Difference between revisions of "Documentation/4.0/Training"

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=Introduction: Slicer 4.0 Tutorials=
 
=Introduction: Slicer 4.0 Tutorials=
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*For "reference manual" style documentation, please visit the [[Documentation/4.0|Slicer 4.0 documentation page]]
 
*For "reference manual" style documentation, please visit the [[Documentation/4.0|Slicer 4.0 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 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]'''
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For information on 3D Slicer version 3.6, see [[Slicer_3.6:Training| the 3.6 Training Pages]].
  
 
=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.
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*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.
 
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|align="right"|
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*The [[media:Slicer4minute-tutorial_SoniaPujol-mj.pdf|Slicer4Minute tutorial]] is a brief introduction to the advanced 3D visualization capabilities of Slicer4.0.
 
*The [[media:Slicer4minute-tutorial_SoniaPujol-mj.pdf|Slicer4Minute tutorial]] is a brief introduction to the advanced 3D visualization capabilities of Slicer4.0.
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*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.
 
*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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[[image:Slicer4minute-image.png|250px|right|Slicer4Minute tutorial]]
 
[[image:Slicer4minute-image.png|250px|right|Slicer4Minute tutorial]]
 
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|}
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==Slicer4 Data Loading and 3D Visualization ==
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*The [[Media:DataLoadingAndVisualizationSlicer4.1_SoniaPujol.pdf | Data loading and 3D visualization]] course guides through the basics of loading and viewing volumes and 3D models in Slicer4 .
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*Author: Sonia Pujol, Ph.D.
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*Audience: End-users
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*The [[Media:3DVisualizationData.zip | 3DVisualization dataset]] contain an MR scan and a series of 3D models of the brain.
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|align="right"|
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[[Image:Slicer4DataLoading_tutorial.png|right|250px|]]
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|}
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=Tutorials for software developers=
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== Slicer4 Programming Tutorial ==
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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.
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*Author: Sonia Pujol, Ph.D., Steve Pieper, Ph.D.
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*Audience: Developers
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*The [[Media:HelloPythonSlicer4.zip‎| HelloPython dataset]] contains three Python files and an MR scan of the brain.
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|align="right"|
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[[Image:HelloPythonTutorial.png|right|250px|]]
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|}
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=Specific functions=
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==Slicer4 Diffusion Tensor Imaging Tutorial ==
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*The [[Media:DiffusionTensorImaging_Slicer4.1_SoniaPujol.pdf | Diffusion Tensor Imaging Tutorial]] course guides through the basics of loading Diffusion Weighted images in Slicer, estimating tensors and generating fiber tracts.
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*Author: Sonia Pujol, Ph.D.
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*Audience: End-users and developers
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*The [[Media:DiffusionMRI_tutorialData.zip |DTI dataset]] contains an MR Diffusion Weighted Imaging scan of the brain.
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|align="right"|
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[[Image:Slicer4DTI Tutorial.png|right|250px|]]
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|}
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==Slicer4 Neurosurgical Planning Tutorial==
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{|width="100%"
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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.
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*Author: Sonia Pujol, Ph.D., Ron Kikinis, M.D.
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*Audience: End-users and developers
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*The [[Media:WhiteMatterExplorationData.zip| White Matter Exploration datasets]] contains a Diffusion Weighted Imaging scan of  brain tumor patient.
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|align="right"|
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[[Image:NeurosurgicalPlanningTutorial.png|right|250px|]]
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|}
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==Slicer4 3D Visualization of DICOM images for Radiology Applications==
 
==Slicer4 3D Visualization of DICOM images for Radiology Applications==
 
{|width="100%"
 
{|width="100%"
 
|
 
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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.  
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*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: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.
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[[Image:Slicer4RSNA_2.png|right|250px|]]
 
[[Image:Slicer4RSNA_2.png|right|250px|]]
 
|}
 
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==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.
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*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 Pohl, 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.
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*The [media:PETCTFusion-TutorialData.zip PETCTFusionData] and [media:ChangeTracker2011.zip] contains a series of MR, CT and PET data.
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*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|]]
 
|}
 
|}
  
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=Specific Functions=
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=Additional resources =
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=Introductions for software developers=
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{|width="100%"
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*This Intro to Slicer4.0 [http://vimeo.com/37671358 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.
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*Audience: First time users interested in a broad overview of Slicer’s features and tools.
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|align="right"|
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[[Image:Webinar.png|250px]]
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|}

Latest revision as of 19:30, 25 April 2014

Home < Documentation < 4.0 < Training


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



Introduction: Slicer 4.0 Tutorials

  • This page contains "How to" tutorials with matched sample data sets. They demonstrate how to use the 3D Slicer environment (version 4.0 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 4.0 documentation page
  • For questions related to the Slicer4 Compendium, please send an e-mail to Sonia Pujol, Ph.D

For information on 3D Slicer version 3.6, see the 3.6 Training Pages.

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.

SlicerWelcome tutorial

Slicer4Minute Tutorial

  • The Slicer4Minute tutorial is a brief introduction to the advanced 3D visualization capabilities of Slicer4.0.
  • 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

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 Pohl, 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

Additional resources

  • This Intro to Slicer4.0 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.

Webinar.png

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