Difference between revisions of "Documentation/4.0/Training"

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*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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=Webinars=
 
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==Tuesday, Feb 28, 2012 12:30 PM - 2:00 PM EST==
 
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This course provides an introduction to the open-source 3DSlicer application, designed for first time users who are interested in a
 
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'''broad overview of Slicer’s features and tools'''. The course introduces 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 course is not an exhaustive or in depth review of all the capabilities of Slicer nor a tutorial for developers.
 
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The course is taught by Julien Finet, an R&D Engineer at Kitware. Dr. Steve Pieper, founder of Isomics, and Jean-Christophe Fillion-Robin, an R&D Engineer at Kitware, were in attendance to answer questions during the course.
 
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|align="right"|
 
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[[Image:WebinarSlicer40.png|250px|link=http://vimeo.com/37671358|Introduction to Slicer 4.0]]
 
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=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.
 
*Audience: First time users who want a general introduction to the software.
 
*Audience: First time users who want a general introduction to the software.
 
|align="right"|
 
|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.
 +
*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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{|width="100%"
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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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{|width="100%"
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|
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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]] contain 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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{|width="100%"
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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 the 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]] contain 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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|
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*The [[Media:NeurosurgicalPlanning_SoniaPujol.pdf | Neurosurgical Planning tutorial]] course guides through white matter exploration
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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.  
 +
*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.
 +
*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.
 
*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.
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=Specific Functions=
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=Introductions for software developers=
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=Additional resources =
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{|width="100%"
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|
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*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 course is not an exhaustive or in depth review of all the capabilities of Slicer nor a tutorial for developers.
 +
*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.
 +
|align="right"|
 +
[[Image:WebinarSlicer40.png|250px|link=http://vimeo.com/37671358|Introduction to Slicer 4.0]]
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|}

Revision as of 16:45, 27 March 2012

Home < Documentation < 4.0 < Training


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


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

  • 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 contain 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 the tensors and generating fiber tracts.
  • Author: Sonia Pujol, Ph.D.
  • Audience: End-users and developers
  • The DTI dataset contain 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 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


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 course is not an exhaustive or in depth review of all the capabilities of Slicer nor a tutorial for developers.
  • 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.

Introduction to Slicer 4.0

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