin creates a job to do the import. This implies that an
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129 import can be monitored, paused or stopped using the :ref:`REST API
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130 for Orthanc jobs <jobs>`.
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131