Application settings

Editing application settings

The application settings dialog allows users to customize application behavior.

After starting Slicer, it can be accessed clicking in menu: Edit / Application Settings.

General

Application startup script can be used to launch any custom Python code when Slicer application is started.

Modules

Skip loading

Select which type of modules to not load at startup. It is also possible to start slicer by temporarily disabling those modules (not saved in settings) by passing the arguments in the command line.

For example, this command will start Slicer without any CLI loaded:

Slicer.exe --disable-cli-modules

Show hidden modules

Some modules don’t have a user interface, they are hidden from the module’s list. For debugging purpose, it is possible to force their display

Temporary directory

Directory where modules can store their temporary outputs if needed.

Additional module paths

List of directories scanned at startup to load additional modules. Any CLI, Loadable or scripted modules located in these paths will be loaded. Extensions are listed in the list, to remove an extension, use the Extensions Manager instead.

It is also possible to start slicer by temporarily adding module paths (not saved in settings) by passing the arguments in the command line.

For example this command will start Slicer trying to load CLIs found in the specified directory:

Slicer.exe --additional-module-paths C:\path\to\lib\Slicer-X.Y\cli-modules

Modules

List of modules loaded, ignored or failed to load in Slicer. An unchecked checkbox indicates that module should not be loaded (ignored) next time Slicer starts. A text color code is used to describe the state of each module:

  • Black: module successfully loaded in Slicer

  • Gray: module not loaded because it has been ignored (unchecked)

  • Red: module failed to load. There are multiple reasons why a module can fail to load.

Look at startup log outputs to have more information. If a module is not loaded in Slicer (ignored or failed), all dependent modules won’t be loaded. You can verify the dependencies of a module in the tooltip of the module.

You can filter the list of modules by untoggling in the advanced (>>) panel the “To Load”, “To Ignore”, “Loaded”, “Ignored” and “Failed” buttons.

Home

Module that is shown when Slicer starts up.

Favorites

List of modules that appear in the Favorites toolbar:

To add a module, drag&drop it from the Modules list above. Then use the advanced panel (>>) to reorganize/delete the modules within the toolbar.

Appearance

Style

The overall theme of Slicer is controlled by the selected Style:

  • Slicer (default): it sets the style based on theme settings set by the operating system. For example, on Windows if [dark mode][(https://blogs.windows.com/windowsexperience/2016/08/08/windows-10-tip-personalize-your-pc-by-enabling-the-dark-theme/)] is turned on for apps, then the Dark Slicer style will be used upon launching Slicer. Currently, automatic detection of dark mode is not available on Linux, therefore use needs to manually select Dark Slicer style for a dark color scheme.

  • Light Slicer: application window background is bright, regardless of operating system settings.

  • Dark Slicer: application window background is dark, regardless of operating system settings.

Information for Advanced Users

Settings file location

Settings are stored in *.ini files. If the settings file is found in application home directory (within organization name or domain subfolder) then that .ini file is used. This can be used for creating a portable application that contains all software and settings in a relocatable folder. Relative paths in settings files are resolved using the application home directory, and therefore are portable along with the application.

If .ini file is not found in the the application home directory then it is searched in user profile:

  • Windows: %USERPROFILE%\AppData\Roaming\NA-MIC\ (typically C:\Users\<your_user_name>\AppData\Roaming\NA-MIC\)

  • Linux: ~/.config/NA-MIC/

  • Mac: ~/.config/www.na-mic.org/

Deleting the *.ini files restores all the settings to default.

There are two types of settings: user specific settings and user and revision specific settings.

User specific settings

This file is named Slicer.ini and it stores settings applying to all versions of Slicer installed by the current user.

To display the exact location of this settings file, open a terminal and type:

./Slicer --settings-path

On Windows:

Slicer.exe --settings-path | more

or enter the following in the Python interactor:

slicer.app.slicerUserSettingsFilePath

User and revision specific settings

This file is named like Slicer-<REVISION>.ini and it stores settings applying to a specific revision of Slicer installed by the current user.

To display the exact location of this settings file, enter the following in the Python interactor:

slicer.app.slicerRevisionUserSettingsFilePath

Application startup file

Each time Slicer starts, it will look up for a startup script file named .slicerrc.py. Content of this file is executed automatically at each startup of Slicer.

The file is searched at multiple location and the first one that is found is used. Searched locations:

  • Application home folder (slicer.app.slicerHome)

  • Path defined in SLICERRC environment variable

  • User profile folder (~/.slicerrc.py)

You can find the path to the startup script in Slicer by opening in the menu: Edit / Application Settings. ‘’Application startup script’’ path is shown in the ‘’General’’ section (or running getSlicerRCFileName() command in Slicer Python console).

Runtime environment variables

The following environment variables can be set before the application is started to fine-tune its behavior:

  • PYTHONNOUSERSITE: if it is set to 1 then import of user site packages is disabled. For example, this will prevent Slicer to reuse packages downloaded/built by Anaconda.

  • QT_SCALE_FACTOR: see Qt documentation. For example, font size can be reduced by running set QT_SCALE_FACTOR=0.5 in the command console and then starting Slicer in that console.

  • QT_ENABLE_HIGHDPI_SCALING: see Qt documentation

  • QT_SCALE_FACTOR_ROUNDING_POLICY: see Qt documentation

  • QTWEBENGINE_REMOTE_DEBUGGING: port number for Qt webengine remote debugger. Default value is 1337.

  • SLICER_OPENGL_PROFILE: Requested OpenGL profile. Valid values are no (no profile), core (core profile), and compatibility (compatibility profile). Default value is compatibility on Windows systems.

  • SLICER_BACKGROUND_THREAD_PRIORITY: Set priority for background processing tasks. On Linux, it may affect the entire process priority. An integer value is expected, default = 20 on Linux and macOS, and -1 on Windows.

  • SLICERRC: Custom application startup file path. Contains a full path to a Python script. By default it is ~/.slicerrc.py (where ~ is the user profile a.k.a user home folder).

  • SLICER_EXTENSIONS_MANAGER_SERVER_URL: URL of the extensions manager backend with the /api path. Default value is retrieved from the settings using the key Extensions/ServerUrl.

  • SLICER_EXTENSIONS_MANAGER_FRONTEND_SERVER_URL: URL of the extension manager frontend displaying the web page. Default value is retrieved from the settings using the key Extensions/FrontendServerUrl.

  • SLICER_EXTENSIONS_MANAGER_SERVER_API: Supported values are Midas_v1 and Girder_v1. Default value is hard-coded to Girder_v1.