annotate Sphinx/source/plugins/neuro.rst @ 927:dfe96daba4f8

python in win installer
author Alain Mazy <am@osimis.io>
date Wed, 29 Mar 2023 11:54:58 +0200
parents 5c1ce758f748
children 05b106383b2a
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
835
1f9f6269543f documentation of the neuroimaging plugin
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
1 .. _neuro:
1f9f6269543f documentation of the neuroimaging plugin
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
2
1f9f6269543f documentation of the neuroimaging plugin
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
3
1f9f6269543f documentation of the neuroimaging plugin
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
4 Neuroimaging plugin
1f9f6269543f documentation of the neuroimaging plugin
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
5 ===================
1f9f6269543f documentation of the neuroimaging plugin
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
6
1f9f6269543f documentation of the neuroimaging plugin
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
7 .. contents::
1f9f6269543f documentation of the neuroimaging plugin
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
8
1f9f6269543f documentation of the neuroimaging plugin
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
9 This **official** plugin by the `ICTEAM institute of UCLouvain
1f9f6269543f documentation of the neuroimaging plugin
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
10 <https://uclouvain.be/en/research-institutes/icteam>`__ extends
1f9f6269543f documentation of the neuroimaging plugin
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
11 Orthanc with features dedicated for neuroimaging:
1f9f6269543f documentation of the neuroimaging plugin
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
12
1f9f6269543f documentation of the neuroimaging plugin
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
13 * Conversion of DICOM series and DICOM instances to the `NIfTI-1
1f9f6269543f documentation of the neuroimaging plugin
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
14 <https://en.wikipedia.org/wiki/Neuroimaging_Informatics_Technology_Initiative>`__
1f9f6269543f documentation of the neuroimaging plugin
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
15 file format, directly from the REST API of Orthanc. This is similar
1f9f6269543f documentation of the neuroimaging plugin
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
16 to `well-known converters
1f9f6269543f documentation of the neuroimaging plugin
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
17 <https://www.sciencedirect.com/science/article/abs/pii/S0165027016300073?via%3Dihub>`__
1f9f6269543f documentation of the neuroimaging plugin
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
18 such as ``dcm2niix``, but smoothly integrated within a PACS server
1f9f6269543f documentation of the neuroimaging plugin
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
19 instead of separate command-line tools.
1f9f6269543f documentation of the neuroimaging plugin
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
20
1f9f6269543f documentation of the neuroimaging plugin
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
21
1f9f6269543f documentation of the neuroimaging plugin
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
22 Compilation
1f9f6269543f documentation of the neuroimaging plugin
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
23 -----------
1f9f6269543f documentation of the neuroimaging plugin
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
24
1f9f6269543f documentation of the neuroimaging plugin
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
25 .. highlight:: bash
1f9f6269543f documentation of the neuroimaging plugin
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
26
1f9f6269543f documentation of the neuroimaging plugin
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
27 Official releases can be `downloaded from the Orthanc homepage
1f9f6269543f documentation of the neuroimaging plugin
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
28 <https://www.orthanc-server.com/browse.php?path=/plugin-neuro>`__. As
1f9f6269543f documentation of the neuroimaging plugin
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
29 an alternative, the `repository containing the source code
919
5c1ce758f748 uclouvain
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 835
diff changeset
30 <https://orthanc.uclouvain.be/hg/orthanc-neuro/>`__ can be accessed using
835
1f9f6269543f documentation of the neuroimaging plugin
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
31 Mercurial.
1f9f6269543f documentation of the neuroimaging plugin
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
32
1f9f6269543f documentation of the neuroimaging plugin
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
33 The procedure to compile this plugin is similar of that for the
1f9f6269543f documentation of the neuroimaging plugin
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
34 :ref:`core of Orthanc <binaries>`. The following commands should work
1f9f6269543f documentation of the neuroimaging plugin
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
35 for most UNIX-like distribution (including GNU/Linux)::
1f9f6269543f documentation of the neuroimaging plugin
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
36
1f9f6269543f documentation of the neuroimaging plugin
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
37 $ mkdir Build
1f9f6269543f documentation of the neuroimaging plugin
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
38 $ cd Build
1f9f6269543f documentation of the neuroimaging plugin
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
39 $ cmake .. -DSTATIC_BUILD=ON -DCMAKE_BUILD_TYPE=Release
1f9f6269543f documentation of the neuroimaging plugin
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
40 $ make
1f9f6269543f documentation of the neuroimaging plugin
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
41
1f9f6269543f documentation of the neuroimaging plugin
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
42 The compilation will produce a shared library ``OrthancNeuro`` that
1f9f6269543f documentation of the neuroimaging plugin
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
43 contains the neuroimaging plugin for Orthanc.
1f9f6269543f documentation of the neuroimaging plugin
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
44
1f9f6269543f documentation of the neuroimaging plugin
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
45 Pre-compiled Linux Standard Base (LSB) binaries `can be downloaded
1f9f6269543f documentation of the neuroimaging plugin
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
46 <https://lsb.orthanc-server.com/plugin-neuro/>`__.
1f9f6269543f documentation of the neuroimaging plugin
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
47
1f9f6269543f documentation of the neuroimaging plugin
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
48 Pre-compiled binaries for Microsoft Windows and macOS `are also
1f9f6269543f documentation of the neuroimaging plugin
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
49 available
1f9f6269543f documentation of the neuroimaging plugin
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
50 <https://www.orthanc-server.com/browse.php?path=/plugin-neuro>`__.
