Latest revision as of 22:12, 22 November 2022

This section is currently out-of-date and may contain errors but is retained for historical reference.

Up-to-date training materials can be found at Documentation/Nightly/Training

1 Introduction: Slicer 4.4 Tutorials
2 General Introduction
3 Tutorials for software developers
- 3.1 Slicer4 Programming Tutorial
- 3.2 Developing and contributing extensions for 3D Slicer
4 Specific functions
5 Summer 2014 Tutorial contest
- 5.1 Cardiac Agatston Tutorial
- 5.2 CMR Toolkit LA workflow
6 Summer 2013 Tutorial contest
7 Summer 2012 Tutorial contest
8 Additional resources
9 External Resources

Introduction: Slicer 4.4 Tutorials

This page contains "How to" tutorials with matched sample data sets. They demonstrate how to use the 3D Slicer environment (version 4.4 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 4.4 documentation page
For questions related to the Slicer4 Compendium, please send an e-mail to Sonia Pujol, Ph.D

Some of these tutorials are based on older releases of 3D Slicer. The concepts are still useful but bear in mind that some interface elements and features will be different in updated versions.

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 the software.
Modules: Welcome to Slicer, Sample Data
Based on: 3D Slicer version 4.0

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.
Modules: Welcome to Slicer, Models
Based on: 3D Slicer version 4.2
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.
Modules: Welcome to Slicer, Sample Data, Models.
Audience: End-users
Based on: 3D Slicer version 4.4
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
Based on: 3D Slicer version 4.4
The HelloPython dataset contains three Python files and an MR scan of the brain.

For additional Python scripts examples, please visit the Script Repository page

Developing and contributing extensions for 3D Slicer

The Developing and contributing extensions for 3D Slicer tutorial is an introduction to the internals of 3D Slicer and the process of contributing a 3D Slicer extension.
Authors: Andrey Fedorov, Jean-Christophe Fillion-Robin, Steve Pieper
Audience: Developers
Based on: 3D Slicer version 4.4

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
Modules: Data, Volumes, DWI to DTI Estimation, Diffusion Tensor Scalar Measurements, Editor, Markups,Tractography Label Map Seeding, Tractography Interactive Seeding
Based on: 3D Slicer Version 4.4.0-2015-05-21 r24272
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: Volumes, Editor, Tractography Label Map Seeding, Tractography Interactive Seeding
Based on: 3D Slicer version 4.3
The White Matter Exploration datasets contains a Diffusion Weighted Imaging scan of brain tumor patient.

Slicer4 3D Visualization of DICOM images for Radiology Applications

The 3D Visualization of DICOM images for Radiology Applications 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., Ron Kikinis, M.D.
Audience: Radiologists and users of Slicer who need a more comprehensive overview over Slicer4 visualization capabilities.
Modules: DICOM, Volumes, Volume Rendering, Models.
Based on: 3D Slicer version 4.3.1_06.29.2014
The 3DVisualizationDICOM_part1 and 3DVisualizationDICOM_part2 datasets 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: Sonia Pujol, Ph.D., Katarzyna Macura, M.D., Ron Kikinis, M.D.
Audience: Radiologists and users of Slicer who need a more comprehensive overview over Slicer4 quantitative imaging capabilities.
Modules: Data, Volumes, Models, Change Tracker, PET Standard Uptake Value Computation
Based on: 3D Slicer version 4.3.1
The Quantitative Imaging dataset contains a series of MR and PET/CT data.

Slicer4 IGT

Slicer IGT tutorials
Authors: Tamas Ungi, M.D, Ph.D., Junichi Tokuda, Ph.D.
Audience: End-users interested in using Slicer for real-time navigated procedures. E.g. navigated needle insertions or other minimally invasive medical procedures.
Modules: SlicerIGT Extension
Based on: Slicer4.3.1-2014.09.14
Data: Slicer-IGT datasets

Slicer4 Non-rigid MR/CT registration for CT-guided liver ablation

Tutorial on non-rigid MR/CT registration for CT-guided liver ablation
Authors: Soichiro Tani, M.D, Atsushi Yamada, Ph.D, Junichi Tokuda, Ph.D, Dominik S. Meier, Ph.D, and Nobuhiko Hata, Ph.D
Audience: End-users interested in using Slicer to fuse pre- and intra-operative images for image-guided interventions.
Modules: N4ITK MRI Bias Correction, Editor, General Registration (BRAINS)
Based on: Slicer 4.4.0-2015-01-26
Data: Pre- and Intra-operative image dataset contains pre-operative MR and intra-operative CT data.

