9/20/22, 12:06 PM
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`Documentation/4.6/SlicerApplication/MainApplicationGUI - Slicer Wiki
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`Documentation/4.6/SlicerApplication/MainApplicationGUI
`
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`Home < Documentation < 4.6 < SlicerApplication < MainApplicationGUI
`
`For the latest Slicer documentation, visit the read-the-docs. (https://slicer.readthedocs.io/en/latest/
`user_guide/getting_started.html)
`
`Overview
`
`Contents
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`1 Overview
`1.1 Application Menu
`■
`1.2 Toolbar
`1.2.1 Load & Save Options
`1.2.2 Module Selection & Navigation
`1.2.3 Core Modules
`1.2.4 Layouts
`1.2.5 Mouse Modes
`1.2.6 Screenshots & Scene Views
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`1.2.7 Crosshair Options
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`1.3 Module Panel
`1.4 Data Probe
`1.5 3D Viewer
`1.6 Slice Viewers
`1.7 Chart Viewers
`1.8 Mouse & Keyboard Across Platforms
`1.8.1 Adjusting Window & Level on All
`Platforms
`1.8.2 Selecting & Manipulating on All
`Platforms
`1.8.3 Viewer Cross-Reference on All
`Platforms
`1.8.4 Zoom In & Out in Slice & 3D
`Viewers
`1.8.5 Pan (Translate) in Slicer & 3D
`Viewers
`1.8.6 Rotate in 3D Viewers
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`2 User FAQ: User Interface
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`2.1 How to overlay 2 volumes ?
`2.2 How to load data from a sequence of jpg,
`tif, or png files?
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`Documentation/4.6/SlicerApplication/MainApplicationGUI - Slicer Wiki
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`Slicer4's main desktop interface provides top-level access to most commonly-used features, and organizes them into logical groupings.
`These groups of features are presented in a number of interface panels on the GUI, as is illustrated in the basic layout below. The
`interface is designed to be easy to learn and remember, to ease navigation of Slicer's large (and growing) functionality, and to easily
`collapse and hide when you don't need to see it.
`Application Menu
`
`Slicer's Application Menu contains many useful features. A brief overview of some of these is given below.
`File Menu
`The File Menu contains options for loading a MRML scene, for downloading sample datasets from the internet, or
`individual datasets of various types. An option for saving scenes and data is also provided here.
`Edit Menu
`The Edit menu contains an option to raise the Application Settings Interface. This interface allows users to customize their
`installation of Slicer. 'Edit->Application Settings can be used to include or suppress various Slicer modules, to customize
`the appearance of your Python Interactor, to select a custom font, to specify a temporary directory, and to accomplish other
`customizations as well.
`View Menu
`This menu contains options to raise the Python Interactor and the Error Log, both useful developer tools. Menu options to
`•
`switch layouts, and to toggle the display of individual toolbars and the module GUI panels are also provided under the View
`Menu.
`
`•
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`Application Menu
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`Slicer File Edit View Help
`ga Add Data
`DICOM
`Download Sample Data
`86 S
`Save
`►
`Recently Loaded
`Close Scene
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`Toolbars
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`Toolbar
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`The Toolbar provides shortcuts to many useful sets of functionality. The following toolbars appear here by default. Customization is
`possible from the Slicer View Menu.
`Load & Save Options
`
`The Load Scene option will raise a browser to select and load a collection of data as a MRML scene. This option clears the existing
`scene and resets the application state. The Save option will raise the "Save Data" Interface which offers a variety of options for saving
`MRML scenes and individual datasets.
`Module Selection & Navigation
`
`The Module Selection & Navigation toolbar provides options for searching for module names, selecting from a module menu, and
`moving backward and forward through the module selection history for convenience.
`
`https://www.slicer.org/wiki/Documentation/4.6/SlicerApplication/MainApplicationGUI
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`Core Modules
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`Documentation/4.6/SlicerApplication/MainApplicationGUI - Slicer Wiki
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`The Core Module Toolbar provides shortcuts to your "Home" module, and some of Slicer's core modules including
`
`Models
`Transforms
`Data
`Volumes
`Annotations
`Interactive Editor
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`Layouts
`
`The Layout Toolbar provides a drop-down menu of layouts useful for many types of studies. When Slicer is exited normally, the
`selected layout is saved and restored as part of the Application state.
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`Layouts
`
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`Four by two slice
`BE Three by three slice
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`Mouse Modes
`
`Persistent
`
`t Ruler
`t , ROI
`t Fiducial
`Slicer has two mouse modes: Transform (which allows interactive rotate, translate and zoom operations), and Place (which permits
`objects to be interactively placed in 3D or 2D). The toolbar icons that switch between these mouse modes are shown from left to right
`above, respectively. Place Fiducial is the default place option as shown above; options to place both Ruler and Region of Interest
`Widgets are also available from the drop-down Place Mode menu. Hint: Transform mode is the default interaction mode. By default,
`Place mode persists for one "place" operation after the Place Mode icon is selected, and then the mode switches back to Transform.
