Documentation/SlicerRT/UsersGuide

Matlab users

• Direct data exchange between Slicer and Matlab can be achieved by using the MatlabBridge extension
• Volumetric images saved by 3D Slicer can be loaded into Matlab using these scripts

Running SlicerRT functions from command-line

An example for completing a complete RT workflow using Slicer GUI: NAMIC_Tutorial_2013June_SelfTest.py Options to start a Ptyhon script:

• Open the Python console in Slicer (CTRL+3) and import scripts and/or enter commands
• Run script commands from command-line:
  Slicer.exe --python-code "slicer.util.loadScene('c:/Slicer_Scenes/20130225_PatientHierarchyTree/2013-02-25-Scene.mrml');
slicer.util.selectModule('PatientHierarchy')"

Start a script from command-line: Slicer.exe --python-scipt "myscript.py" If you don't want the Slicer window to appear while the scripts are running add these switches to the command-line: --no-splash --no-main-window See related pages about python scripting

Troubleshooting

• Problem:
  On OpenSuse linux: Some SlicerRT modules are not loaded, logged error is "cannot open shared object file: No such file or directory"
  Solution:
  Start Slicer with command: LD_LIBRARY_PATH=/home/karl/.config/NA-MIC/Extensions-22288/SlicerRT/lib/Slicer-4.2/qt-loadable-modules ./Slicer

Known limitations

• DICOM-RT import
  • RTSTRUCT import: structure set plane normal has to be parallel to the IS axis
  • RTIMAGE import: Datasets exported by the Corvus treatment planning system cannot be loaded properly (geometry cannot be computed for the RT image), because apparently ReferencedSOPInstanceUID points to the SeriesInstanceUID of the plan, which is not standard.
• DVH plotting
  • Cannot move the legend on DVH plots (#68)
  • The V metrics volume is computed from the DVH value corresponding to the closest dose to the one below and above the requested dose using linear interpolation (#74)