Latest revision as of 22:13, 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This section is currently out-of-date and may contain errors but is retained for historical reference.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

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 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

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:

User Contributions

See the User Contributions Page for more content.

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-<noinclude>{{documentation/versioncheck}}</noinclude>
+<noinclude>{{documentation/historicaltraining}}</noinclude>
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 {|width="100%"
 |
-*[http://wiki.na-mic.org/Wiki/index.php/CardiacMRIToolkit_TutorialContestSummer2013 Cardiac MRI Toolkit]
+*[[Media:Cardiac MRI Toolkit Tutorial Summer2013.pdf|Cardiac MRI Toolkit]]
 *Authors:   Salma Bengali, Josh Cates, SCI, Utah
-*Dataset:  [http://wiki.na-mic.org/Wiki/index.php/File:Cardiac_MRI_Toolkit_Tutorial_Data.zip Cardiac MRI Toolkit Tutorial Data]
+*Dataset:  [[Media:Cardiac_MRI_Toolkit_Tutorial_Data.zip|Cardiac MRI Toolkit Tutorial Dataset]]
+|align="right"|
+[[Image:CMRToolkit_Tutorial_Image.png|250px]]
+|}
 ==HelloCLI==
 {|width="100%"
 |
-*[http://wiki.na-mic.org/Wiki/index.php/HelloCLI_TutorialContestSummer2013 HelloCLI]
+*[[Media:Hello_CLI_TutorialContestSummer2013.pdf|HelloCLI]]
 *Authors:   Nadya Shusharina, Greg Sharp, MGH, Boston
-*Dataset:  [http://wiki.na-mic.org/Wiki/index.php/File:Hello_CLI_TutorialContestSummer2013.zip HelloCLI Dataset]
+*Dataset:  [[Media:Hello_CLI_TutorialContestSummer2013.zip‎|HelloCLI Dataset]]
+|align="right"|
+[[Image:Cli_icon.png|300px]]
+|}
 ==SlicerRT==
 {|width="100%"
 |
-*[http://wiki.na-mic.org/Wiki/index.php/SlicerRT_TutorialContestSummer2013 SlicerRT]
+*[[Media:SlicerRT_TutorialContestSummer2013.pdf|SlicerRT Tutorial]]
-*Authors:    Csaba Pinter, Andras Lasso(Queen's), Kevin Wang(PMH, Toronto)
+*Authors:    Csaba Pinter, Andras Lasso (Queen's), Kevin Wang (PMH, Toronto)
-*Dataset:  [http://wiki.na-mic.org/Wiki/index.php/File:CsabaPinter-SlicerRtTutorial_Namic2013June.zip SlicerRT Dataset]
+*Dataset:  [[Media:CsabaPinter-SlicerRtTutorial_Namic2013June.zip|SlicerRT Dataset]]
+|align="right"|
+[[Image:667px-SlicerRT_0.10_IsocenterShiftingEvaluation.png|250px]]
+|}
+==DTIPrep==
+{|width="100%"
+|
+*[[Media:DTIPrep_TutorialContestSummer2013.pdf|DTIPrep]]
+*Authors:    Dave Welch, SINAPSE, IOWA
+*Dataset:  [[Media:DTIPrepData_TutorialContestSummer2013.zip|DTIPrep Dataset]]
 =Summer 2012 Tutorial contest=
@@ Line 168: / Line 184: @@
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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
 |align="right"|
@@ Line 181: / Line 197: @@
 * 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 [https://wiki.cancerimagingarchive.net/display/Public/Prostate-Diagnosis 5 subjects from TCIA’s Prostate-Diagnosis image collection].  The [http://www.slicer.org/slicerWiki/index.php/File:ProstateDx-01-0006-1.zip archive] contains both the DICOM images and the NRRD file for one of the 5 available subjects.
+*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 [https://wiki.cancerimagingarchive.net/display/Public/Prostate-Diagnosis 5 subjects from TCIA’s Prostate-Diagnosis image collection].  The [http://www.slicer.org/wiki/File:ProstateDx-01-0006-1.zip archive] contains both the DICOM images and the NRRD file for one of the 5 available subjects.
 |align="right"|[[Image:NCIA-prostate.png|250px]]
 |-

Difference between revisions of "Documentation/4.2/Training"