Documentation/4.2/Training

For the latest Slicer documentation, visit the read-the-docs.

Introduction: Slicer 4.2 Tutorials

• This page contains "How to" tutorials with matched sample data sets. They demonstrate how to use the 3D Slicer environment (version 4.2 release) to accomplish certain tasks.
• For tutorials for other versions of Slicer, please visit the Slicer training portal.
• For "reference manual" style documentation, please visit the Slicer 4.2 documentation page.
• For an overview of Slicer and its abilities please see 3D Slicer as an Image Computing Platform for the Quantitative Imaging Network.
• For questions related to the Slicer4 Compendium, please send an e-mail to Sonia Pujol, Ph.D..

General Introduction

Slicer Welcome Tutorial

The SlicerWelcome tutorial is an introduction to Slicer based on the Welcome module. Author: Sonia Pujol, Ph.D. Audience: First time users who want a general introduction to Slicer.

Slicer4Minute Tutorial

The Slicer4Minute tutorial is a brief introduction to the advanced 3D visualization capabilities of Slicer 4.0. Author: Sonia Pujol, Ph.D. Audience: First time users who want to discover Slicer in 4 minutes. The Slicer4Minute dataset contains an MR scan of the brain and 3D reconstructions of the anatomy

Slicer4 Data Loading and 3D Visualization

The Data loading and 3D visualization course guides through the basics of loading and viewing volumes and 3D models in Slicer4 . Author: Sonia Pujol, Ph.D. Audience: End-users The 3DVisualization dataset contain an MR scan and a series of 3D models of the brain.

Tutorials for software developers

Slicer4 Programming Tutorial

The Hello Python Programming tutorial course guides through the integration of a python module in Slicer4. Author: Sonia Pujol, Ph.D., Steve Pieper, Ph.D. Audience: Developers The HelloPython dataset contains three Python files and an MR scan of the brain.

Specific functions

Slicer4 Diffusion Tensor Imaging Tutorial

The Diffusion Tensor Imaging Tutorial course guides through the basics of loading Diffusion Weighted images in Slicer, estimating tensors and generating fiber tracts. Author: Sonia Pujol, Ph.D. Audience: End-users and developers The DTI dataset contains an MR Diffusion Weighted Imaging scan of the brain.

Slicer4 Neurosurgical Planning Tutorial

The Neurosurgical Planning tutorial course guides through the generation of fiber tracts in the vicinity of a tumor. Author: Sonia Pujol, Ph.D., Ron Kikinis, M.D. Audience: End-users and developers Modules presented: Main GUI, add data, interactive editor, tractography interactive seeding, tractography display. The White Matter Exploration datasets contains a single tensor Diffusion Tensor data set of a patient with a brain tumor.

Slicer4 3D Visualization of DICOM images for Radiology Applications

The Slicer4RSNA course guides through 3D data loading and visualization of DICOM images for Radiology Applications in Slicer4. Author: Sonia Pujol, Ph.D., Kitt Shaffer, M.D., Ph.D. Audience: Radiologists and users of Slicer who need a more comprehensive overview over Slicer4 visualization capabilities. The Slicer4RSNAdataset1 and Slicer4RSNAdataset2 contain a series of MR and CT scans, and 3D models of the brain, lung and liver.

Slicer4 Quantitative Imaging tutorial

The Slicer4 Quantitative Imaging tutorial guides through the use for Slicer for quantifying small volumetric changes in slow-growing tumors, and for calculating Standardized Uptake Value (SUV) from PET/CT data. Authors: Jeffrey Yap, Ph.D., Ron Kikinis, M.D., Randy Gollub, M.D., Ph.D., Wendy Plesniak, Ph.D., Nicole Aucoin, B.Sc., Sonia Pujol, Ph.D., Valerie Humblet, Ph.D., Andriy Fedorov, Ph.D., Kilian Poh, Ph.D., Ender Konugolu, Ph.D. Audience: Radiologists and users of Slicer who need a more comprehensive overview over Slicer4 quantitative imaging capabilities. The PETCTFusion and Change Tracker datasets contain a series of MR, CT and PET data.

