Difference between revisions of "Documentation/4.2/Training"

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<noinclude>{{documentation/historicaltraining}}</noinclude>
 
__TOC__
 
__TOC__
  
  
 
=Introduction: Slicer {{documentation/version}} Tutorials=
 
=Introduction: Slicer {{documentation/version}} Tutorials=
−
 
 
*This page contains "How to" tutorials with matched sample data sets. They demonstrate how to use the 3D Slicer environment (version {{documentation/version}} release) to accomplish certain tasks.  
 
*This page contains "How to" tutorials with matched sample data sets. They demonstrate how to use the 3D Slicer environment (version {{documentation/version}} release) to accomplish certain tasks.  
 
*For tutorials for other versions of Slicer, please visit the [[Training| Slicer training portal]].
 
*For tutorials for other versions of Slicer, please visit the [[Training| Slicer training portal]].
−
*For "reference manual" style documentation, please visit the [[Documentation/{{documentation/version}}|Slicer {{documentation/version}} documentation page]]
+
*For "reference manual" style documentation, please visit the [[Documentation/{{documentation/version}}|Slicer {{documentation/version}} documentation]] page.
−
*For questions related to the Slicer4 Compendium, please send an e-mail to '''[http://www.na-mic.org/Wiki/index.php/User:SPujol Sonia Pujol, Ph.D]'''
+
*For an overview of Slicer and its abilities please see [http://www.slicer.org/publications/item/view/2219 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 '''[http://www.na-mic.org/Wiki/index.php/User:SPujol Sonia Pujol, Ph.D.]'''.
  
 
=General Introduction=
 
=General Introduction=
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*The [[media:SlicerWelcome-tutorial_SoniaPujol.pdf|SlicerWelcome tutorial]] is an introduction to Slicer based on the Welcome module.
 
*The [[media:SlicerWelcome-tutorial_SoniaPujol.pdf|SlicerWelcome tutorial]] is an introduction to Slicer based on the Welcome module.
 
*Author: Sonia Pujol, Ph.D.
 
*Author: Sonia Pujol, Ph.D.
−
*Audience: First time users who want a general introduction to the software.
+
*Audience: First time users who want a general introduction to Slicer.
 
|align="right"|
 
|align="right"|
 
[[image:SlicerWelcome-image.png|250px|SlicerWelcome tutorial]]
 
[[image:SlicerWelcome-image.png|250px|SlicerWelcome tutorial]]
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*Author: Sonia Pujol, Ph.D., Ron Kikinis, M.D.
 
*Author: Sonia Pujol, Ph.D., Ron Kikinis, M.D.
 
*Audience: End-users and developers
 
*Audience: End-users and developers
−
*The [[Media:WhiteMatterExplorationData.zip| White Matter Exploration datasets]] contains a Diffusion Weighted Imaging scan of brain tumor patient.
+
*Modules presented: Main GUI, add data, interactive editor, tractography interactive seeding, tractography display.
 +
*The [[Media:WhiteMatterExplorationData.zip| White Matter Exploration datasets]] contains a single tensor Diffusion Tensor data set of a patient with a brain tumor.
 
|align="right"|
 
|align="right"|
 
[[Image:NeurosurgicalPlanningTutorial.png|right|250px|]]
 
[[Image:NeurosurgicalPlanningTutorial.png|right|250px|]]
 
|}
 
|}
−
 
  
 
==Slicer4 3D Visualization of DICOM images for Radiology Applications==
 
==Slicer4 3D Visualization of DICOM images for Radiology Applications==
 
{|width="100%"
 
{|width="100%"
 
|
 
|
−
*The [[Media:3DVisualizationDICOMforRadiologyApplications_SoniaPujol_KittShaffer_RSNA2011.pdf | Slicer4RSNA]] course guides through 3D data loading and visualization of DICOM images for Radiology Applications in Slicer4.  
+
*The [[Media:3DVisualizationDICOM_RadiologyApplications_SoniaPujol_RSNA2012.pdf | 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.
 
*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.
 
