# HG changeset patch
# User Sebastien Jodogne <s.jodogne@gmail.com>
# Date 1650978242 -7200
# Node ID 1f9f6269543f5ab17317ba51a9971ca5cb137f88
# Parent  0b35dcbb127cd43cdf0b47c83e50fcb464596c88
documentation of the neuroimaging plugin

diff -r 0b35dcbb127c -r 1f9f6269543f Sphinx/source/contributing.rst
--- a/Sphinx/source/contributing.rst	Fri Apr 22 09:13:49 2022 +0200
+++ b/Sphinx/source/contributing.rst	Tue Apr 26 15:04:02 2022 +0200
@@ -115,11 +115,6 @@
       that it manages the worklists (i.e. add/remove items) with a
       REST API or HL7 messages, instead of reading them from some
       folder on the filesystem.
-    + Conversion to/from `NIfTI
-      <https://www.sciencedirect.com/science/article/abs/pii/S0165027016300073?via%3Dihub>`__
-      and/or `BIDS
-      <https://en.wikipedia.org/wiki/Brain_Imaging_Data_Structure>`__,
-      notably for neuroimaging.
     + `Encapsulate a video into a DICOM file
       <https://stackoverflow.com/questions/28698888/creating-h-264-avc-dicom-file-with-dcmtk/28737338#28737338>`__
       by calling some REST route, similarly to the
diff -r 0b35dcbb127c -r 1f9f6269543f Sphinx/source/plugins.rst
--- a/Sphinx/source/plugins.rst	Fri Apr 22 09:13:49 2022 +0200
+++ b/Sphinx/source/plugins.rst	Tue Apr 26 15:04:02 2022 +0200
@@ -80,6 +80,7 @@
 
    plugins/tcia.rst
    plugins/indexer.rst
+   plugins/neuro.rst
 
 .. _plugins-contributed:
 
diff -r 0b35dcbb127c -r 1f9f6269543f Sphinx/source/plugins/neuro.rst
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/Sphinx/source/plugins/neuro.rst	Tue Apr 26 15:04:02 2022 +0200
@@ -0,0 +1,105 @@
+.. _neuro:
+
+
+Neuroimaging plugin
+===================
+
+.. contents::
+
+This **official** plugin by the `ICTEAM institute of UCLouvain
+<https://uclouvain.be/en/research-institutes/icteam>`__ extends
+Orthanc with features dedicated for neuroimaging:
+
+* Conversion of DICOM series and DICOM instances to the `NIfTI-1
+  <https://en.wikipedia.org/wiki/Neuroimaging_Informatics_Technology_Initiative>`__
+  file format, directly from the REST API of Orthanc. This is similar
+  to `well-known converters
+  <https://www.sciencedirect.com/science/article/abs/pii/S0165027016300073?via%3Dihub>`__
+  such as ``dcm2niix``, but smoothly integrated within a PACS server
+  instead of separate command-line tools.
+
+
+Compilation
+-----------
+
+.. highlight:: bash
+
+Official releases can be `downloaded from the Orthanc homepage
+<https://www.orthanc-server.com/browse.php?path=/plugin-neuro>`__. As
+an alternative, the `repository containing the source code
+<https://hg.orthanc-server.com/orthanc-neuro/>`__ can be accessed using
+Mercurial.
+
+The procedure to compile this plugin is similar of that for the
+:ref:`core of Orthanc <binaries>`. The following commands should work
+for most UNIX-like distribution (including GNU/Linux)::
+
+  $ mkdir Build
+  $ cd Build
+  $ cmake .. -DSTATIC_BUILD=ON -DCMAKE_BUILD_TYPE=Release
+  $ make
+
+The compilation will produce a shared library ``OrthancNeuro`` that
+contains the neuroimaging plugin for Orthanc.
+
+Pre-compiled Linux Standard Base (LSB) binaries `can be downloaded
+<https://lsb.orthanc-server.com/plugin-neuro/>`__.
+
+Pre-compiled binaries for Microsoft Windows and macOS `are also
+available
+<https://www.orthanc-server.com/browse.php?path=/plugin-neuro>`__.
+
+Furthermore, the :ref:`Docker images <docker>`
+``jodogne/orthanc-plugins`` and ``osimis/orthanc`` also contain the
+plugin.
+
+
+Usage
+-----
+
+Configuration
+^^^^^^^^^^^^^
+
+.. highlight:: json
+
+Here is a minimal sample :ref:`configuration file <configuration>` to
+use this plugin::
+
+  {
+    "Plugins" : [
+      "/home/user/OrthancNeuro/Build/libOrthancNeuro.so"
+    ]
+  }
+
+Orthanc must of course be restarted after the modification of its
+configuration file.
+
+If you wish to convert DICOM instances using the JPEG2k transfer
+syntax, don't forget to also enable the :ref:`GDCM plugin <gdcm>`.
+
+
+Conversion to NIFTI
+^^^^^^^^^^^^^^^^^^^
+
+When the plugin is enabled, the built-in **Orthanc Explorer** user
+interface will provide a yellow button entitled ``Export to NIfTI`` at
+the series and instance levels.
+
+The same feature is accessible to external software through the **REST
+API of Orthanc** at the following URIs:
+
+* ``/series/{id}/nifti`` to convert the DICOM series whose
+  :ref:`Orthanc ID <orthanc-ids>` is ``{id}`` to one uncompressed
+  NIfTI-1 file (file extension ``.nii``).
+
+* ``/series/{id}/nifti?compress`` to convert the DICOM series whose
+  :ref:`Orthanc ID <orthanc-ids>` is ``{id}`` to one gzip-compressed
+  NIfTI-1 file (file extension ``.nii.gz``).
+
+* ``/instances/{id}/nifti`` to convert the DICOM instance whose
+  :ref:`Orthanc ID <orthanc-ids>` is ``{id}`` to one uncompressed
+  NIfTI-1 file (file extension ``.nii``).
+
+* ``/instances/{id}/nifti?compress`` to convert the DICOM instance whose
+  :ref:`Orthanc ID <orthanc-ids>` is ``{id}`` to one gzip-compressed
+  NIfTI-1 file (file extension ``.nii.gz``).