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`Documentation/4.6/SlicerApplication/MainApplicationGUI - Slicer Wiki
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`https://www.slicer.org./wiki/Documentation/4.6/SlicerApplication/MainApplicationGUI
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`9Weo1eByQUGpPD2jyauqo8
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`PDF REFERENCE #: rsfXXw1s3SGyHqw52JakKB
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`
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`A Page Vault
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`Medivis Exhibit 1016
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`1
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`

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`Document title: Documentation/4.6/SlicerApplication/MainApplicationGUI - Slicer Wiki
`Capture URL: https://www.slicer.org./wiki/Documentation/4.6/SlicerApplication/MainApplicationGUI
`Capture timestamp (UTC): Mon, 15 May 2023 15:15:36 GMT
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`Page 1 of 6
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`& login
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`request account
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`discussion
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`view source
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`history
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`Documentation/4.6/SlicerApplication/MainApplicationGUl
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`Jump to: navigation, search
`
`Home < Documentation < 4.6 < SlicerApplication < MainApplicationGUI
`
`For the latest Slicer documentation, visit the read-the-docs.@
`
`Overview
`
`41 Overview
`
`a
`
`1.1 Application Menu
`
`1.2 Toolbar
`
`1.2.1
`
`.
`Load & Save Options
`
`1.2.2 Module Selection & Navigation
`Bere Ra
`
`1.2.4 Layouts
`
`1.2.5 Mouse Modes
`
`1.2.6 Screenshots & Scene Views
`
`3DSlicer
`
`About slicer
`= Introduction
`» Acknowledgments
`
`=» News
`
`» Contact Us
`
`» Licensing
`=» Commercial Use
`
`Publication
`= Publication DB
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`= Help
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`= Developer FAQ
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`Links
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`a Wiki
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`1.2.7 Crosshair Options
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`Search
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`| Go |
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`Tools
`= What links here
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`» Related changes
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`
`= Printable version
`= Permanent link
`
`= Page information
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`= Cite this page
`
`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
`
`2 User FAQ: User Interface
`
`2.1 How to overlay 2 volumes ?
`
`2.2 How to load data from a sequence of jpg, tif, or png files?
`
`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
`
`= Edit 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.
`
`» The Edit menu contains an option to raise the Application Settings Interface. This interface allows users to customize their installation of Slicer. ‘Edit-
`-
`«a
`’
`:
`moa
`_
`©
`mo
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`Medivis Exhibit 1016
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`2
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`

`

`Document title: Documentation/4.6/SlicerApplication/MainApplicationGUI - Slicer Wiki
`Capture URL: https://www.slicer.org./wiki/Documentation/4.6/SlicerApplication/MainApplicationGUI
`Capture timestamp (UTC): Mon, 15 May 2023 15:15:36 GMT
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`Page 2 of 6
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`EN
`UR Re rt
`An option for saving scenes and data is also provided here.
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`= Edit Menu
`
`Rp se ee
`
`TE PRAE WN
`
`ty pe
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`= 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.
`
`Application Menu
`
`Slicer
`
`Help
`
`View
`Edit
`& Add Data
`& DICOM
`
`#0
`
`3S
`>
`s8W
`
`Application Settings
`& Cut
`
`|
`
`362
`3X
`
`(J Copy
`(1) Paste
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`.
`
`#C
`3eV
`
`Help
`@ Python Interactor
`GJ Extension Manager
`
`¥ Module Panel
`Toolbars
`(B Layout
`
`© Error Log
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`3
`34
`
`#5
`>
`>
`
`#0
`
`EB Download Sample Data
`é Save
`Recently Loaded
`Close Scene
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`=
`
`
`
`Toolbar
`
`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.
`
`Core Modules
`
`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
`
`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.
`
`Layouts
`
`Four-Up Quantitative
`EB Four-Up Tabie
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`Medivis Exhibit 1016
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`3
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`Document title: Documentation/4.6/SlicerApplication/MainApplicationGUI - Slicer Wiki
`Capture URL: https://www.slicer.org./wiki/Documentation/4.6/SlicerApplication/MainApplicationGUI
`Capture timestamp (UTC): Mon, 15 May 2023 15:15:36 GMT
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`Page 3 of 6
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`Mouse Modes
`
`Red slice only
`Yellow slice only
`[5 Green slice only
`[i] Tabbed 3D
`[BH Tabbed slice
`compare
`[El Compare Widescreen
`
`= Compare Grid
`FR Three over three
`HA Three Over Three Quantitative
`FRR Four over four
`EB Two over Two
`[I Side by side
`HB Four by three slice
`HER Four by two slice
`
`HB Tree by three slice
`
`,
`»
`
`>
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`ty
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`Persistent
`
`t, Ruler
`*. ROI
`¢
`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.
`
`Screenshots & Scene Views
`
`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.
`
`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
`
`+H
`
`Navigation
`
`© No crosshair
`
`Basic crosshair
`
`Basic + intersection
`
`Small basic crosshair
`
`Small basic + intersection
`
`©
`
`Fine crosshair
`
`Medium crosshair
`
`Thick crosshair
`
`Slice intersections
`
`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.
`
`Medivis Exhibit 1016
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`4
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`

