Difference between revisions of "Documentation/SlicerRT/UsersGuide"
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| − | = Matlab users = | + | = Frequently asked questions = |
| − | * Direct data exchange between Slicer and Matlab can be achieved by using the [ | + | == Matlab users == |
| + | * Direct data exchange between Slicer and Matlab can be achieved by using the [[Documentation/Nightly/Extensions/MatlabBridge|MatlabBridge extension]] | ||
* Volumetric images saved by 3D Slicer can be loaded into Matlab using [http://www.mathworks.com/matlabcentral/fileexchange/29344 these scripts] | * Volumetric images saved by 3D Slicer can be loaded into Matlab using [http://www.mathworks.com/matlabcentral/fileexchange/29344 these scripts] | ||
| − | = Running SlicerRT functions from command-line = | + | == Running SlicerRT functions from command-line == |
| − | An example for completing a complete RT workflow using Slicer GUI: [http:// | + | An example for completing a complete RT workflow using Slicer GUI: [http://subversion.assembla.com/svn/slicerrt/trunk/SlicerRt/src/Testing/Python/IGRTWorkflow_SelfTest.py IGRTWorkflow_SelfTest.py] |
<!-- Original link: https://subversion.assembla.com/svn/slicerrt/trunk/SlicerRt/src/Testing/Python/NAMIC_Tutorial_2013June_SelfTest.py --> | <!-- Original link: https://subversion.assembla.com/svn/slicerrt/trunk/SlicerRt/src/Testing/Python/NAMIC_Tutorial_2013June_SelfTest.py --> | ||
Options to start a Ptyhon script: | Options to start a Ptyhon script: | ||
* Open the Python console in Slicer (CTRL+3) and import scripts and/or enter commands | * Open the Python console in Slicer (CTRL+3) and import scripts and/or enter commands | ||
| − | * Run script commands from command-line:<br><code>Slicer.exe --python-code "slicer.util.loadScene('c:/Slicer_Scenes/20130225_PatientHierarchyTree/2013-02-25-Scene.mrml');<br>slicer.util.selectModule(' | + | * Run script commands from command-line:<br><code>Slicer.exe --python-code "slicer.util.loadScene('c:/Slicer_Scenes/20130225_PatientHierarchyTree/2013-02-25-Scene.mrml');<br>slicer.util.selectModule('SubjectHierarchy')"</code> |
Start a script from command-line: Slicer.exe --python-scipt "myscript.py" | 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 | 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 [ | + | See related pages about [[Documentation/Nightly/Developers/Python_scripting|python scripting]] |
| + | |||
| + | == Creating segmentations from labelmaps/models == | ||
| + | TODO | ||
= Troubleshooting = | = Troubleshooting = | ||
| − | * | + | * ''Problem'':<br>On OpenSuse linux: Some SlicerRT modules are not loaded, logged error is "''cannot open shared object file: No such file or directory''"<br>''Solution'':<br>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 = | = Known limitations = | ||
| − | + | == DICOM-RT import == | |
| − | + | * 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 ([http://www.donotlink.com/bEt #68]) | |
| − | |||
<!-- Original link: https://www.assembla.com/spaces/slicerrt/tickets/68 --> | <!-- Original link: https://www.assembla.com/spaces/slicerrt/tickets/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 ([http://www.donotlink.com/bEu #74]) | |
<!-- Original link: https://www.assembla.com/spaces/slicerrt/tickets/74 --> | <!-- Original link: https://www.assembla.com/spaces/slicerrt/tickets/74 --> | ||
Latest revision as of 02:23, 27 November 2019
Home < Documentation < SlicerRT < UsersGuideContents
Frequently asked questions
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: IGRTWorkflow_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('SubjectHierarchy')"
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
Creating segmentations from labelmaps/models
TODO
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
- 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.
