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Welcome to the 3D Slicer3.2 User Training 101

  • The information on this page applies to 3D Slicer version 3.2.
  • Slicer 3 has been designed as
    • an easy-to-use application for 3D image analysis and visualization,
    • an open-source environment for software development,
    • a technology delivery platform for community breakthroughs.
  • Slicer3 is distributed under a BSD open source license, and is designed to enable a collaborative development environment.
  • This page contains training materials and data sets for self-guided training in the use of Slicer3
  • For questions about the materials on this page, please send an e-mail to Sonia Pujol, Ph.D. (spujol at
Slicer Logo
Slicer logo

Software Installation

The Slicer download page contains links for downloading the different versions of Slicer 3.

Training Compendium

Category Tutorial Sample Data Image
1.1 Data Loading and 3D Visualization in Slicer3 SlicerSampleVisualization.tar.gz‎
1.2 Manual segmentation with 3D Slicer OrbitSegmentationt.png
1.3 EM Segmentation Course

Background Materials: EMSegmenter History



EM Segmenter
1.4 Affine and Deformable Registration in Slicer 3 SlicerSampleRegistration.tgz

1.5 Processing of Diffusion Weighted Imaging and Diffusion Tensor Imaging data in Slicer3

Background Materials:DT-MRI module.
Glyphs and tracts
1.6 Detecting subtle change in pathology

This tutorial consists of two MR scans of a patient with meningioma. Meningioma Case
1.7 Detecting white matter lesions in lupus

This tutorial teaches how to use an automated, multi-level method to segment white matter brain lesions in lupus.

Lupus Tutorial Data (.tgz) (.zip)
Lesion Segmentation
1.8 FreeSurfer Course

This tutorial teaches how to visualize FreeSurfer segmentations and parcellation maps of the brain.

FreeSurfer Tutorial Data
FreeSurfer segmentation
2.1 Programming into Slicer3

This tutorial is intended for engineers and scientists who want to integrate stand-alone programs outside of the Slicer3 source tree. Programming
2.2 Image Guided Therapy Planning Tutorial

This tutorial takes the trainee through a complete workup for neurosurgical patient specific mapping.See pages 58 to 80 of this tutorial on using the "Simple region growing" segmentation module.
Background Materials: Neurosurgical Planning. Neurosurgical Planning Overview
3.1 Slicer3 as a research tool for image guided therapy research (IGT)

This tutorial is intended for engineers and scientists who want to use Slicer 3 for IGT research.

Slicer with robots
3.2 SPL-PNL Brain Atlas Tutorial

This three-dimensional brain atlas dataset, derived from a volumetric, whole-head MRI scan, contains the original MRI-scan, a complete set of label maps, three-dimensional reconstructions (200+ structures) and a tutorial.
Background Materials: SPL-PNL Brain Atlas.

SPL-PNL Brain Atlas Brain Atlas
3.3 SPL Abdominal Atlas Tutorial

This three-dimensional abdominal atlas was derived from a computed tomography (CT) scan, using semi-automated image segmentation and three-dimensional reconstruction techniques. The dataset contains the original CT scan, detailed label maps, three-dimensional reconstructions and a tutorial.
Background Materials: SPL Abdominal Atlas.

SPL Abdominal Atlas Abdominal Atlas
3.4 Using XNAT Desktop and Slicer3 for remote data handling

This tutorial is intended for researchers who wish to upload local datasets to a remote XNAT repository like XNAT Central and retrieve catalog files that can be opened inside Slicer.

XNAT Desktop Manager
3.5 Harnessing Grid Computational Resources and integration with Slicer through the Grid Wizard Enterprise system

These tutorials are intended for researchers who wish to utilize distributed computational resources.

Grid Wizard Enterprise GWE OverviewFeatured Study Case (YouTube)
3.6 YouTube Video: Using "GWE's Record Set Explorer"

This tutorial is intended for researchers who wish to interactively review local or remote datasets; such as input values of parameter exploration experiements, their output results, result sets of XNAT queries or any other type of dataset.

(there you can find: binaries, installation guides, source code, other useful documentation and project related information)

RSE browsing through the results of a parameter exploration experiment
  • Category 1 = Basic functionality
  • Category 2 = Advanced functionality
  • Category 3 = Specialized application packages

Additional Materials

For a variety of data sets for downloading, check the following link.
Back to Training:Main