Difference between revisions of "Documentation/4.3/Training"

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*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 the software.
 +
*Based on: 3D Slicer version 4.0
 
|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.
 
*Author: Sonia Pujol, Ph.D.
 
*Audience: First time users who want to discover Slicer in 4 minutes.
 
*Audience: First time users who want to discover Slicer in 4 minutes.
 +
*Based on: 3D Slicer version 4.0
 
*The [[media:Slicer4minute.zip|Slicer4Minute dataset]] contains an MR scan of the brain and 3D reconstructions of the anatomy
 
*The [[media:Slicer4minute.zip|Slicer4Minute dataset]] contains an MR scan of the brain and 3D reconstructions of the anatomy
 
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*Author: Sonia Pujol, Ph.D.
 
*Author: Sonia Pujol, Ph.D.
 
*Audience: End-users
 
*Audience: End-users
 +
*Based on: 3D Slicer version 4.1
 
*The [[Media:3DVisualizationData.zip | 3DVisualization dataset]] contain an MR scan and a series of 3D models of the brain.
 
*The [[Media:3DVisualizationData.zip | 3DVisualization dataset]] contain an MR scan and a series of 3D models of the brain.
 
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*The [[Media:Slicer4_ProgrammingTutorial_SPujol-SPieper.pdf | Hello Python Programming tutorial]] course guides through the integration of a python module in Slicer4.  
 
*The [[Media:Slicer4_ProgrammingTutorial_SPujol-SPieper.pdf | Hello Python Programming tutorial]] course guides through the integration of a python module in Slicer4.  
 
*Author: Sonia Pujol, Ph.D., Steve Pieper, Ph.D.
 
*Author: Sonia Pujol, Ph.D., Steve Pieper, Ph.D.
−
*Audience: Developers
+
*Audience: Developers
 +
*Based on: 3D Slicer version 4.1
 
*The [[Media:HelloPythonSlicer4.zip‎| HelloPython dataset]] contains three Python files and an MR scan of the brain.
 
*The [[Media:HelloPythonSlicer4.zip‎| HelloPython dataset]] contains three Python files and an MR scan of the brain.
 
|align="right"|
 
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*Author: Sonia Pujol, Ph.D.
 
*Author: Sonia Pujol, Ph.D.
 
*Audience: End-users and developers
 
*Audience: End-users and developers
 +
*Based on: 3D Slicer version 4.1
 
*The [[Media:DiffusionMRI_tutorialData.zip |DTI dataset]] contains an MR Diffusion Weighted Imaging scan of the brain.
 
*The [[Media:DiffusionMRI_tutorialData.zip |DTI dataset]] contains an MR Diffusion Weighted Imaging scan of the brain.
 
|align="right"|
 
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*The [[Media:NeurosurgicalPlanning_SoniaPujol.pdf | Neurosurgical Planning tutorial]] course guides through the generation of fiber tracts in the vicinity of a tumor.
 
*The [[Media:NeurosurgicalPlanning_SoniaPujol.pdf | 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.
 
*Author: Sonia Pujol, Ph.D., Ron Kikinis, M.D.
−
*Audience: End-users and developers
+
*Audience: End-users and developers
 +
*Based on: 3D Slicer version 4.1
 
*The [[Media:WhiteMatterExplorationData.zip| White Matter Exploration datasets]] contains a Diffusion Weighted Imaging scan of  brain tumor patient.
 
*The [[Media:WhiteMatterExplorationData.zip| White Matter Exploration datasets]] contains a Diffusion Weighted Imaging scan of  brain tumor patient.
 
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*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:3DVisualizationDICOMforRadiologyApplications_SoniaPujol_KittShaffer_RSNA2011.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.
 +
*Based on: 3D Slicer version 4.0
 
*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: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.
 
|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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*The [[media:Slicer4QuantitativeImaging.pdf| 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.
 
*The [[media:Slicer4QuantitativeImaging.pdf| 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.
 
*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.
+
*Audience: Radiologists and users of Slicer who need a more comprehensive overview over Slicer4 quantitative imaging capabilities.
 +
*Based on: 3D Slicer version 4.0
 
*The [[media:PETCTFusion-TutorialData.zip| PETCTFusion]] and [[media:ChangeTracker2011.zip|Change Tracker]] datasets contain a series of MR, CT and PET data.
 
*The [[media:PETCTFusion-TutorialData.zip| PETCTFusion]] and [[media:ChangeTracker2011.zip|Change Tracker]] datasets contain a series of MR, CT and PET data.
 
|align="right"|
 
|align="right"|
 
[[Image:Slicer4_QuantitativeImaging.png|right|250px|]]
 
[[Image:Slicer4_QuantitativeImaging.png|right|250px|]]
 
|}
 
|}
−
 
  
 
=Summer 2012 Tutorial contest (under construction)=  
 
=Summer 2012 Tutorial contest (under construction)=  

Revision as of 14:50, 6 September 2013

Home < Documentation < 4.3 < Training


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



Introduction: Slicer 4.3 Tutorials

  • This page contains "How to" tutorials with matched sample data sets. They demonstrate how to use the 3D Slicer environment (version 4.3 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 4.3 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.
  • Based on: 3D Slicer version 4.0

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.
  • Based on: 3D Slicer version 4.0
  • The Slicer4Minute dataset contains an MR scan of the brain and 3D reconstructions of the anatomy
Slicer4Minute tutorial

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
  • Based on: 3D Slicer version 4.1
  • The 3DVisualization dataset contain an MR scan and a series of 3D models of the brain.
Slicer4DataLoading tutorial.png

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 4.1
  • The HelloPython dataset contains three Python files and an MR scan of the brain.
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
  • Based on: 3D Slicer version 4.1
  • 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
  • Based on: 3D Slicer version 4.1
  • The White Matter Exploration datasets contains a Diffusion Weighted Imaging scan of brain tumor patient.
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.
  • Based on: 3D Slicer version 4.0
  • 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.
  • Based on: 3D Slicer version 4.0
  • The PETCTFusion and Change Tracker datasets contain a series of MR, CT and PET data.
Slicer4 QuantitativeImaging.png

Summer 2012 Tutorial contest (under construction)

Automatic Left Atrial Scar Segmenter

Qualitative and quantitative comparison of two RT dose distributions

Dose accumulation for adaptive radiation therapy

WebGL Export

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

OpenIGTLink

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
 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:

Team Contributions

See the collection of videos on the Kitware vimeo album.

User Contributions

See the User Contributions Page for more content.

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