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documentation of the neuroimaging plugin
author Sebastien Jodogne <s.jodogne@gmail.com>
date Tue, 26 Apr 2022 15:04:02 +0200
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834:0b35dcbb127c 835:1f9f6269543f
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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``).