Neuroimaging plugin

This official plugin by the ICTEAM institute of UCLouvain extends Orthanc with features dedicated for neuroimaging:

  • Conversion of DICOM series and DICOM instances to the NIfTI-1 file format, directly from the REST API of Orthanc. This is similar to well-known converters such as dcm2niix, but smoothly integrated within a PACS server instead of separate command-line tools.

Compilation

Official releases can be downloaded from the Orthanc homepage. As an alternative, the repository containing the source code can be accessed using Mercurial.

The procedure to compile this plugin is similar of that for the core of Orthanc. 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.

Pre-compiled binaries for Microsoft Windows and macOS are also available.

Furthermore, the Docker images jodogne/orthanc-plugins and osimis/orthanc also contain the plugin.

Usage

Configuration

Here is a minimal sample configuration file 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 GDCM plugin.

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 Orthanc ID is {id} to one uncompressed NIfTI-1 file (file extension .nii).
  • /series/{id}/nifti?compress to convert the DICOM series whose Orthanc ID is {id} to one gzip-compressed NIfTI-1 file (file extension .nii.gz).
  • /instances/{id}/nifti to convert the DICOM instance whose Orthanc ID is {id} to one uncompressed NIfTI-1 file (file extension .nii).
  • /instances/{id}/nifti?compress to convert the DICOM instance whose Orthanc ID is {id} to one gzip-compressed NIfTI-1 file (file extension .nii.gz).