*Audience: Radiologists and users of Slicer who need a more comprehensive overview over Slicer4 visualization capabilities.
−
*The [[Media:3DVisualizationData RSNA2011 part1.zip | Slicer4RSNAdataset1]] and [[Media:3DVisualizationData RSNA2011 part2.zip | Slicer4RSNAdataset2]] contain a series of MR and CT scans, and 3D models of the brain, lung and liver.
+
*The [[Media:3Dvisualization_DICOM_Data-RSNA2012-Part1.zip | Slicer4RSNAdataset1]] and [[Media:3Dvisualization_DICOM_Data-RSNA2012-Part2.zip| Slicer4RSNAdataset2]] contain a series of MR and CT scans, and 3D models of the brain, lung and liver.
 
|align="right"|
 
|align="right"|
 
[[Image:Slicer4RSNA_2.png|right|250px|]]
 
[[Image:Slicer4RSNA_2.png|right|250px|]]
 
|}
 
|}
−
 
  
 
==Slicer4 Quantitative Imaging tutorial==
 
==Slicer4 Quantitative Imaging tutorial==
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[[Image:Slicer4_QuantitativeImaging.png|right|250px|]]
 
[[Image:Slicer4_QuantitativeImaging.png|right|250px|]]
 
|}
 
|}
 +
=Summer 2013 Tutorial contest=
  
 +
==Cardiac MRI Toolkit==
 +
{|width="100%"
 +
|
 +
*[[Media:Cardiac MRI Toolkit Tutorial Summer2013.pdf|Cardiac MRI Toolkit]]
 +
*Authors:  Salma Bengali, Josh Cates, SCI, Utah
 +
*Dataset:  [[Media:Cardiac_MRI_Toolkit_Tutorial_Data.zip|Cardiac MRI Toolkit Tutorial Dataset]]
 +
|align="right"|
 +
[[Image:CMRToolkit_Tutorial_Image.png|250px]]
 +
|}
  
−
=Summer 2012 Tutorial contest (under construction)=  
+
==HelloCLI==
 +
{|width="100%"
 +
|
 +
*[[Media:Hello_CLI_TutorialContestSummer2013.pdf|HelloCLI]]
 +
*Authors:  Nadya Shusharina, Greg Sharp, MGH, Boston
 +
*Dataset:  [[Media:Hello_CLI_TutorialContestSummer2013.zip‎|HelloCLI Dataset]]
 +
|align="right"|
 +
[[Image:Cli_icon.png|300px]]
 +
|}
 +
 
 +
==SlicerRT==
 +
{|width="100%"
 +
|
 +
*[[Media:SlicerRT_TutorialContestSummer2013.pdf|SlicerRT Tutorial]]
 +
*Authors:    Csaba Pinter, Andras Lasso (Queen's), Kevin Wang (PMH, Toronto)
 +
*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=  
  
 
==Automatic Left Atrial Scar Segmenter ==
 
==Automatic Left Atrial Scar Segmenter ==
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*Dataset: [http://wiki.na-mic.org/Wiki/index.php/File:CARMA-LA-Scar_TutorialContestSummer2012.zip CARMA-LA-Scar data]
 
*Dataset: [http://wiki.na-mic.org/Wiki/index.php/File:CARMA-LA-Scar_TutorialContestSummer2012.zip CARMA-LA-Scar data]
 
|align="right"|
 
|align="right"|
 +
[[Image:carma_afib_auto_scar.png|250px]]
 
|}
 
|}
  
−
==Qualitative and quantitative comparison of two RT dose distributions==
+
==Qualitative and quantitative comparison of two RT dose distributions==
 
{|width="100%"
 
{|width="100%"
 
|
 
|
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*Authors:  James Shackleford, Nadya Shusharina, Greg Sharp, MGH
 
*Authors:  James Shackleford, Nadya Shusharina, Greg Sharp, MGH
 
|align="right"|
 
|align="right"|
 +
[[Image:SynteticDoseDistribution.png|250px]]
 
|}
 
|}
  
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*Authors:  Kevin Wang, Csaba Pinter, Andras Lasso, PMH, Queen's
 
*Authors:  Kevin Wang, Csaba Pinter, Andras Lasso, PMH, Queen's
 
|align="right"|
 
|align="right"|
 +
[[Image:Wang-DoseAccumulationforAdaptiveRadiationTherapy TutorialContestSummer2012-fig1.png|250px]]
 
|}
 
|}
  
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*Authors:  Nicolas Rannou, Daniel Haehn, Children's Hospital
 
