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Welcome to the 3D Slicer3.2 User Training 101

This page is under construction The information on this page applies to 3D Slicer version 3. If you are looking for materials about Slicer version 2, please go to the following location.

  • 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 Visualization in Slicer3 SlicerSampleVisualization.tar.gz‎
1.2 EM Segmentation Course

Older materials: EM Pages, 1, 2

Older Materials: 1
EM Segmenter
1.3 Affine and deformable registration in Slicer 3 SlicerSampleRegistration.tgz SlicerRegistration
1.4 Processing of DWI and DTI data in Slicer3 (pdf) (under construction)

Processing of DWI and DTI data in Slicer3 (ppt)
This tutorial takes the trainee through the slicer3 diffusion display and processing options. See here for background info.

Download diffusion MRI data for the tutorial
Glyphs and tracts
1.5 Detecting subtle change in pathology

This tutorial consists of two MR scans of a patient with meningioma. (xcat file) Meningioma Case
1.6 Detecting white matter lesions in lupus

This tutorial consists of five MR scans of patients with lupus.

Lupus-Tutorial-Data Lesion Segmentation
2.1 Plug-ins for Slicer3: Course for Developers

This tutorial is intended for engineers and scientists who want to integrate external programs with Slicer3. Plug-In
2.2 Image Guided Therapy Planning Tutorial

See here for background info. 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. 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

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. See here for more information.

SPL-PNL Brain Atlas Brain Atlas
3.3 SPL Abdominal Atlas

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. See here for more information.

SPL Abdominal Atlas Abdominal Atlas
3.4 Slicer 3 as a Research Tool for Microscopy Data

This tutorial is intended for researchers who wish to utilize Slicer 3 with microscopy data. If you are interested in more microscopy data, you can visit the Cell Centered Database for freely available data sets.

Microscopy Sample Data (90 MB) Astrocyte Visualized in Slicer
3.5 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
  • 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