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3D Slicer

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3D Slicer is an application used to visualize and analyze medical image datasets like CT scans or MRI dataset. In this course, we will use also use Slicer to segment and render anatomical objects in these datasets.

3D Slicer has a documentation site here.

Useful Slicer Documentation

Interface

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Application Menu

Slicer has four fairly simple menus

Toolbar

The Toolbar provides quick access to commonly used functions.

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Viewers

There are two types of viewers in 3D Slicer

  • 2D Viewers: Display orthogonal cross-sections of the volume data
  • 3D Viewers: Displays 3D Renderings and/or orthogonal slices in 3D space.

In the default view, there are three 2D slice viewers: Red, Yellow, and Green, which typically correspond to, axial, sagittal, and coronal anatomical plane (see The Red, Yellow, and Green Slice viewers shown above) and one 3D viewer which shows anything being rendered in 3D.

Changing the Viewer Layout

You can change the layout of the Slice Viewers using the layout menu in the toolbar:

layout menu

Viewer Controls

You can change what's displayed in the viewers by clicking on the pushpin icon in the top left corner of each 2D viewer to display the following controls:

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2D Slice View Controller Top row

Clicking on the push-pin only reveals the top row of controls:

  • Link - change the settings across all viewers
  • Eye Icon - display the orthogonal slice in the 3D viewer
  • Orientation - select which orthogonal plane to display (e.g. coronal, sagittal, etc.)
  • Background layer - choose the main volume to display in the viewer

The rest of the 2D controllers

To reveal the additional settings, you need to click on the >> icon

For the 2D viewers, you should now see more controls with some pop-up labels - Label - show the segmentation data in the label layer - Foreground - You can overlay to volumes on top of each other. One is set to the foreground layer and one to the background layer - Background - The background layer for the volumes - Opacity - sets the amount of mixed opacity for the foreground and background layers

Modules

The modules contain all of the fine-toothed controls for Slicer.

You set the current module by selecting its name from the Modules menu in the Toolbar:

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Welcome Module

The default module is the welcome module which contains key controls for loading data, customizing slicer, and downloading sample data. It also contains several panels of information about using Slicer.

Welcome Module Main Buttons

  • Add DICOM data - loading DICOM datasets

  • Add Data - load Slicer data

  • Download Sample Data - download and display sample datasets

  • Customize Slicer - Opens Slicer preferences

  • Explore Added Data - Brings up the data module, which shows any data that has been loaded into Slicer

Welcome Module Collapsing Tabs

Each panel (indicated by a black triangle) contains basic information on how to interact with the software

  • The Main Window - information about the interface

  • Loading and Saving - how to load and save stuff

  • Display - Display different types of data (like Volumes versus rendered volumes)

  • Mouse and Keyboard - info about using the mouse

  • Documentation & Tutorials

  • Data Probe: This panel is available in most module interfaces. It contains pixel information when the mouse is hovering over a pixel in one of the 2D viewers