*Authors:  Nicolas Rannou, Daniel Haehn, Children's Hospital
 
|align="right"|
 
|align="right"|
 +
[[Image:WebdGLExport.png|250px]]
 
|}
 
|}
  
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{|width="100%"
 
{|width="100%"
 
|
 
|
−
*[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
 
*Authors:  Junichi Tokuda, BWH
 
|align="right"|
 
|align="right"|
 +
[[Image:OpenIGTLink-Tracking.png|250px]]
 
|}
 
|}
  
 
=Additional resources =
 
=Additional resources =
 +
 
{|width="100%"
 
{|width="100%"
 +
|
 +
*Title: [https://wiki.cancerimagingarchive.net/display/Public/Hands-on+Tutorial+-+Using+3D+Slicer+with+the+Prostate-Diagnosis+data Visualizing Prostate-Diagnosis images and segmentations] tutorial from [http://cancerimagingarchive.net/about-archive.html  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 [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]]
 +
|-
 
|
 
|
 
* This ''Slicer 4.1 [http://vimeo.com/41096643 webinar]'' presents the new features and improvements of the release, and a brief overview of work for the next release.
 
* This ''Slicer 4.1 [http://vimeo.com/41096643 webinar]'' presents the new features and improvements of the release, and a brief overview of work for the next release.
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|align="right"|[[Image:RegLib Banner.png|250px]]
 
|align="right"|[[Image:RegLib Banner.png|250px]]
 
|}
 
|}
 +
 +
= 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:
 +
 +
* [http://openpaleo.blogspot.com/2008/12/3d-slicer-tutorial.html Open Source Paleontologist: 3D Slicer: The Tutorial]
 +
* [http://openpaleo.blogspot.com/2008/12/3d-slicer-tutorial-part-ii.html Open Source Paleontologist: 3D Slicer: The Tutorial Part II]
 +
* [http://openpaleo.blogspot.com/2008/12/3d-slicer-tutorial-part-iii.html Open Source Paleontologist: 3D Slicer: The Tutorial Part III]
 +
* [http://openpaleo.blogspot.com/2008/12/3d-slicer-tutorial-part-iv.html Open Source Paleontologist: 3D Slicer: The Tutorial Part IV]
 +
* [http://openpaleo.blogspot.com/2009/03/3d-slicer-tutorial-part-v.html Open Source Paleontologist: 3D Slicer: The Tutorial Part V]
 +
* [http://openpaleo.blogspot.com/2009/03/3d-slicer-tutorial-part-vi.html Open Source Paleontologist: 3D Slicer: The Tutorial Part VI]
 +
 +
== User Contributions ==
 +
See the [[Documentation/{{documentation/version}}/Training/UserContributions|User Contributions Page]] for more content.

Latest revision as of 22:13, 22 November 2022

Home < Documentation < 4.2 < Training
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

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.

SlicerWelcome tutorial

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
Slicer4Minute tutorial

Slicer4 Data Loading and 3D Visualization

Slicer4DataLoading tutorial.png

Tutorials for software developers

Slicer4 Programming Tutorial

HelloPythonTutorial.png

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.
Slicer4DTI Tutorial.png

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.
NeurosurgicalPlanningTutorial.png

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.
Slicer4RSNA 2.png

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.
Slicer4 QuantitativeImaging.png

Summer 2013 Tutorial contest

Cardiac MRI Toolkit

CMRToolkit Tutorial Image.png

HelloCLI

Cli icon.png

SlicerRT

667px-SlicerRT 0.10 IsocenterShiftingEvaluation.png

DTIPrep

Summer 2012 Tutorial contest

Automatic Left Atrial Scar Segmenter

Carma afib auto scar.png

Qualitative and quantitative comparison of two RT dose distributions

SynteticDoseDistribution.png

Dose accumulation for adaptive radiation therapy

Wang-DoseAccumulationforAdaptiveRadiationTherapy TutorialContestSummer2012-fig1.png

WebGL Export

  • WebdGLExport
  • Authors: Nicolas Rannou, Daniel Haehn, Children's Hospital

WebdGLExport.png

OpenIGTLink

OpenIGTLink-Tracking.png

Additional resources

NCIA-prostate.png
  • 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
 Webinar-Slicer-4.1.png
  • 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
 Webinar.png
  • 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
 RegLib Banner.png

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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