Difference between revisions of "Documentation/4.5/Training"

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=Introduction: Slicer {{documentation/version}} Tutorials=
 
=Introduction: Slicer {{documentation/version}} Tutorials=
  
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*This page contains step-by-step tutorials with pre-computed data sets. They demonstrate how to use the 3D Slicer environment (version {{documentation/version}} release) to accomplish certain tasks.
 
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*For tutorials for other versions of Slicer, please visit the [[Training| Slicer training portal]].
 
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*For "reference manual" style documentation, please visit the [[Documentation/{{documentation/version}}|Slicer {{documentation/version}} documentation page]]
 
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*For questions related to the 3D Slicer compendium and the organization of 3D Slicer training events, please send an e-mail to '''[http://www.na-mic.org/Wiki/index.php/User:SPujol Sonia Pujol, Ph.D, Director of Training]'''
 
  
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*The 3D Slicer compendium contains step-by-step tutorials with pre-computed anonymized data sets. The tutorials demonstrate how to use the 3D Slicer platform (version {{documentation/version}} release) to accomplish certain tasks and clinical research workflows.
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{{documentation/banner|text=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.}}
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*For questions related to the 3D Slicer compendium and for the organization of 3D Slicer training events, please contact '''[http://www.na-mic.org/Wiki/index.php/User:SPujol Sonia Pujol, Ph.D, Director of Training]'''
 +
*For tutorials for previous versions of Slicer, please visit the [[Training| 3D Slicer training portal]].
 +
*For "reference manual" style documentation, please visit the [[Documentation/{{documentation/version}}| 3D Slicer {{documentation/version}} documentation page]]
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{{documentation/banner|text=Some of these tutorials are based on previous release versions of 3D Slicer.  The concepts are still useful but bear in mind that some interface elements and features may be different in updated versions.}}
  
 
=General Introduction=
 
=General Introduction=
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{|width="100%"
 
{|width="100%"
 
|
 
|
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*The [http://www.na-mic.org/Wiki/images/7/71/3DDataLoadingandVisualization_SoniaPujol_slicer4.4.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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*The [[Media:3DDataLoadingandVisualization_Slicer4.5_SoniaPujol.pdf | 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.
 
*Author: Sonia Pujol, Ph.D.
 
*Modules: Welcome to Slicer, Sample Data, Models.
 
*Modules: Welcome to Slicer, Sample Data, Models.
 
*Audience: End-users
 
*Audience: End-users
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*Based on: 3D Slicer version 4.4
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*Based on: 3D Slicer version 4.5
 
*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.
 
|align="right"|
 
|align="right"|
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{|width="100%"
 
{|width="100%"
 
|
 
|
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*The [[Media:DiffusionMRIanalysis_Tutorial_Slicer4.5_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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*The [[Media:DiffusionMRIanalysisTutorial_Slicer4.5_SoniaPujol.pdf |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.
 
*Author: Sonia Pujol, Ph.D.
 
*Audience: End-users and developers
 
*Audience: End-users and developers
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*Modules: Data, Volumes, Models, Change Tracker, PET Standard Uptake Value Computation
 
*Modules: Data, Volumes, Models, Change Tracker, PET Standard Uptake Value Computation
 
*Based on: 3D Slicer version 4.5
 
*Based on: 3D Slicer version 4.5
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*The [[media:QuantitaiveImaging.zip‎| Quantitative Imaging dataset]]  contains a series of MR and PET/CT data.
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*The [[media:QuantitativeImaging.zip‎| Quantitative Imaging dataset]]  contains a series of MR and PET/CT data.
 
|align="right"|
 
|align="right"|
 
[[Image:QuantitaiveImaging_tutorial.png|right|250px|]]
 
[[Image:QuantitaiveImaging_tutorial.png|right|250px|]]
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{|width="100%"
 
{|width="100%"
 
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|
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* The [http://www.na-mic.org/Wiki/images/8/8c/RegistrationTutorial_SoniaPujol_UNC2015.pdf Slicer 4 Image registration Tutorial]  shows how to perform intra- and inter-subject registration within Slicer.
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* The [https://www.slicer.org/wiki/File:RegistrationTutorial_3DSlicer4.5_spujol.pdf Registration tutorial]  shows how to perform intra- and inter-subject registration within Slicer.
 
* Authors: Sonia Pujol, Ph.D., Dominik Meier, Ph.D., Ron Kikinis, M.D.
 