`Place mode can be made persistent (useful for creating multiple fiducial points, rulers, etc.) by checking the Persistent checkbox shown
`rightmost in the Mouse Mode Toolbar.
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`https://www.slicer.org/wiki/Documentation/4.6/SlicerApplication/MainApplicationGUI
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`Screenshots & Scene Views
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`Documentation/4.6/SlicerApplication/MainApplicationGUI - Slicer Wiki
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`This toolbar presents options for capturing screenshots (1st icon) and Scene Views (2nd icon) and restoring saved scene views (3rd
`icon).
`
`A Screenshot can be taken at multiples of the resolution visible on the screen. This allows the taking of higher quality pictures for
`publication. Saving the screenshots is possible in the save menu. At that time the format of the file can be specified. More
`information on saving is in the Load and Save toolbar.
`A Scene View is a description of the state of the MRML scene at the time of its capture that can be restored at any time. This
`mechanism is useful for preparing and viewing multiple interesting presentations of a complicated dataset. More information in
`the Scene Views module.
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`Crosshair Options
`
`The Crosshair Toolbar provides a set of options for customizing the appearance and behavior of the crosshairs across all Slice Viewers.
`
`Crosshair Options
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`B"
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`• No crosshair
`Basc crosshair
`Basic • intersection
`Small basic crosshair
`Small basic • intersection
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`• Fine crosshair
`Median crosshair
`Thick crossbar
`
`Sice intersections
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`Module Panel
`
`Any selected module in Slicer will display its user interface in the Module Panel. The panel may be undocked (by left-clicking &
`dragging the panel chrome or by selecting its undock icon; hidden by selecting the hide (X) icon, or have its display toggled by selecting
`View->Module Panel. The panel can be re-docked by double-clicking on its chrome.
`Data Probe
`
`The Data Probe interactively reports data values at voxels indexed by the current mouse position in all layers (Label, Foreground and
`Background).
`
`See the Data Probe documentation for more information about the data values displayed.
`3D Viewer
`
`Access the 3D Viewer Controller by mousing over the push-pin icon in the top left corner of any 3D Viewer.
`
`The panel may be opened persistently by clicking the push-pin icon which effectively "pins" it open. Clicking again "unpins" the
`panel.
`Next to the push-pin, a unique ID may be found that distinguishes this 3D viewer from other 3D viewers that may have been
`created when other layouts were selected.
`Finally there is a Center the View button to set the virtual camera to show everything that is visible in the viewer at that point.
`
`https://www.slicer.org/wiki/Documentation/4.6/SlicerApplication/MainApplicationGUI
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`Documentation/4.6/SlicerApplication/MainApplicationGUI - Slicer Wiki
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`The panel contains options for setting the viewpoint direction, and configuring the appearance and behavior of any 3D Viewer.
`This includes buttons to set slicer to rock or orbit in the irghtmost column. The eye icon contains controls for visibility of the
`orientation letters and the bounding box in the 3D viewer.
`Depth peeling is a multipass technique to render translucent polygonal geometry without sorting polygons. It can be used to solve
`semi-transparent surface model rendering issues.
`
`30 Viewer Controller
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`Slice Viewers
`
`Access any Slice Viewer's Controller by mousing over its push-pin icon in the top left corner of any slice viewer. The panel may also be
`opened persistently by clicking the push-pin icon. Next to the push-pin a unique ID may be found that distinguishes the particular Slice
`Viewer from other Slice Viewers that may have been created when other layouts were selected. A Slice Scrollbar is provided for
`manually sweeping through slices and a slice number entry widget is also provided at the top right of the display for manually indexing
`a particular slice. Each Slice Viewer contains options for displaying each of the layers (Foreground, Background and Label). For the
`Foreground and Label layers, the opacity of the layer can be controlled by using the spinbox opacity widget (pointed by the "Opacity"
`annotation in the figure below). In addition, the visibility of the Label layer can be toggled between the "contour" and "solid" mode (see
`"Label contour" button in the diagram below).
`
`Some Slice Viewer configuration options may be applied to one or all Slice Viewers by using the Link option. When viewers are
`unlinked, an option applies only to the viewer being adjusted. When viewers are linked, the option will apply to all Slice Viewers. The
`application of an operation or interaction when viewers are linked is propagated to the other viewers only after the interaction with the
`current viewer is complete. For example, zooming within a viewer when the viewers are linked will interactively zoom the current
`viewer and upon completion of the interaction, the effect of the zoom will be propagated to the other viewers. The Hot-Link setting
`modifies this behavior such the effect of an interaction is immediately applied to all viewers. Link and Unlink are persistent settings.
