Slicer3 Minute Tutorial
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1 Slicer3 Minute Tutorial Surgical Planning Laboratory Harvard Medical School Sonia Pujol, PhD
2 Slicer3 Minute Tutorial This tutorial is a short introduction to the advanced 3D visualization capabilities of the Slicer3 software for medical image analysis.
3 The Slicer3 Software An end-user application for image analysis An open-source environment for software development A software platform that is both easy to use for clinical researchers and easy to extend for programmers
4 Download the Material Slicer3 is a multi-platform software running on Windows, Linux, and Mac OSX. Download and install the Slicer3.6 software from the Slicer web site Disclaimer It is the responsibility of the user of 3DSlicer to comply with both the terms of the license and with the applicable laws, regulations and rules.
5 Download Slicer3.6 Slicer3 is under active development by the medical research community. Frequent releases incorporating cutting-edge medical image analysis capabilities. This tutorial uses the current Slicer3.6.1 release version.
6 Download Slicer3.6 Select Type of download: Nightly Builds
7 Download Slicer3.6 Select the corresponding release:
8 Download the Material Slicer3 is a multi-platform software running on Windows, Linux, and Mac OSX. Download the training dataset: Slicer3minuteDataset.zip
9 Tutorial Dataset The Slicer3minute dataset is composed of an MR scan of the brain and 3D surface reconstructions of anatomical structures. The data are part of the SPL Brain Atlas developed by Talos et al. The atlas is available at:
10 Start Slicer3 Linux/Mac users Launch the Slicer3executable located in the Slicer3.6 directory Windows users Select Start All Programs Slicer Slicer3
11 Slicer Welcome The SlicerWelcome module is the module displayed by default. This module gives an overview of the GUI of Slicer3, and data loading & saving functionalities.
12 Loading a 3D Scene Select File Load Scene from the File menu
13 Loading a 3D Scene Browse to the location of the Slicer3MinuteDataset directory and select the scene file slicer3minute.mrml , ARR Click on Open to load the scene --
14 Loading a 3D Scene Slicer displays a 3D model of the head in the 3DViewer, and anatomical MR slices of the brain in the 2D Slice Viewer. 3D Viewer 2D Slice Viewer
15 Loading a 3D Scene Left click on the Modules menu and select All Modules to display the list of over 100 modules available for image analysis and 3D visualization.
16 Loading a 3D Scene To access the Models module, browse through the list of modules or click on the icon in the toolbar button.
17 Loading a 3D Scene Slicer displays the GUI of the Models module
18 3D Visualization Position the mouse in the 3D Viewer, hold down the left mouse button and drag to rotate the model.
19 3D Visualization Click on the Slice Visibility icon to display the axial slice in the 3D Viewer
20 3D Visualization Select the Skin model and turn the opacity of the model from 1.0 to 0.0.
21 3D Visualization The model of the skull bone and eyeballs appear in the 3D viewer.
22 3D Visualization Click on the Slice Visibility icon to display the coronal slice in the 3D Viewer
23 3D Visualization Select the 3D model skull_bone in the Model Hierarchy, and select the Clipping option.
24 3D Visualization Browse through the coronal slices to expose the 3D model of the white matter and left and right optic nerves.
25 3D Visualization Select the hemispheric_white_matter model in the Model Hierarchy and turn off its visibility.
26 3D Visualization Slicer displays the optic nerve, optic chiasm and optic tracts overlaid on the MR images of the brain.
27 3D Visualization Windows/Linux users: Position the mouse in the 3D Viewer, hold down the right mouse button and move the mouse down to zoom in. Mac users: Position the mouse in the 3D Viewer, hold down the apple button and the mouse button and move the mouse down to zoom in.
28 3D Visualization Slicer3 displays a closer view of 3D anatomical structures overlaid on 2D MR slices
29 Slicer3 Minute Tutorial Slicer3 is an open-source software for image analysis and 3D visualization Slicer3 core functionalities, 95 available modules and built-in libraries represent more than 2.8 million lines of code Slicer3 is a multi-institution effort to share the latest advances in image analysis with the scientific and clinical community. spujol at bwh.harvard.edu
30 Acknowledgments National Alliance for Medical Image Computing NIH U54EB Neuroimage Analysis Center NIH P41RR013218
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