Documentation/4.3/ScriptRepository

For the latest Slicer documentation, visit the read-the-docs.

Community-contributed modules

Usage: save the .py file to a directory, add the directory to the additional module paths in the Slicer application settings.

Segmentation

• FillRoi.py: Fill a region of interest in a labelmap volume with a constant value. This can be used after an automatic segmentation for removing certain regions of a volume.

Filters

• VolumeMasker.py: Update a target volume with the results of setting all input volume voxels to 0 except for those that correspond to a selected label value in an input label map (Used for example in the volume rendering in [https://www.youtube.com/watch?v=dfu2gugHLHs this video).

DICOM

• dicom header browser to easily scroll through dicom files using dcmdump.

Community-contributed examples

Usage: Copy-paste the shown code lines or linked .py file contents into Python console in Slicer.

Capture

• Get a MRML node in the scene based on the node name and call methods of that object. For the MRHead sample data:

 vol=slicer.util.getNode('MR*')
 vol.GetImageData().GetDimensions()

• Capture the full Slicer screen and save it into a file

 img = qt.QPixmap.grabWidget(slicer.util.mainWindow()).toImage()
 img.save('c:/tmp/test.png')

• • To capture the content of a slice viewer:

 viewNames = slicer.app.layoutManager().sliceViewNames()
 img = qt.QPixmap.grabWidget(slicer.app.layoutManager().sliceWidget(viewNames[0]))

• CaptureRotationVideo.py: Capture a video of the scene rotating in the 3D view

Launching Slicer

• How to open an .mrb file with Slicer at the command line?

 Slicer.exe --python-code "slicer.util.loadScene( 'f:/2013-08-23-Scene.mrb' )"

• How to run a script in the Slicer environment in batch mode (without showing any graphical user interface)?

 Slicer.exe --python-code "doSomething; doSomethingElse; etc." --testing --no-splash --no-main-window

• To create an animated gifs of the saved frames, you can use the following tools:
  • [sips (Mac only) to convert single frame to GIF format (cannot save as .gif with QImage)
  • [gifsicle] to combine individual frames into a single animated gif (gifsicle is a command line tool, so you can batch it!)