Customize Slicer

The two main ways to customize Slicer:

1. the Application Settings
2. the Extension Manager

Application Settings

The Application settings contain settings that control Slicer Appearance and performance

Modules

The modules tab contains settings for loading extensions (modules), setting the default startup module, and customizing the toolbar

Modify the Toolbar

The toolbar is broken down into panels, which can be shown/hidden by right-clicking on a blank area of the toolbar to bring up a contextual menu:

The favorites panel, to the right of the arrows, can be modified in the Application settings: Modules tab

Views

Add Orientation Marker

It is convenient to display the human orientation marker in the viewers at startup.

the Orientation marker makes it much easier to understand the orientation of the orthogonal slices or the current view in the 3D viewer

To set the Slice View defaults:

1. In the Edit menu, select "Application Settings"
2. In the dialog window, select the "Views" tab
3. Use the following settings:

When you make changes to the default settings, Slicer requires that you restart the app. Click OK to restart when prompted

Remove Slice Edge

Slice edges are colored rectangles in the 3D view that indicate the orthogonal planes. To remove these from the display uncheck "Show slice edge in 3D."

Volume Rendering

If you have issues rendering volumes, try changing the default rendering to "VTK CPU Ray Casting"

Installing Extensions

Extensions are customized modules to handle specialized tasks. For the Slicer exercises, we will use the following extensions

• segEditExtraFX

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• LungCTAnalyzer

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• TotalSegmentator

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• HDBrainExtraction

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• PyTorch

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You add extensions as follows

1. Click on the Extension Manager toolbar button to bring up the Manager.
2. On the Side bar, Select a Category, like "Segmentation"
3. Find Extension of interest, like "segEditExtraFX"
4. Click the Install Button
5. Repeat
6. When you are finished installing extensions, restart Slicer.

Pro-Tip: If the extension manager isn't working

Try Clicking on the "Check for Updates" button and then on "Try again", and see if that fixes things.