1f9f6269543f documentation of the neuroimaging plugin
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
51
1f9f6269543f documentation of the neuroimaging plugin
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
52 Furthermore, the :ref:`Docker images <docker>`
1f9f6269543f documentation of the neuroimaging plugin
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
53 ``jodogne/orthanc-plugins`` and ``osimis/orthanc`` also contain the
1f9f6269543f documentation of the neuroimaging plugin
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
54 plugin.
1f9f6269543f documentation of the neuroimaging plugin
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
55
1f9f6269543f documentation of the neuroimaging plugin
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
56
1f9f6269543f documentation of the neuroimaging plugin
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
57 Usage
1f9f6269543f documentation of the neuroimaging plugin
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
58 -----
1f9f6269543f documentation of the neuroimaging plugin
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
59
1f9f6269543f documentation of the neuroimaging plugin
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
60 Configuration
1f9f6269543f documentation of the neuroimaging plugin
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
61 ^^^^^^^^^^^^^
1f9f6269543f documentation of the neuroimaging plugin
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
62
1f9f6269543f documentation of the neuroimaging plugin
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
63 .. highlight:: json
1f9f6269543f documentation of the neuroimaging plugin
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
64
1f9f6269543f documentation of the neuroimaging plugin
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
65 Here is a minimal sample :ref:`configuration file <configuration>` to
1f9f6269543f documentation of the neuroimaging plugin
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
66 use this plugin::
1f9f6269543f documentation of the neuroimaging plugin
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
67
1f9f6269543f documentation of the neuroimaging plugin
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
68 {
1f9f6269543f documentation of the neuroimaging plugin
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
69 "Plugins" : [
1f9f6269543f documentation of the neuroimaging plugin
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
70 "/home/user/OrthancNeuro/Build/libOrthancNeuro.so"
1f9f6269543f documentation of the neuroimaging plugin
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
71 ]
1f9f6269543f documentation of the neuroimaging plugin
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
72 }
1f9f6269543f documentation of the neuroimaging plugin
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
73
1f9f6269543f documentation of the neuroimaging plugin
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
74 Orthanc must of course be restarted after the modification of its
1f9f6269543f documentation of the neuroimaging plugin
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
75 configuration file.
1f9f6269543f documentation of the neuroimaging plugin
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
76
1f9f6269543f documentation of the neuroimaging plugin
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
77 If you wish to convert DICOM instances using the JPEG2k transfer
1f9f6269543f documentation of the neuroimaging plugin
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
78 syntax, don't forget to also enable the :ref:`GDCM plugin <gdcm>`.
1f9f6269543f documentation of the neuroimaging plugin
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
79
1f9f6269543f documentation of the neuroimaging plugin
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
80
1f9f6269543f documentation of the neuroimaging plugin
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
81 Conversion to NIFTI
1f9f6269543f documentation of the neuroimaging plugin
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
82 ^^^^^^^^^^^^^^^^^^^
1f9f6269543f documentation of the neuroimaging plugin
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
83
1f9f6269543f documentation of the neuroimaging plugin
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
84 When the plugin is enabled, the built-in **Orthanc Explorer** user
1f9f6269543f documentation of the neuroimaging plugin
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
85 interface will provide a yellow button entitled ``Export to NIfTI`` at
1f9f6269543f documentation of the neuroimaging plugin
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
86 the series and instance levels.
1f9f6269543f documentation of the neuroimaging plugin
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
87
1f9f6269543f documentation of the neuroimaging plugin
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
88 The same feature is accessible to external software through the **REST
1f9f6269543f documentation of the neuroimaging plugin
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
89 API of Orthanc** at the following URIs:
1f9f6269543f documentation of the neuroimaging plugin
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
90
1f9f6269543f documentation of the neuroimaging plugin
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
91 * ``/series/{id}/nifti`` to convert the DICOM series whose
1f9f6269543f documentation of the neuroimaging plugin
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
92 :ref:`Orthanc ID <orthanc-ids>` is ``{id}`` to one uncompressed
1f9f6269543f documentation of the neuroimaging plugin
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
93 NIfTI-1 file (file extension ``.nii``).
1f9f6269543f documentation of the neuroimaging plugin
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
94
1f9f6269543f documentation of the neuroimaging plugin
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
95 * ``/series/{id}/nifti?compress`` to convert the DICOM series whose
1f9f6269543f documentation of the neuroimaging plugin
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
96 :ref:`Orthanc ID <orthanc-ids>` is ``{id}`` to one gzip-compressed
1f9f6269543f documentation of the neuroimaging plugin
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
97 NIfTI-1 file (file extension ``.nii.gz``).
1f9f6269543f documentation of the neuroimaging plugin
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
98
1f9f6269543f documentation of the neuroimaging plugin
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
99 * ``/instances/{id}/nifti`` to convert the DICOM instance whose
1f9f6269543f documentation of the neuroimaging plugin
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
100 :ref:`Orthanc ID <orthanc-ids>` is ``{id}`` to one uncompressed
1f9f6269543f documentation of the neuroimaging plugin
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
101 NIfTI-1 file (file extension ``.nii``).
1f9f6269543f documentation of the neuroimaging plugin
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
102
1f9f6269543f documentation of the neuroimaging plugin
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
103 * ``/instances/{id}/nifti?compress`` to convert the DICOM instance whose
1f9f6269543f documentation of the neuroimaging plugin
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
104 :ref:`Orthanc ID <orthanc-ids>` is ``{id}`` to one gzip-compressed
1f9f6269543f documentation of the neuroimaging plugin
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
105 NIfTI-1 file (file extension ``.nii.gz``).