* Authors: Sonia Pujol, Ph.D., Dominik Meier, Ph.D., Ron Kikinis, M.D.
 
* Audience: Users and developers interested in image registration
 
* Audience: Users and developers interested in image registration
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See [[Documentation/{{documentation/version}}/Registration/RegistrationLibrary|the Registration Library for worked out registration examples with data]].
 
See [[Documentation/{{documentation/version}}/Registration/RegistrationLibrary|the Registration Library for worked out registration examples with data]].
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== Fast GrowCut ==
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{|width="100%"
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|
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* The [[media:FastGrowCutTutorial.pdf |Fast GrowCut tutorial]]  shows how to perform a segmentation using the Fast GrowCut effect in Slicer.
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* Authors: Hillary Lia
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* Audience: Users interested in segmentation
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|align="right"|[[File:FastGrowCutLogo.png|200px]]
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|}
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== Other ==
 
== Other ==
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=Winter 2016 Tutorial contest=
 
=Winter 2016 Tutorial contest=
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==Subject Hierarchy==
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{|width="100%"
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|
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*The [http://wiki.na-mic.org/Wiki/images/2/27/SubjectHierarchy.TutorialContestWinter2016.pdf Subject Hierarchy] tutorial demonstrates the basic usage and potential of Slicer’s data manager module Subject Hierarchy using a two-timepoint radiotherapy phantom dataset.
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*Author: Csaba Pinter, Queen's University, Canada
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*Dataset:  [http://slicer.kitware.com/midas3/download/item/205404/SlicerRT_WorldCongress_TutorialIGRT_Dataset.zip SlicerRT_WorldCongress_TutorialIGRT_Dataset] The tutorial dataset is a two-timepoint phantom dataset taken from a RANDO head&neck phantom. It contains two studies, the planning one is a DICOM study consisting of a CT grayscale image and radiotherapy data: contours, dose distribution, treatment beams, plan information. The second timepoint consists of a CT NRRD volume and a dose NRRD volume.
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|align="right"|
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[[File:SubjectHierarchyTutorial.png | 200px]].
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|}
  
 
==Fiber Bundle Selection and Scalar Measurements==
 
==Fiber Bundle Selection and Scalar Measurements==
 
{|width="100%"
 
{|width="100%"
 
|
 
|
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*The [http://wiki.na-mic.org/Wiki/index.php/File:FiberBundleSelectionAndScalarMeasurement_TutorialContestWinter2016.pdf Fiber Bundle Selection and Scalar Measurements] tutorial guides through the use of the Diffusion Bundle Selection module and the Fiber Tract Scalar Measurement module for diffusion MRI tractography data analysis.
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*The [[media:FiberBundleSelectionAndScalarMeasurement_TutorialContestWinter2016.pdf | Fiber Bundle Selection and Scalar Measurements]] tutorial guides through the use of the Diffusion Bundle Selection module and the Fiber Tract Scalar Measurement module for diffusion MRI tractography data analysis.
 
*Author: Fan Zhang, University of Sydney Australia, Brigham and Women's Hospital
 
*Author: Fan Zhang, University of Sydney Australia, Brigham and Women's Hospital
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*Dataset:  [http://wiki.na-mic.org/Wiki/index.php/File:FiberBundleSelectionAndScalarMeasurement_TutorialContestWinter2016.zip Fiber Bundle Selection And Scalar Measurement Tutorial Dataset]
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*Dataset:  [[media:FiberBundleSelectionAndScalarMeasurement_TutorialContestWinter2016.zip| Fiber Bundle Selection And Scalar Measurement Tutorial Dataset]]
 
|align="right"|
 
|align="right"|
 
[[File:FiberBundleSelectionAndScalarMeasurement_TutorialContestWinter2016_Snapshot.png|200px]]
 
