Graphical User Interface (GUI)

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GUI

The acronym GUI stands for Graphical User Interface, and refers to the way the program presents the information it handles to the user; more colloquially, it is defined as the appearance and layout of program windows.

Main components

This is the interface of 3D Slicer when it's just opened (Figure 1):

Figure 1: Interfaz genérica

1. Main menu
2. Toolbar
3. Modules panel
4. 3D visualization
5. 2D Display
6. Data window

Menús

The menu from which the files and all program functions are managed (Figure 2).

Figure 2: Main Menu

It consists of four sections:

File

(Figure 3)

Figure 3: File

• Add Data: to load the contents of both files and folders. It allows you to open files in the format nrrd, mrml and vtk among others. The mrml (Medical Reality Markup Language) files are files that contain all the elements that make up a scene but are contained in a single file; the vtk (Visualization Tool Kit) and nrrd (Nearly Raw Raster Data) files contain multidimensional structures.
• DICOM: to load DICOM format files and communicate with a PACS server.
• Download Sample Data: it allows to download the sample files that come with the software, it is necessary an internet connection the first time that each file is opened, then they are stored on the hard disk.
• Save: Saves the scene in which you are working or parts of it. You can save everything packed in a single file mrml or in individual files.
• Recently Loaded: to open the latest files/scenes that have been worked with
• Close Scene: Close the scene.
• Exit: Exit the program.

Edit

(Figure 4)

Figure 4: Edit

• Application settings : opens the window with the program's customization options
• Cut : Cut selected item to clipboard
• Copy : copies the selected element to the clipboard
• Paste : paste from the clipboard

View

(Figure 5)

Figure 5: View

• Extension Manager: Extension manager
• Module Panel: enable or disable visibility of the module panel
• Python Interactor: Open the Python console window
• Toolbars: select the sections of the taskbar to display
• Layout: change the layout of the different windows of the program
• Reset to default: return to the initial display options
• Home: return to the welcome module
• Error Log: consult the error log

Help

(Figure 6)

Figure 6: Help

• Keyboard Shortcuts: list of keyboard shortcuts
• Interface Documentation: online, opens the Slicer website of the program documentation
• Browse tutorials: online, opens the Slicer tutorials website
• Slicer Publications: online, opens the Slicer Publications website
• Visual Blog: online, open Slicer's blog
• Report a Bug: send error log to developers
• About 3D Slicer: opens the program information screen

Toolbar

On the toolbar, located below the menu, there is a selection for quick access to some of the most frequently used functions in the program:

Load/Save

(Figure 7)

Figure 7: Load/Save

• DATA: DATA: Load files or folders, it is equivalent to the command Add Data of the file menu.
• DCM: for loading DICOM files.
• SAVE: Saves the scene or files in use, it is equivalent to the command' Save of the menu file.

Module Selection

(Figure 8)

Figure 8: Module Selection

• magnifying glass: allows you to search for modules by name
• Dropdown: Displays all modules installed in Slicer. First it shows the most common ones and then, by means of side pull-ups, it shows the complete list of all available ones.
• Last modules: it allows you to navigate between the last modules used
• previous: go backwards in the navigation between modules in the module panel
• next: go back forward in the navigation between modules in the module panel

Favorite Modules

(Figure 9)

Figure 9: Favorite Modules

Displays a default selection of the most general Slicer modules, these are: data, transformations, volumes and models

Layout Selection

(Figure 10)

Figure 10: Layout Selection

Used to switch between the different display options of the program interface, changing the window layout. Equivalent to the View menu command.

Mouse Interaction

(Figure 11)

Figure 11: Mouse Interaction

Used to change the behavior of the mouse pointer. The options are:

• Personalized: the way we want it to be permanent, by default it will be Fiducial
• Ruler: by means of two clicks on the scene it is possible to measure the distance between the two marked points.
• ROI: delimit a 3D box on the scene, containing a part of the model that we want to highlight
• Fiducial: to manipulate the scene: rotate, zoom in... (it's the default mode)

Capture/Restore

(Figure 12)

Figure 12: Capture/Restore

Used for capturing screen images.

Crosshair Selection

(Figure 13)

Figure 13: Crosshair Selection

Switches between the different reticle/crosshair options, used especially in 2D display windows to know the exact position of the mouse cursor.

Extensions

(Figure 14)

Figure 14: Extensions

Opens the extensions manager, it is equivalent to the View menu command.

Sequence browser

(Figure 15)

Figure 15: Sequence browser

Video stream playback controls.

Module panel

Window in which the options of the active module are shown. This window can be de-anchored from the main program window to gain more screen space. The selection of the module to be worked with is done from the drop-down panel of the toolbar (); this panel shows first a list of the most relevant modules and then the complete list of all the modules installed in our version of Slicer 3D.

Figure 16: Modules list

As the content of this panel varies according to the module being worked on at any given time, its parts will be described when explaining each of the modules to be used in this course.

