Mercurial > hg > orthanc-book
changeset 835:1f9f6269543f
documentation of the neuroimaging plugin
author | Sebastien Jodogne <s.jodogne@gmail.com> |
---|---|
date | Tue, 26 Apr 2022 15:04:02 +0200 |
parents | 0b35dcbb127c |
children | a9c35bf108fa |
files | Sphinx/source/contributing.rst Sphinx/source/plugins.rst Sphinx/source/plugins/neuro.rst |
diffstat | 3 files changed, 106 insertions(+), 5 deletions(-) [+] |
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--- 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
--- 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:
--- /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``).