Documentation/SlicerRT/UsersGuide - Revision history

Grundlett: Text replacement - "\[http:\/\/www\.slicer\.org\/slicerWiki\/index\.php\/([^ ]+) ([^]]+)]" to "$2"

2019-11-27T02:23:42Z

Text replacement - "\[http:\/\/www\.slicer\.org\/slicerWiki\/index\.php\/([^ ]+) ([^]]+)]" to "$2"

Pinter at 20:14, 8 July 2015

2015-07-08T20:14:32Z

Pinter: /* Running SlicerRT functions from command-line */

2015-07-08T20:11:46Z

Running SlicerRT functions from command-line

Pinter at 21:12, 2 July 2015

2015-07-02T21:12:20Z

Pinter: Page created

2013-10-08T16:15:55Z

Page created

New page

= Matlab users =
* Direct data exchange between Slicer and Matlab can be achieved by using the [http://www.slicer.org/slicerWiki/index.php/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]

= Running SlicerRT functions from command-line =
An example for completing a complete RT workflow using Slicer GUI: [http://www.donotlink.com/bEs 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: <code>Slicer.exe --python-code "slicer.util.loadScene('c:/Slicer_Scenes/20130225_PatientHierarchyTree/2013-02-25-Scene.mrml'); slicer.util.selectModule('PatientHierarchy')"</code>
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 [http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Developers/Python_scripting 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 ([http://www.donotlink.com/bEt #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])

@@ Line 1: / Line 1: @@
 = Frequently asked questions =
 == Matlab users ==
-* Direct data exchange between Slicer and Matlab can be achieved by using the [http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Extensions/MatlabBridge MatlabBridge extension]
+* 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]
@@ Line 12: / Line 12: @@
 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 [http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Developers/Python_scripting python scripting]
+See related pages about [[Documentation/Nightly/Developers/Python_scripting|python scripting]]
 == Creating segmentations from labelmaps/models ==

@@ Line 1: / Line 1: @@
-= Matlab users =
+= Frequently asked questions =
 * Direct data exchange between Slicer and Matlab can be achieved by using the [http://www.slicer.org/slicerWiki/index.php/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]
-= Running SlicerRT functions from command-line =
+== Running SlicerRT functions from command-line ==
 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 -->
@@ Line 12: / Line 13: @@
 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 [http://www.slicer.org/slicerWiki/index.php/Documentation/Nightly/Developers/Python_scripting python scripting]
 = 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''
+* ''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 =
-*  DICOM-RT import
+== 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.
+* 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
+== DVH plotting ==
-** Cannot move the legend on DVH plots ([http://www.donotlink.com/bEt #68])
+* Cannot move the legend on DVH plots ([http://www.donotlink.com/bEt #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])
+* 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 -->