Mercurial > hg > orthanc-book
comparison Sphinx/source/plugins/neuro.rst @ 835:1f9f6269543f
documentation of the neuroimaging plugin
author | Sebastien Jodogne <s.jodogne@gmail.com> |
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date | Tue, 26 Apr 2022 15:04:02 +0200 |
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children | 5c1ce758f748 |
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1 .. _neuro: | |
2 | |
3 | |
4 Neuroimaging plugin | |
5 =================== | |
6 | |
7 .. contents:: | |
8 | |
9 This **official** plugin by the `ICTEAM institute of UCLouvain | |
10 <https://uclouvain.be/en/research-institutes/icteam>`__ extends | |
11 Orthanc with features dedicated for neuroimaging: | |
12 | |
13 * Conversion of DICOM series and DICOM instances to the `NIfTI-1 | |
14 <https://en.wikipedia.org/wiki/Neuroimaging_Informatics_Technology_Initiative>`__ | |
15 file format, directly from the REST API of Orthanc. This is similar | |
16 to `well-known converters | |
17 <https://www.sciencedirect.com/science/article/abs/pii/S0165027016300073?via%3Dihub>`__ | |
18 such as ``dcm2niix``, but smoothly integrated within a PACS server | |
19 instead of separate command-line tools. | |
20 | |
21 | |
22 Compilation | |
23 ----------- | |
24 | |
25 .. highlight:: bash | |
26 | |
27 Official releases can be `downloaded from the Orthanc homepage | |
28 <https://www.orthanc-server.com/browse.php?path=/plugin-neuro>`__. As | |
29 an alternative, the `repository containing the source code | |
30 <https://hg.orthanc-server.com/orthanc-neuro/>`__ can be accessed using | |
31 Mercurial. | |
32 | |
33 The procedure to compile this plugin is similar of that for the | |
34 :ref:`core of Orthanc <binaries>`. The following commands should work | |
35 for most UNIX-like distribution (including GNU/Linux):: | |
36 | |
37 $ mkdir Build | |
38 $ cd Build | |
39 $ cmake .. -DSTATIC_BUILD=ON -DCMAKE_BUILD_TYPE=Release | |
40 $ make | |
41 | |
42 The compilation will produce a shared library ``OrthancNeuro`` that | |
43 contains the neuroimaging plugin for Orthanc. | |
44 | |
45 Pre-compiled Linux Standard Base (LSB) binaries `can be downloaded | |
46 <https://lsb.orthanc-server.com/plugin-neuro/>`__. | |
47 | |
48 Pre-compiled binaries for Microsoft Windows and macOS `are also | |
49 available | |
50 <https://www.orthanc-server.com/browse.php?path=/plugin-neuro>`__. | |
51 | |
52 Furthermore, the :ref:`Docker images <docker>` | |
53 ``jodogne/orthanc-plugins`` and ``osimis/orthanc`` also contain the | |
54 plugin. | |
55 | |
56 | |
57 Usage | |
58 ----- | |
59 | |
60 Configuration | |
61 ^^^^^^^^^^^^^ | |
62 | |
63 .. highlight:: json | |
64 | |
65 Here is a minimal sample :ref:`configuration file <configuration>` to | |
66 use this plugin:: | |
67 | |
68 { | |
69 "Plugins" : [ | |
70 "/home/user/OrthancNeuro/Build/libOrthancNeuro.so" | |
71 ] | |
72 } | |
73 | |
74 Orthanc must of course be restarted after the modification of its | |
75 configuration file. | |
76 | |
77 If you wish to convert DICOM instances using the JPEG2k transfer | |
78 syntax, don't forget to also enable the :ref:`GDCM plugin <gdcm>`. | |
79 | |
80 | |
81 Conversion to NIFTI | |
82 ^^^^^^^^^^^^^^^^^^^ | |
83 | |
84 When the plugin is enabled, the built-in **Orthanc Explorer** user | |
85 interface will provide a yellow button entitled ``Export to NIfTI`` at | |
86 the series and instance levels. | |
87 | |
88 The same feature is accessible to external software through the **REST | |
89 API of Orthanc** at the following URIs: | |
90 | |
91 * ``/series/{id}/nifti`` to convert the DICOM series whose | |
92 :ref:`Orthanc ID <orthanc-ids>` is ``{id}`` to one uncompressed | |
93 NIfTI-1 file (file extension ``.nii``). | |
94 | |
95 * ``/series/{id}/nifti?compress`` to convert the DICOM series whose | |
96 :ref:`Orthanc ID <orthanc-ids>` is ``{id}`` to one gzip-compressed | |
97 NIfTI-1 file (file extension ``.nii.gz``). | |
98 | |
99 * ``/instances/{id}/nifti`` to convert the DICOM instance whose | |
100 :ref:`Orthanc ID <orthanc-ids>` is ``{id}`` to one uncompressed | |
101 NIfTI-1 file (file extension ``.nii``). | |
102 | |
103 * ``/instances/{id}/nifti?compress`` to convert the DICOM instance whose | |
104 :ref:`Orthanc ID <orthanc-ids>` is ``{id}`` to one gzip-compressed | |
105 NIfTI-1 file (file extension ``.nii.gz``). |