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author Alain Mazy <am@osimis.io>
date Thu, 02 Feb 2023 12:13:34 +0100
parents 1f9f6269543f
children 5c1ce758f748
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1 .. _neuro:
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2
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3
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4 Neuroimaging 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://uclouvain.be/en/research-institutes/icteam>`__ extends
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11 Orthanc with features dedicated for neuroimaging:
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12
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13 * Conversion of DICOM series and DICOM instances to the `NIfTI-1
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14 <https://en.wikipedia.org/wiki/Neuroimaging_Informatics_Technology_Initiative>`__
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15 file format, directly from the REST API of Orthanc. This is similar
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16 to `well-known converters
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17 <https://www.sciencedirect.com/science/article/abs/pii/S0165027016300073?via%3Dihub>`__
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18 such as ``dcm2niix``, but smoothly integrated within a PACS server
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19 instead of separate command-line tools.
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20
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21
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22 Compilation
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23 -----------
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24
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25 .. highlight:: bash
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26
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27 Official releases can be `downloaded from the Orthanc homepage
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28 <https://www.orthanc-server.com/browse.php?path=/plugin-neuro>`__. As
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29 an alternative, the `repository containing the source code
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30 <https://hg.orthanc-server.com/orthanc-neuro/>`__ can be accessed using
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31 Mercurial.
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32
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33 The procedure to compile this plugin is similar of that for the
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34 :ref:`core of Orthanc <binaries>`. The following commands should work
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35 for most UNIX-like distribution (including GNU/Linux)::
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36
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37 $ mkdir Build
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38 $ cd Build
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39 $ cmake .. -DSTATIC_BUILD=ON -DCMAKE_BUILD_TYPE=Release
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40 $ make
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41
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42 The compilation will produce a shared library ``OrthancNeuro`` that
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43 contains the neuroimaging plugin for Orthanc.
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44
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45 Pre-compiled Linux Standard Base (LSB) binaries `can be downloaded
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46 <https://lsb.orthanc-server.com/plugin-neuro/>`__.
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47
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48 Pre-compiled binaries for Microsoft Windows and macOS `are also
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49 available
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50 <https://www.orthanc-server.com/browse.php?path=/plugin-neuro>`__.
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51
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52 Furthermore, the :ref:`Docker images <docker>`
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53 ``jodogne/orthanc-plugins`` and ``osimis/orthanc`` also contain the
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54 plugin.
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55
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56
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57 Usage
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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 .. highlight:: json
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64
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65 Here is a minimal sample :ref:`configuration file <configuration>` to
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66 use this plugin::
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67
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68 {
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69 "Plugins" : [
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70 "/home/user/OrthancNeuro/Build/libOrthancNeuro.so"
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71 ]
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72 }
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73
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74 Orthanc must of course be restarted after the modification of its
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75 configuration file.
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76
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77 If you wish to convert DICOM instances using the JPEG2k transfer
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78 syntax, don't forget to also enable the :ref:`GDCM plugin <gdcm>`.
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79
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80
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81 Conversion to NIFTI
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82 ^^^^^^^^^^^^^^^^^^^
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83
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84 When the plugin is enabled, the built-in **Orthanc Explorer** user
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85 interface will provide a yellow button entitled ``Export to NIfTI`` at
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86 the series and instance levels.
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87
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88 The same feature is accessible to external software through the **REST
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89 API of Orthanc** at the following URIs:
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90
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91 * ``/series/{id}/nifti`` to convert the DICOM series whose
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92 :ref:`Orthanc ID <orthanc-ids>` is ``{id}`` to one uncompressed
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93 NIfTI-1 file (file extension ``.nii``).
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94
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95 * ``/series/{id}/nifti?compress`` to convert the DICOM series whose
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96 :ref:`Orthanc ID <orthanc-ids>` is ``{id}`` to one gzip-compressed
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97 NIfTI-1 file (file extension ``.nii.gz``).
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98
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99 * ``/instances/{id}/nifti`` to convert the DICOM instance whose
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100 :ref:`Orthanc ID <orthanc-ids>` is ``{id}`` to one uncompressed
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101 NIfTI-1 file (file extension ``.nii``).
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102
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103 * ``/instances/{id}/nifti?compress`` to convert the DICOM instance whose
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104 :ref:`Orthanc ID <orthanc-ids>` is ``{id}`` to one gzip-compressed
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105 NIfTI-1 file (file extension ``.nii.gz``).