Summer 2013 Tutorial contest

Cardiac MRI Toolkit

Cardiac MRI Toolkit Authors: Salma Bengali, Josh Cates, SCI, Utah Dataset: Cardiac MRI Toolkit Tutorial Dataset

HelloCLI

HelloCLI Authors: Nadya Shusharina, Greg Sharp, MGH, Boston Dataset: HelloCLI Dataset SlicerRT SlicerRT Authors: Csaba Pinter, Andras Lasso (Queen's), Kevin Wang (PMH, Toronto) Dataset: SlicerRT Dataset DTIPrep DTIPrep Authors: Dave Welch, SINAPSE, IOWA Dataset: DTIPrep Dataset Summer 2012 Tutorial contest Automatic Left Atrial Scar Segmenter Automatic Left Atrial Scar Segmenter Authors: Greg Gardner, Josh Cates, SCI, Utah Dataset: CARMA-LA-Scar data Qualitative and quantitative comparison of two RT dose distributions Qualitative and quantitative comparison of two RT dose distributions Authors: James Shackleford, Nadya Shusharina, Greg Sharp, MGH Dose accumulation for adaptive radiation therapy Dose accumulation for adaptive radiation therapy Authors: Kevin Wang, Csaba Pinter, Andras Lasso, PMH, Queen's WebGL Export WebdGLExport Authors: Nicolas Rannou, Daniel Haehn, Children's Hospital OpenIGTLink OpenIGTLink Authors: Junichi Tokuda, BWH Additional resources Title: Visualizing Prostate-Diagnosis images and segmentations tutorial from The Cancer Imaging Archive (TCIA). Author: Justin Kirby Audience: Novice 3D Slicer users interested in visualizing prostate segmentations hosted on TCIA. Summary: 3D Slicer was used to generate NRRD segmentations of the following prostate components: prostate gland boundary; internal capsule; central gland, peripheral zone; seminal vesicles; urethra; cancer – dominant nodule; neurovascular bundle; penile bulb; ejaculatory duct; veru-montanum; rectum. These segmentations are currently available for 5 subjects from TCIA’s Prostate-Diagnosis image collection. The archive contains both the DICOM images and the NRRD file for one of the 5 available subjects. This Slicer 4.1 webinar presents the new features and improvements of the release, and a brief overview of work for the next release. Authors: Steve Pieper Ph.D. Audience: First time users and developers interested in Slicer 4.1 new features. Length: 0h20m This Intro to Slicer 4.0 webinar provides an introduction to 3DSlicer, and demonstrates core functionalities such as loading, visualizing and saving data. Basic processing tools, including manual registration, manual segmentation and tractography tools are also highlighted. This webinar is a general overview. For in depth information see the modules above and the documentation pages. Authors: Julien Finet, M.S., Steve Pieper, Ph.D., Jean-Christophe Fillion-Robin, M.S. Audience: First time users interested in a broad overview of Slicer’s features and tools. Length: 1h20m The Slicer Registration Case Library provides many real-life example cases of using the Slicer registration tools. They include the dataset and step-by-step instructions to follow and try yourself. Author: Dominik Meier, Ph.D. Audience: users interested learning/applying Slicer image registration technology External Resources Using the Editor This set of tutorials about the use of slicer in paleontology is very well written and provides step-by-step instructions. Even though it covers slicer version 3.4, many of the concepts and techniques have applicability to the new version and to any 3D imaging field: Open Source Paleontologist: 3D Slicer: The Tutorial Open Source Paleontologist: 3D Slicer: The Tutorial Part II Open Source Paleontologist: 3D Slicer: The Tutorial Part III Open Source Paleontologist: 3D Slicer: The Tutorial Part IV Open Source Paleontologist: 3D Slicer: The Tutorial Part V Open Source Paleontologist: 3D Slicer: The Tutorial Part VI User Contributions See the User Contributions Page for more content.