Slicer4 3D Printing

This Slicer 4.3 3D printing tutorial shows how to prepare 3D Slicer data for 3D printing.
Authors: Nabgha Farhat, MSc
Audience: Users and developers interested in 3D printing

Other

Additional (non-curated) videos-based demonstrations using 3D Slicer are accessible on You Tube.

Summer 2014 Tutorial contest

Cardiac Agatston Tutorial

Cardiac Agatston Scoring Tutorial
Authors: Jessica Forbes, Hans Johnson, University of Iowa
Dataset: Cardiac Agatston Scoring Tutorial Dataset

CMR Toolkit LA workflow

CMR Toolkit LA Workflow Tutorial
Authors: Salma Bengali, Josh Cates, University of Utah
Dataset: CMRToolkitLAWorkflow Dataset

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 Tutorial
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

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:

Team Contributions

See the collection of videos on the Kitware vimeo album.

User Contributions

See the User Contributions Page for more content.

YouTube videos about 3D Slicer

3D Slicer YouTube channel

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 *Audience: End-users and developers
 *Modules: Data, Volumes, DWI to DTI Estimation, Diffusion Tensor Scalar Measurements, Editor, Markups,Tractography Label Map Seeding, Tractography Interactive Seeding
-*Based on: 3D Slicer version 4.3
+*Based on: [http://www.na-mic.org/Wiki/index.php/3DSlicer_4.4_r24272 3D Slicer Version 4.4.0-2015-05-21 r24272]
 *The [[Media:DiffusionMRI_tutorialData.zip |DTI dataset]] contains an MR Diffusion Weighted Imaging scan of the brain.
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 [[Image:SlicetIGT.png|right|150px|]]
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-== Slicer4 Non-rigid registration of MR and CT images for CT-guided liver ablation ==
+== Slicer4 Non-rigid MR/CT registration for CT-guided liver ablation ==
 {|width="100%"
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-*link
+*[[Media:NRR-CTgLiverAblation.pdf| Tutorial on non-rigid MR/CT registration for CT-guided liver ablation]]
-*Authors:
+*Authors: Soichiro Tani, M.D, Atsushi Yamada, Ph.D,  Junichi Tokuda, Ph.D, Dominik S. Meier, Ph.D, and Nobuhiko Hata, Ph.D
-*Audience: End-users interested in using Slicer for real-time navigated procedures.
+*Audience: End-users interested in using Slicer to fuse pre- and intra-operative images for image-guided interventions.
-*Modules:
+*Modules: N4ITK MRI Bias Correction, Editor, General Registration (BRAINS)
-*Based on: Slicer version
+*Based on: Slicer 4.4.0-2015-01-26
 *Data: [[Media:NRR-CTgLiverAblation.zip|Pre- and Intra-operative image dataset]] contains pre-operative MR and intra-operative CT data.
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+[[Image:NRR-CTgLiverAblation.png|right|250px|]]
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-*[http://wiki.slicer.org/slicerWiki/images/f/f1/OpenIGTLinkTutorial_Slicer4.1.0_JunichiTokuda_Apr2012.pdf OpenIGTLink]
+*[http://www.slicer.org/w/img_auth.php/f/f1/OpenIGTLinkTutorial_Slicer4.1.0_JunichiTokuda_Apr2012.pdf OpenIGTLink]
 *Authors:  Junichi Tokuda, BWH
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 :Author: Dominik Meier, Ph.D.
 :Audience:  users interested learning/applying Slicer image registration technology
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 |}
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 [http://www.youtube.com/results?search_query=3d+slicer&sm=3 YouTube videos about 3D Slicer]
+[https://www.youtube.com/channel/UC11x1iQ7ydSIFYw4L6wveXg/playlists 3D Slicer YouTube channel]

Difference between revisions of "Documentation/4.4/Training"