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`Document title: Documentation/4.6/SlicerApplication/MainApplicationGUI - Slicer Wiki
`Capture URL: https://www.slicer.org./wiki/Documentation/4.6/SlicerApplication/MainApplicationGUI
`Capture timestamp (UTC): Mon, 15 May 2023 15:15:36 GMT
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`Page 4 of 6
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`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.
`
`= 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.
`
`3D Viewer Controller
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`o
`4 ||
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`|e #
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`Options for centering, projection,
`visibility, zoom, 3D viewing, rotation and
`
`Stl]
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`Options for setting viewpoint
`as
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`s
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`-
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`P
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`R
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`L
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`A
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`Slice Viewers
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`
`
`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
`
`View Unique ID
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`wel tee Dele ey
`
`Rt a
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`ert a el)
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`PS
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`
`
`ele Tem
`toe
`Pert tated ned
`Pe need
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`| o
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`
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`Chart Viewers
`
`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.
`
`
`
`
`
`
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`Medivis Exhibit 1016
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`5
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`

`

`Document title: Documentation/4.6/SlicerApplication/MainApplicationGUI - Slicer Wiki
`Capture URL: https://www.slicer.org./wiki/Documentation/4.6/SlicerApplication/MainApplicationGUI
`Capture timestamp (UTC): Mon, 15 May 2023 15:15:36 GMT
`
`Page 5 of 6
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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: Ctri+Left-click & drag down & up
`
`= Mac with trackpad: two-finger click & drag
`
`Pan (Translate) in Slicer & 3D Viewers
`
`= 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
`
`= Windows, Mac & Linux with
`
`= 3-Button Mouse: Left-click & drag
`
`= 2-Button Mouse: Left-click & drag
`
`= 1-Button Mouse: Left-click & drag
`
`User FAQ: User Interface
`
`How to overlay 2 volumes ?
`
`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?
`
`Medivis Exhibit 1016
`
`6
`
`

`

`Document title: Documentation/4.6/SlicerApplication/MainApplicationGUI - Slicer Wiki
`Capture URL: https://www.slicer.org./wiki/Documentation/4.6/SlicerApplication/MainApplicationGUI
`Capture timestamp (UTC): Mon, 15 May 2023 15:15:36 GMT
`
`Page 6 of 6
`
`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: Ctri+Left-click & drag down & up
`
`= Mac with trackpad: two-finger click & drag
`
`Pan (Translate) in Slicer & 3D Viewers
`
`= 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
`
`= Windows, Mac & Linux with
`
`= 3-Button Mouse: Left-click & drag
`
`= 2-Button Mouse: Left-click & drag
`
`= 1-Button Mouse: Left-click & drag
`
`User FAQ: User Interface
`
`How to overlay 2 volumes ?
`
`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?
`
`. Choose from the menu: File / Add Data
`
`. Click Choose File(s) to Add button and select any of the files in the sequence in the displayed dialog
`
`. Click on Show Options and uncheck the Single File option
`
`. Click OK to load the volume
`
`. Go to the Volumes module
`
`. Choose the loaded image as Active Volume
`
`. In the Volume Information section set the correct /mage Spacing and Image Origin values
`
`. 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
`
`ONO nF WN =
`
`Category: Documentation/4.6/SlicerApplication
`
`
`
`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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`Medivis Exhibit 1016
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`7
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