Data Probe

Located at the bottom of the module panel, it is always visible regardless of the selected module. Shows spatial information about the position of the mouse pointer when it is over one of the 2D display windows:

Figure 17: Data Probe

Axes of visualisation

It is important to review the axes according to which the objects are oriented in Slicer, these axes are the ones traditionally used in radiology and are those represented in the , defined in that order:

Figure 18: Ejes

• R-L (Right-Left): corresponds to the sagittal plane.
• A-P (Anterior-Posterior): corresponding to the coronal plane.
• S-I (Superior-Inferior): corresponding to the axial plane

Data Probe window information

In the case of the image, the mouse pointer was located on the red 2D window, on a pixel defined by the RAS coordinates, these are established while the patient is standing and looking at the observer:

• R 49.3: on the axis from left to right of the patient
• P 35.2: on the axis from front to rear of the patient
• I 35.0: on the axis from top to bottom of the patient

The letter designating the axis indicates in which direction the coordinates grow.

To the right of this first line of text indicates what flat is showing in the window, and the spaced between the sections of the same; this will come determined by the file of data with which was working .

The other three lines give information, if there is it, on the label (L*abel), first plane (*F*oreground) and bottom (*B*ackground); if there is not information for this field, will show the indication *None, in contrary case will show the name of the volume and the coordinates *IJK of the pixel on which is situated the mouse together with the value of the tone of grey corresponding.

The IJK coordinates refer to the specific section and not to the set of sections, they will be discussed later.

3D Visualization

Where the three-dimensional reconstruction of the loaded data is shown.

Figure 19: 3D view

Visualization options

Figure 20: Visualization options

On the left side of the menu, it shows the three display axes, this serves to re-orient the currently active 3D view. Clicking on the initial of the end of the axis takes the 3D view to the selected axis and orientation, which is useful when you have been manipulating the 3D view and want to have it presented again in a known orientation.

The other options, listed by rows, are:

• • Row 1
• Center/fit the 3d view on the screen
• Switch between orthographic or perspective rendering
• Show/hide rules
• Options for glasses and 3D screens
  • Row 2
• Increase zoom
• Rotate the 3D view horizontally
• Show/hide the orientation marks of the representation axes
• Mostar FPS
  • Row 3
• Decrease zoom
• Balance the 3D view horizontally
• Graphic options of the window (axis labels, background, color...)

Mouse options

• Left button
  • click and hold: to freely rotate the 3D view on all three axes
• Right button
  • click and hold moving up-down: zoom in or out of the 3D view
  • click and hold moving left-right: no effect

2D Visualisation

The information displayed in these windows will certainly be more familiar to medical professionals used to working with images of anatomical sections resulting from a scanner.

Figure 21: 2D View

Axes of visualisation

In the three 2D views available, each sub-window is identified by its colour: red, yellow and green. By default, each of the three different visualization planes appears in each window:

• Axial: red, corresponds to the S-I axis
• Sagital: yellow, corresponds to the L-R axis
• Coronal: green, A-P axis

These windows can show representations completely alien to the three planes that have been talked about so far.

Figure 22: 2D View_detail

Display options

Clicking on the button with the pinch drawing in the upper left corner of the window opens the menu with the view information shown in the window:

Figure 23: 2D View_menu

• Open / Closed Rings: Links / unlocks the display options between the three 2D windows
• Open / closed eye: shows / hide in the 3D view the corresponding section, which is very useful to know quickly which place of the 3D model we are seeing in this window
• Expanding with the name of the plane being represented
• Expandable with the available volumes in the scene that we have open at that moment in the slicer

Continuing with the top bar of the

• he letter R, Y or G identifies the window as red (R: red), yellow (Y: yellow) or green (G: green).
• The following icon adjusts the image to the entire window, restoring the zoom level if it has changed.
• Moving left and right, the handle on the top bar of the window will show the section corresponding to the representation plane along its axis. At the right end of the upper bar appears, in this case, the letter R, which corresponds to the R-L axis; the red window has the letter S, corresponding to the S-I axis and the green one the letter A, corresponding to the A-P axis (see ). The number that accompanies this letter indicates the position of the image along its axis of the section shown.

Layers

Each 3D visualization window displays 3 layers. clicking on the icon' >> (near the pin) opens the layer menu (see ):

Figure 24: Layers

The layers are as follows:

• FG (foreground): front layer
• BG (background): background layer
• L (Label): layer for the Label map

When a volume is loaded, it is displayed by default in the BG layer; and if a set of labels is loaded, it will be displayed in the L layer.

Mouse options

• Left button
  • click and hold moving up-down: changes the brightness of the image in all three windows simultaneously
  • click and hold moving left-right: changes the saturation of the image in all three windows simultaneously
• Right button
  • click and hold moving up-down: Zooms in or out of sight in 2D
  • click and hold moving left-right: no effect

Progress bar and error logging

Located at the bottom of the bottom of the Slicer 3D window, it will display status messages.

Figure 25: Status Bar

By clicking on the red button in the lower right corner you can access the error log, where the different messages generated by the program since it started are shown:

Figure 26: Error Log

It can be filtered according to:

• Errors
• Warnings
• Messages

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