Mercurial > hg > orthanc-book
annotate Sphinx/source/plugins/neuro.rst @ 1027:60b0b7ea409b
migration to orthancteam
author | Sebastien Jodogne <s.jodogne@gmail.com> |
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date | Fri, 02 Feb 2024 14:16:55 +0100 |
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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://orthanc.uclouvain.be/downloads/sources/orthanc-neuro/index.html>`__. As |
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29 an alternative, the `repository containing the source code |
919 | 30 <https://orthanc.uclouvain.be/hg/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://orthanc.uclouvain.be/downloads/linux-standard-base/orthanc-neuro/index.html>`__. |
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47 |
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48 Pre-compiled binaries for `Microsoft Windows <https://orthanc.uclouvain.be/downloads/windows-32/orthanc-neuro/index.html>`__ |
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49 and `macOS <https://orthanc.uclouvain.be/downloads/macos/orthanc-neuro/index.html>`__ are available as well. |
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50 |
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51 Furthermore, the :ref:`Docker images <docker>` |
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52 ``jodogne/orthanc-plugins`` and ``orthancteam/orthanc`` also contain the |
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53 plugin. |
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54 |
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55 |
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56 Usage |
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57 ----- |
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58 |
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59 Configuration |
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60 ^^^^^^^^^^^^^ |
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61 |
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62 .. highlight:: json |
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63 |
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64 Here is a minimal sample :ref:`configuration file <configuration>` to |
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65 use this plugin:: |
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66 |
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67 { |
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68 "Plugins" : [ |
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69 "/home/user/OrthancNeuro/Build/libOrthancNeuro.so" |
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70 ] |
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71 } |
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72 |
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73 Orthanc must of course be restarted after the modification of its |
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74 configuration file. |
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75 |
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76 If you wish to convert DICOM instances using the JPEG2k transfer |
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77 syntax, don't forget to also enable the :ref:`GDCM plugin <gdcm>`. |
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78 |
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79 |
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80 Conversion to NIFTI |
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81 ^^^^^^^^^^^^^^^^^^^ |
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82 |
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83 When the plugin is enabled, the built-in **Orthanc Explorer** user |
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84 interface will provide a yellow button entitled ``Export to NIfTI`` at |
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85 the series and instance levels. |
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86 |
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87 The same feature is accessible to external software through the **REST |
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88 API of Orthanc** at the following URIs: |
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89 |
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90 * ``/series/{id}/nifti`` to convert the DICOM series whose |
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91 :ref:`Orthanc ID <orthanc-ids>` is ``{id}`` to one uncompressed |
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92 NIfTI-1 file (file extension ``.nii``). |
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93 |
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94 * ``/series/{id}/nifti?compress`` to convert the DICOM series whose |
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95 :ref:`Orthanc ID <orthanc-ids>` is ``{id}`` to one gzip-compressed |
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96 NIfTI-1 file (file extension ``.nii.gz``). |
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97 |
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98 * ``/instances/{id}/nifti`` to convert the DICOM instance whose |
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99 :ref:`Orthanc ID <orthanc-ids>` is ``{id}`` to one uncompressed |
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100 NIfTI-1 file (file extension ``.nii``). |
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101 |
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102 * ``/instances/{id}/nifti?compress`` to convert the DICOM instance whose |
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103 :ref:`Orthanc ID <orthanc-ids>` is ``{id}`` to one gzip-compressed |
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104 NIfTI-1 file (file extension ``.nii.gz``). |