Mercurial > hg > orthanc-book

annotate Sphinx/source/plugins/neuro.rst @ 1057:5a3c238575f8

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
documentation of stl
author Sebastien Jodogne <s.jodogne@gmail.com>
date Tue, 09 Apr 2024 16:29:42 +0200
parents 89bb195dfbc0
children
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
1056
89bb195dfbc0 starting stl documentation
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1027
diff changeset
10 <https://orthanc.uclouvain.be/>`__ extends Orthanc with features
89bb195dfbc0 starting stl documentation
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1027
diff changeset
11 dedicated for neuroimaging:
835
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
993
05b106383b2a migration to UCLouvain servers
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 919
diff changeset
28 <https://orthanc.uclouvain.be/downloads/sources/orthanc-neuro/index.html>`__. As
835
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
993
05b106383b2a migration to UCLouvain servers
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 919
diff changeset
46 <https://orthanc.uclouvain.be/downloads/linux-standard-base/orthanc-neuro/index.html>`__.
835
1f9f6269543f documentation of the neuroimaging plugin
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
47
993
05b106383b2a migration to UCLouvain servers
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 919
diff changeset
48 Pre-compiled binaries for `Microsoft Windows <https://orthanc.uclouvain.be/downloads/windows-32/orthanc-neuro/index.html>`__
05b106383b2a migration to UCLouvain servers
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 919
diff changeset
49 and `macOS <https://orthanc.uclouvain.be/downloads/macos/orthanc-neuro/index.html>`__ are available as well.
835
1f9f6269543f documentation of the neuroimaging plugin
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
50
1f9f6269543f documentation of the neuroimaging plugin
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
51 Furthermore, the :ref:`Docker images <docker>`
1027
60b0b7ea409b migration to orthancteam
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 993
diff changeset
52 ``jodogne/orthanc-plugins`` and ``orthancteam/orthanc`` also contain the
835
1f9f6269543f documentation of the neuroimaging plugin
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
53 plugin.
1f9f6269543f documentation of the neuroimaging plugin
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
54
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 Usage
1f9f6269543f documentation of the neuroimaging plugin
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
57 -----
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 Configuration
1f9f6269543f documentation of the neuroimaging plugin
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
60 ^^^^^^^^^^^^^
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 .. highlight:: json
1f9f6269543f documentation of the neuroimaging plugin
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
63
1f9f6269543f documentation of the neuroimaging plugin
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
64 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
65 use this plugin::
1f9f6269543f documentation of the neuroimaging plugin
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
66
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 "Plugins" : [
1f9f6269543f documentation of the neuroimaging plugin
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
69 "/home/user/OrthancNeuro/Build/libOrthancNeuro.so"
1f9f6269543f documentation of the neuroimaging plugin
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
70 ]
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 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
74 configuration file.
1f9f6269543f documentation of the neuroimaging plugin
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
75
1f9f6269543f documentation of the neuroimaging plugin
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
76 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
77 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
78
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 Conversion to NIFTI
1f9f6269543f documentation of the neuroimaging plugin
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
81 ^^^^^^^^^^^^^^^^^^^
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 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
84 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
85 the series and instance levels.
1f9f6269543f documentation of the neuroimaging plugin
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
86
1f9f6269543f documentation of the neuroimaging plugin
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
87 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
88 API of Orthanc** at the following URIs:
1f9f6269543f documentation of the neuroimaging plugin
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
89
1f9f6269543f documentation of the neuroimaging plugin
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
90 * ``/series/{id}/nifti`` to convert the DICOM series whose
1f9f6269543f documentation of the neuroimaging plugin
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
91 :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
92 NIfTI-1 file (file extension ``.nii``).
1f9f6269543f documentation of the neuroimaging plugin
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
93
1f9f6269543f documentation of the neuroimaging plugin
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
94 * ``/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
95 :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
96 NIfTI-1 file (file extension ``.nii.gz``).
1f9f6269543f documentation of the neuroimaging plugin
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
97
1f9f6269543f documentation of the neuroimaging plugin
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
98 * ``/instances/{id}/nifti`` to convert the DICOM instance whose
1f9f6269543f documentation of the neuroimaging plugin
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
99 :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
100 NIfTI-1 file (file extension ``.nii``).
1f9f6269543f documentation of the neuroimaging plugin
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
101
1f9f6269543f documentation of the neuroimaging plugin
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
102 * ``/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
103 :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
104 NIfTI-1 file (file extension ``.nii.gz``).