[[File:FiberBundleSelectionAndScalarMeasurement_TutorialContestWinter2016_Snapshot.png|200px]]
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|}
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==Plastimatch ==
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{|width="100%"
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|
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*The [http://www.na-mic.org/Wiki/images/5/5c/Plastimatch_TutorialContestWinter2016.pdf Plastimatch tutorial] guides through registration and wrapping of DICOM and DICOM-RT data using the Plastimatch extension of 3D Slicer.
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*Author: Gregory Sharp, Massachusetts General Hospital
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*Dataset:  [http://www.na-mic.org/Wiki/index.php/File:Plastimatch_TutorialContestWinter2016.zip Plastimatch Tutorial Dataset]
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|align="right"|
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[[File:PlastimatchTutorial_Winter2016Contest.png|200px]]
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|}
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==UKF ==
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{|width="100%"
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|
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*The [http://www.na-mic.org/Wiki/images/3/3e/UKF-Tractography_TutorialContestWinter2016.pdf UKF tutorial] guides through the use of the Unscented Kalman Filter (UKF) tractography module.
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*Author: Pegah Kahali, Brigham and Women's Hopital
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*Dataset:  [http://www.na-mic.org/Wiki/index.php/File:UKF-Tractography_TutorialContestWinter2016.zip UKF tutorial Dataset]
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|align="right"|
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[[File:UKF_Winter2016.png|200px]]
 
|}
 
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*[http://wiki.slicer.org/slicerWiki/images/f/f1/OpenIGTLinkTutorial_Slicer4.1.0_JunichiTokuda_Apr2012.pdf OpenIGTLink]
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*[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"|
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:Author: Dominik Meier, Ph.D.
 
:Author: Dominik Meier, Ph.D.
 
:Audience:  users interested learning/applying Slicer image registration technology
 
:Audience:  users interested learning/applying Slicer image registration technology
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|align="right"|[[Image:RegLib_table.png|250px|link=http://wiki.slicer.org/slicerWiki/index.php/Documentation/{{documentation/version}}/Registration/RegistrationLibrary]]
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|align="right"|[[Image:RegLib_table.png|250px|link=http://wiki.slicer.org/wiki/Documentation/{{documentation/version}}/Registration/RegistrationLibrary]]
 
|}
 
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Latest revision as of 22:15, 22 November 2022

Home < Documentation < 4.5 < 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 4.5 Tutorials

  • The 3D Slicer compendium contains step-by-step tutorials with pre-computed anonymized data sets. The tutorials demonstrate how to use the 3D Slicer platform (version 4.5 release) to accomplish certain tasks and clinical research workflows.
  • For questions related to the 3D Slicer compendium and for the organization of 3D Slicer training events, please contact Sonia Pujol, Ph.D, Director of Training
  • For tutorials for previous versions of Slicer, please visit the 3D Slicer training portal.
  • For "reference manual" style documentation, please visit the 3D Slicer 4.5 documentation page

Some of these tutorials are based on previous release versions of 3D Slicer. The concepts are still useful but bear in mind that some interface elements and features may 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.
  • Modules: Welcome to Slicer, Sample Data
  • Based on: 3D Slicer version 4.5

SlicerWelcome tutorial

Slicer4Minute Tutorial

  • The Slicer4Minute tutorial is a brief introduction to the advanced 3D visualization capabilities of Slicer 4.5.
  • Author: Sonia Pujol, Ph.D.
  • Audience: First time users who want to discover Slicer in 4 minutes.
  • Modules: Welcome to Slicer, Models
  • Based on: 3D Slicer version 4.5
  • The Slicer4Minute dataset contains an MR scan of the brain and 3D models of the head.
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.
  • Modules: Welcome to Slicer, Sample Data, Models.
  • Audience: End-users
  • Based on: 3D Slicer version 4.5
  • 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 4.5
  • The HelloPython dataset contains three Python files and an MR scan of the brain.
HelloPythonTutorial.png

For additional Python scripts examples, please visit the Script Repository page

Developing and contributing extensions for 3D Slicer

Contributing3DSlicerExtension.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
  • Modules: Data, Volumes, DWI to DTI Estimation, Diffusion Tensor Scalar Measurements, Editor, Markups,Tractography Label Map Seeding, Tractography Interactive Seeding
  • Based on: 3D Slicer version 4.5
  • 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: Volumes, Editor, Tractography Label Map Seeding, Tractography Interactive Seeding
  • Based on: 3D Slicer version 4.5
  • 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 3D Visualization of DICOM images for Radiology Applications course guides through 3D data loading and visualization of DICOM images for Radiology Applications in Slicer4.5.
  • Author: Sonia Pujol, Ph.D., Kitt Shaffer, M.D., Ph.D., Ron Kikinis, M.D.
  • Audience: Radiologists and users of Slicer who need a more comprehensive overview over Slicer4 visualization capabilities.
  • Modules: DICOM, Volumes, Volume Rendering, Models.
  • Based on: 3D Slicer version 4.5
  • The 3DVisualizationDICOM_part1 and 3DVisualizationDICOM_part2 datasets 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: Sonia Pujol, Ph.D., Katarzyna Macura, M.D., Ron Kikinis, M.D.
  • Audience: Radiologists and users of Slicer who need a more comprehensive overview over Slicer4 quantitative imaging capabilities.
  • Modules: Data, Volumes, Models, Change Tracker, PET Standard Uptake Value Computation
  • Based on: 3D Slicer version 4.5
  • The Quantitative Imaging dataset contains a series of MR and PET/CT data.
QuantitaiveImaging tutorial.png