`The linking behavior for Slice Viewer settings and interactions is further describe here.
`
`Slice View Controller
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`https://www.slicer.org/wiki/Documentation/4.6/SlicerApplication/MainApplicationGUI
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`Chart Viewers
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`Documentation/4.6/SlicerApplication/MainApplicationGUI - Slicer Wiki
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`Access any Chart Viewer's Controller by mousing over its push-pin icon in the top left corner of any chart viewer. The panel may also
`be opened persistently by clicking the push-pin icon. Next to the push-pin a unique ID may be found that distinguishes the particular
`Chart Viewer from other Chart Viewers that may have been created when other layouts were selected. Each Chart Viewer contains
`options for controlling the content and display of a Chart.
`
`The content and display of a Chart is controlled by selecting a specific Chart for the Chart Viewer. A Chart Viewer can switch between
`multiple Charts by selecting different Charts from the Scene. The type of the chart can Line, Bar, or Scatter. The style can be modified
`by toggling the display of Lines and Markers for the data or by toggling the display of a Grid or the Legend. The content of the Chart
`can be modified by adding and removing individual Arrays from the Chart. The Chart's Title, X-axis Label, and Y-axis Label can be
`edited using the controls in the Chart Viewer's Controller.
`Mouse & Keyboard Across Platforms
`
`Below is basic information about how to use the three-, two-, and one-button mouse (or trackpad) on Windows, Mac, and Linux
`platforms to perform basic interaction operations in Slicer.
`
`Adjusting Window & Level on All Platforms
`
`Left-clicking and dragging the mouse in any Slice viewer is a quick way to adjust Window and Level. Adjust the middle value (level) of
`the greyscale window by moving the mouse up (increase level) or down (decrease level), and adjust the greyscale window size by
`moving the mouse to the left (decrease window size) or right (increase window size). Slicer's Volumes Module provides a "Display"
`interface panel for making more precise adjustments.
`
`Selecting & Manipulating on All Platforms
`
`Mousing over any "pickable" object in any of Slicer's viewers will cause the cursor to change from a "pointer" into a "picking hand".
`When the cursor shows a picking hand, left-clicking and dragging the mouse will pick and manipulate the object. Releasing the mouse
`button will deselect the object.
`
`Viewer Cross-Reference on All Platforms
`
`Holding down the Shift-Key while moving the mouse in any Slice Viewer will cause other Slice Viewers to interactively scroll to the
`same RAS position indexed by the mouse. This feature is useful when inspecting multiple registered studies.
`
`Zoom In & Out in Slice & 3D Viewers
`
`Windows, Mac & Linux with
`3-Button Mouse: Right-click & drag down & up
`2-Button Mouse: Right-click & drag down & up
`1-Button Mouse: Ctrl+Left-click & drag down & up
`Mac with trackpad: two-finger click & drag
`
`•
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`•
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`Pan (Translate) in Slicer & 3D Viewers
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`•
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`Windows, Mac & Linux with
`3-Button Mouse: Middle-click & drag
`2-Button Mouse: Shift+Left-click & drag
`1-Button Mouse: Shift+Left-click & drag
`Rotate in 3D Viewers
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`•
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`Windows, Mac & Linux with
`3-Button Mouse: Left-click & drag
`2-Button Mouse: Left-click & drag
`1-Button Mouse: Left-click & drag
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`https://www.slicer.org/wiki/Documentation/4.6/SlicerApplication/MainApplicationGUI
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`User FAQ: User Interface
`How to overlay 2 volumes ?
`
`Documentation/4.6/SlicerApplication/MainApplicationGUI - Slicer Wiki
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`1. Load the two volumes
`2. Use the slice viewer controls to select one of the volumes as the foreground and one as the background.
`3. Change the opacity of the Foreground to your liking.
`4. If you click on the link symbol, this happens to all viewers
`How to load data from a sequence of jpg, tif, or png files?
`
`1. Choose from the menu: File / Add Data
`2. Click Choose File(s) to Add button and select any of the files in the sequence in the displayed dialog
`3. Click on Show Options and uncheck the Single File option
`4. Click OK to load the volume
`5. Go to the Volumes module
`6. Choose the loaded image as Active Volume
`7. In the Volume Information section set the correct Image Spacing and Image Origin values
`8. Most modules require grayscale image as input. The loaded color image can be converted to a grayscale image by using the
`Vector to scalar volume module
`
`Retrieved from "https://www.slicer.org/w/index.php?title=Documentation/4.6/SlicerApplication/MainApplicationGUI&oldid=48012"
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`This page was last edited on 7 November 2016, at 08:06.
`Content is available under Creative Commons Attribution-ShareAlike unless otherwise noted.
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