Slicer interface
Contenido
Parts of the interface
This is the interface of 3D Slicer when it's just opened (Figure 1):
- Main menu
- Toolbar
- Modules panel
- 3D visualization
- 2D Display
- Data window
Menú principal
The menu from which the files and all program functions are managed (Figure 2).
It consists of four sections:
*File
(Figure 3)
- Add Data : to load the contents of both files and folders. It allows to open files format 'nrrd' , 'mrml' and 'vtk' among others. Mrml files are files that contain all the elements that make up a scene but contained in a single file; the vtk files are individual solid and the nrrd files are XXXXX files.
- DICOM : to load DICOM format files and communicate with a PACS server.
- Download Sample Data : allows you to download sample files that come with the software, an internet connection is required the first time each file is opened, then stored on the hard disk.
- Save : Save the scene in which you are working or parts of it. All packages can be stored in a single 'mrml' file or in individual files.
Edit
(Figure 4)
- 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)
- Extension Manager : Extension Manager
- Module Panel : to enable or disable the visibility of the module panel
- Python Interactor : open the Python console window
- Toolbars : Select the sections of the taskbar to display
- Layout : changes 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 : check the error log
Help
(Figure 6)
- Keyboard Shortcuts : list of keyboard shortcuts
- Interface Documentation : online, open the Slicer website of the program documentation
- Browse tutorials : online, open the Slicer website for tutorials
- Slicer Publications : online, open the Slicer publications website
- Visual Blog : online, open Slicer's blog
- Report to Bug : sends error log to developers
- About 3D Slicer : opens the program information screen
Toolbar
A selection of some of the most commonly used functions
- Load / Save (Figure 7)
Figure 7: Load / Save </ caption>
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- DATA: allows loading files or folders, is equivalent to the 'Add Data' 'command in the file menu.
- DCM: for loading DICOM files.
- SAVE: save the scene or files with which you are working, it is equivalent to the command Save of the file menu.
- Module Selection
(???)
<figure id="fig:ModuleSelection">
- Magnifier: allows you to search for modules by name
- drop-down: shows all installed modules in Slicer. First it shows the most common ones and then, through lateral drop-downs, it shows the complete list of all available
- last modules: allows to navigate between the last modules used
- previous: to go back in the navigation between modules of the panel of modules
- next: go forward in navigation between module modules
- Favorite Modules
(Figure 8)
Muestra una selección por defecto de los módulos más generales de Slicer, estos son: datos, transformaciones, volúmenes y modelos
- *Layout Selection
(Figure 9)
To change between the different options of visualization of the interface of the program, varying the organization of the windows. Equivalent to the View menu command.
- Mouse Interaction
(Figure 10)
To change the behaviour of the pointer of the mouse. The options are:
- Persistent: the way we want it to be permanent, default is going to be Fiducial
- Ruler: clicking twice on the scene it is possible to measure the distance between the two points indicated
- ROI: delimits a 3D box on the scene, containing a part of the model that interests us to highlight
- Fiducial: to manipulate the scene: rotate, zoom ... (it is the default mode)
- Capture/Restore
(Figure 11)
For capturing images from the screen.
- Crosshair Selection
(Figure 12)
Switch between different reticle options, it is especially used in 2D viewing windows to know the exact position of the mouse cursor.
- Extensions
(Figure 13)
Open the extension manager, it is equivalent to the command in the View menu.
- Sequence browser
(Figure 14)
Controls playback of video streams.
Module Panel
Window showing the active module options. This window can be unzipped from the main window of the program, to gain more screen space.
As its contents vary according to the module that is working at each moment, its parts will be described when explaining each of the modules to be used in this course.
3D Display
Where the reconstruction in three dimensions of the data that has been loaded is shown.
Axes of visualisation
It is important to review the axes according to which objects are oriented in Slicer, these axes are those used traditionally in radiology and are represented in the ???, defined in that order:
- 'R-L' '(Right-Left): corresponds to the sagittal plane
- 'A-S' (Anterior-Posterior): corresponds to the coronal plane
- 'S-I' '(Upper-Lower): corresponds to the axial plane
Display options
In the left part of the menu it shows the three axes of visualization, this serves to re-orient the active 3D view at that moment. Clicking on the initial of the end of the axis passes the 3D view to the selected axis and orientation, which is useful when the 3D view has been manipulated and you want to have it presented again in a known orientation.
The other options, listed by rows, are:
- Row 1
- Center the 3d view on the screen
- Switch between spelling or perspective rendering
- show / hide rules
- Options for glasses and 3D screens
- Row 2
- Zoom in
- Rotate the 3D view horizontally
- Show / Hide Orientation Markings of Representation Axes
- Show FPS
- Row 3
- Zoom out
- Balance the 3D view horizontally
- Graphic window options (axes labels, background, color ...)
Mouse Commands
- Left button
- Right button
Visualización 2D
The three 2D views available, each sub-window is identified by its color: red, yellow and green. By default in each of the windows appears each one of the three different planes of visualization:
- Axial: red
- Sagittal: yellow
- Coronal: green
This assignment of planes to each window can be changed according to the needs of the user, being able to show in these windows representations completely alien to the three planes that have been talked about until now.
Clicking the button with the drawing of thumbtack in the upper left corner of the window displays the menu with the information of the view shown in the window:
- 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
The letter R, Y or G identifies the window, such 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.
Shifting right and left the handle of 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, the letter R appears, in this case, corresponding to the R-L axis; the red window has the letter S, corresponding to the axis S-I and the green one the letter A, corresponding to the axis A-P (see ???). The number that accompanies this letter indicates the position of the image shown along its corresponding axis.
Mouse Commands
Clicking and dragging with:
- Left button
- vertically: change the brightness of the image in all three windows simultaneously
- horizontally: change the saturation of the image in the three windows simultaneously
- Right button
- change the zoom of the window