Slicer4 IGT

  • Slicer IGT tutorials
  • Authors: Tamas Ungi, M.D, Ph.D., Junichi Tokuda, Ph.D.
  • Audience: End-users interested in using Slicer for real-time navigated procedures. E.g. navigated needle insertions or other minimally invasive medical procedures.
  • Modules: SlicerIGT Extension
  • Based on: Slicer4.3.1-2014.09.14
  • Data: Slicer-IGT datasets
SlicetIGT.png

Slicer4 3D Printing

  • This Slicer 4.3 3D printing tutorial shows how to prepare 3D Slicer data for 3D printing.
  • Authors: Nabgha Farhat, MSc
  • Audience: Users and developers interested in 3D printing
 3DPrinting tutorial.png

Slicer4 Image Registration

  • The Registration tutorial shows how to perform intra- and inter-subject registration within Slicer.
  • Authors: Sonia Pujol, Ph.D., Dominik Meier, Ph.D., Ron Kikinis, M.D.
  • Audience: Users and developers interested in image registration
  • Dataset: 3D Slicer Registration Data
 Registration Slicer4.png

See the Registration Library for worked out registration examples with data.

Fast GrowCut

  • The Fast GrowCut tutorial shows how to perform a segmentation using the Fast GrowCut effect in Slicer.
  • Authors: Hillary Lia
  • Audience: Users interested in segmentation
 FastGrowCutLogo.png


Other

Additional (non-curated) videos-based demonstrations using 3D Slicer are accessible on You Tube.

Winter 2016 Tutorial contest

Subject Hierarchy

  • The Subject Hierarchy tutorial demonstrates the basic usage and potential of Slicer’s data manager module Subject Hierarchy using a two-timepoint radiotherapy phantom dataset.
  • Author: Csaba Pinter, Queen's University, Canada
  • Dataset: SlicerRT_WorldCongress_TutorialIGRT_Dataset The tutorial dataset is a two-timepoint phantom dataset taken from a RANDO head&neck phantom. It contains two studies, the planning one is a DICOM study consisting of a CT grayscale image and radiotherapy data: contours, dose distribution, treatment beams, plan information. The second timepoint consists of a CT NRRD volume and a dose NRRD volume.

SubjectHierarchyTutorial.png.

Fiber Bundle Selection and Scalar Measurements

FiberBundleSelectionAndScalarMeasurement TutorialContestWinter2016 Snapshot.png

Plastimatch

PlastimatchTutorial Winter2016Contest.png

UKF

  • The UKF tutorial guides through the use of the Unscented Kalman Filter (UKF) tractography module.
  • Author: Pegah Kahali, Brigham and Women's Hopital
  • Dataset: UKF tutorial Dataset

UKF Winter2016.png

Summer 2014 Tutorial contest

Cardiac Agatston Tutorial

CardiacAgatstonMeasuresModuleScreenshot.jpg

CMR Toolkit LA workflow

Utah SummerContest2014 tutorial.png

Summer 2013 Tutorial contest

Cardiac MRI Toolkit

CMRToolkit Tutorial Image.png

HelloCLI

Cli icon.png

SlicerRT

667px-SlicerRT 0.10 IsocenterShiftingEvaluation.png

DTIPrep

DTIPrep-tutorial.png

Summer 2012 Tutorial contest

Automatic Left Atrial Scar Segmenter

Carma afib auto scar.png

Qualitative and quantitative comparison of two RT dose distributions

PlastimatchDose.png

Dose accumulation for adaptive radiation therapy

  • Tutorial presentation: pptx pdf
  • Dataset: download from MIDAS
  • Authors: Csaba Pinter, Andras Lasso, Queen's

SlicerRT 0.12 DoseVolumeHistogram Ent AllStructures.png

WebGL Export

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

WebGLExport.png

OpenIGTLink

OpenIGTLink.png

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 table.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.

YouTube videos about 3D Slicer

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