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Home < Slicer3.4:Training

Software Installation

  • The Slicer download page contains information on how to obtain a compiled version of Slicer for a variety of platforms and where to find the source code for Slicer 3.

Software Documentation

  • For the Slicer 3.4 manual pages please click here. These pages are the reference manual for Slicer 3.4 and briefly explain the functionality found in panels and modules.

Older Versions

Slicer 3.4 Tutorials

  • The following table contains "How to" tutorials with matched sample data sets. They demonstrate how to use the 3D Slicer environment ( version 3.4) to accomplish certain tasks.
Category Tutorial Sample Data
Basic Slicer3Minute Tutorial

The Slicer3Minute tutorial is an introduction to the advanced 3D visualization capabilities of Slicer3.4.

Audience: First time users.
Slicer3Minute dataset

The Slicer3Minute dataset contains an MR scan of the brain and 3D reconstructions of the anatomy
Core Slicer3Visualization Tutorial

The Slicer3Visualization tutorial guides through 3D data loading and visualization in Slicer3.4.

Audience: All beginning users including clinicians, scientists, engineers and programmers.
Slicer3Visualization dataset

The Slicer3VisualizationDataset contains two MR scans of the brain, a pre-computed labelmap and 3D reconstructions of the anatomy.
DataLoadingAndVisualization SPujol.png
Core Programming in Slicer3 Tutorial

The Programming in Slicer3 tutorial is an introduction to the the integration of stand-alone programs outside of the Slicer3 source tree.

Audience: Programmers and Engineers.
HelloWorld Plugin

The HelloWorld tutorial dataset contains an MR scan of the brain and pre-computed xml and C++ files for integrating the Hello World plug-in to Slicer3.
Specialized 3D Visualization of FreeSurfer Data

The course guides through 3D visualization of FreeSurfer brain segmentations, surface reconstruction and parcellation results in Slicer3.4.

Audience: All users.
FreeSurfer Tutorial dataset

The FreeSurfer dataset contains an MR scan of the brain and pre-computed FreeSurfer segmentation and cortical surface reconstructions.
Specialized Automatic Segmentation Tutorial

The course guides through the process of using the Expectation-Maximization Segmentation algorithm to automatically segment brain structures from MRI data.

Audience: Programmers and Engineers.
Automatic Segmentation dataset

Specialized Neurosurgical Planning Tutorial

This tutorial takes the trainee through a complete workup for neurosurgical patient-specific mapping. Also see this tutorial for information on how to use Slicer's affine registration, simple region growing, model maker and tractography modules.

Audience: All users interested in image-guided therapy.
Neurosurgical Planning dataset

Specialized Advanced Navigation Tutorial

Illustrates Slicer3's tracking capabilities using a tracking device (the NDI Aurora), and provides an overview of the OpenIGTLink protocol .

Audience: All users interested in using tracking devices.
Advanced Navigation Data

Specialized LEGO IGT and Medical Robotics Tutorial

Provides an overview of all of the main components of image-guided therapy and medical robotics, including imaging, pre-operative planning, targetting by tracking, navigation and registration .

Audience: Users new to image-guided therapy in Slicer3.
LEGO tutorial data


Slicer Tutorial Contest

(under construction)

The following tutorials were part of the Summer 2009 Slicer tutorial contest and Winter 2009 Slicer tutorial contest.

Contest Tutorial Sample Data Image
Summer 2009 Confocal Microscopy Microscopy Confocal Dataset MicroscopyTutorial.png
Summer 2009 ARCTIC: Automatic Regional Cortical ThICkness V2.1 ARCTIC Data Corticalthickness.png
Summer 2009 ‎Trans-rectal MR guided prostate biopsy MR guided prostate biopsy Dataset TransRectalBiopsy.png
Summer 2009 Python Stochastic Tractography Module Stochastic Tractography Data StochasticTractographyTutorial2.png
Summer 2009 White Matter Lesions Segmentation V2.2 Lesion Segmentation Tutorial Data LupusTutorial2.PNG
Winter 2009 IA FEMesh Tutorial Mesh Tutorial Example Data Femesh-in-trunk-120808.png
Winter 2009 Non-Human Primate Segmentation Tutorial Non-Human Primate Segmentation Data Non-HumanPrimateSegmentation.png
Winter 2009 MR Guided Prostate Interventions MR Guided Prostate Interventions Data ProstatePlanningOverview.jpg
Winter 2009 Basic Navigation Tutorial Basic Navigation Data 300px-IGTBasicNavigationSummary.png
Winter 2009 Python Stochastic Tractography Tutorial V1.0 Stochastic Tractography Data StochasticTractographyTutorial2.png
Winter 2009 ARCTIC: Automatic Regional Cortical ThICkness V1.0 ARCTIC Data ArcticLogo.png
Winter 2009 White Matter Lesions Segmentation V2.0 Lesion Segmentation Tutorial Data Lupus3.png
Winter 2009 Segmentation of the Orbit -- OrbitSegmentationt.png