Difference between revisions of "Documentation/Nightly/Training"

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<noinclude>{{documentation/versioncheck}}</noinclude>
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=Introduction: Slicer Tutorials=
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=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 to accomplish certain tasks.
−
*For tutorials for other versions of Slicer, please visit the [[Training| Slicer training portal]].
+
*For "reference manual" style documentation, please see the [https://slicer.readthedocs.io/en/latest/ Slicer manual on ReadTheDocs].
−
*For "reference manual" style documentation, please visit the [[Documentation/{{documentation/version}}|Slicer {{documentation/version}} documentation page]]
+
*For questions related to 3D Slicer training materials and to the organization of 3D Slicer training workshops, please send an e-mail to '''[https://scholar.harvard.edu/soniapujol/home Sonia Pujol, Ph.D., Director of Training and Education of 3D Slicer.]'''
−
*For questions related to the Slicer4 Training Compendium, please send an e-mail to '''[http://www.na-mic.org/Wiki/index.php/User:SPujol Sonia Pujol, Ph.D., Director of Training of 3D Slicer.]'''
 
  
 +
*Some of these tutorials are based on older releases of 3D Slicer and are being upgraded to Slicer 5.0. The concepts are still useful but some interface elements and features may be different in updated versions. For tutorials for older versions of Slicer, please visit the [[Training| Slicer training portal]].
  
−
* 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.
+
__TOC__
  
−
__TOC__
+
=Quick Start Guide=
 +
 
 +
==Downloading and Installing Slicer==
 +
{| width="100%"
 +
|
 +
*The [https://spujol.github.io/3DSlicerQuickStartGuide/ Quick Start Guide] shows how to install and start 3D Slicer
 +
*Author: Sonia Pujol, Ph.D.
 +
*Based on 3D Slicer 5.0 / 4.11
 +
| align="right" |
 +
[[image:QuickStart_image.png|250px|SlicerWelcome tutorial]]
 +
|}
  
 
=General Introduction=
 
=General Introduction=
  
 
==Slicer Welcome Tutorial==
 
==Slicer Welcome Tutorial==
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{|width="100%"
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{| width="100%"
 
|
 
|
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*The [[media:SlicerWelcome-tutorial_Slicer4.5.pdf|SlicerWelcome tutorial]] is an introduction to Slicer based on the Welcome module.
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*The [https://www.dropbox.com/s/vn8sqlof2kag2kk/SlicerWelcome-tutorial_Slicer4.8_SoniaPujol.pdf?dl=0 Slicer Welcome tutorial] is an introduction to Slicer.
 
*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
 
*Modules: Welcome to Slicer, Sample Data
 
*Modules: Welcome to Slicer, Sample Data
−
*Based on: 3D Slicer version 4.6
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*Based on 3D Slicer 4.8
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|align="right"|
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*Compatible with Slicer 4.10.1
 +
| align="right" |
 
[[image:SlicerWelcome-image.png|250px|SlicerWelcome tutorial]]
 
[[image:SlicerWelcome-image.png|250px|SlicerWelcome tutorial]]
 
|}
 
|}
  
 
==Slicer4Minute Tutorial==
 
==Slicer4Minute Tutorial==
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{|width="100%"
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{| width="100%"
 
|
 
|
−
*The [[media:Slicer4.5minute_SoniaPujol.pdf|Slicer4Minute tutorial]]  is a brief introduction to the advanced 3D visualization capabilities of Slicer 4.5.
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*The [https://www.dropbox.com/s/v3lyivwgdoro7yn/Slicer4.10minute_SoniaPujol.pdf?dl=0| Slicer4 Minute Tutorial]  is a brief introduction to the advanced 3D visualization capabilities of Slicer.
 
*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
 
*Modules: Welcome to Slicer, Models
 
*Modules: Welcome to Slicer, Models
−
*Based on: 3D Slicer version 4.5
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*Based on Slicer version 4.8
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*The [[media:Slicer4minute.zip|Slicer4Minute dataset]] contains an MR scan of the brain and 3D reconstructions of the anatomy
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*Compatible with Slicer 4.10.1
−
|align="right"|
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*The [[Media:Slicer4minute.zip|Slicer4Minute dataset]] contains an MR scan of the brain and 3D reconstructions of the anatomy
 +
| align="right" |
 
[[image:Slicer4minute-image.png|250px|right|Slicer4Minute tutorial]]
 
[[image:Slicer4minute-image.png|250px|right|Slicer4Minute tutorial]]
 
|}
 
|}
  
−
==Slicer4 Data Loading and 3D Visualization ==
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=3D Visualization=
−
{|width="100%"
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==Data Loading and 3D Visualization==
 +
{| width="100%"
 
|
 
|
−
*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 .  
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*Slicer 5.0
 +
**The [https://spujol.github.io/SlicerVisualizationTutorial/ Slicer 5.0 Basics of data loading and visualization tutorial] shows how to load and visualize DICOM images and 3D models in 3D Slicer. [https://docs.google.com/presentation/d/12Lbq-QBCxP2p9FkF3_YM5Ng7pItfspMG0FP_20wQglA/edit?usp=sharing French version]
 +
**Author: Sonia Pujol, Ph.D.
 +
**Modules: DICOM, Volume Rendering, Models
 +
**Audience: End-users
 +
**Based on: 3D Slicer version 5.0/4.11
 +
**The [https://www.dropbox.com/s/03emcqnlec4t2s5/3DVisualizationDataset.zip?dl=1 Data Loading and Visualization dataset] contains a thoraco-abdominal CT scan, an MRI brain dataset and 3D models of brain structures.
 +
 
 +
 
 +
*Slicer 4.10
 +
**The [http://slicer.kitware.com/midas3/download/item/356408/20180430_DataLoadingAndVisualizationTutorial.pdf Data loading and visualization] ([http://slicer.kitware.com/midas3/download/item/356409/20180430_DataLoadingAndVisualizationTutorial.pptx pptx]) course guides through the basics of loading and viewing volumes and 3D models in Slicer 4.10.
 +
**Author: Csaba Pinter
 +
**Modules: Welcome to Slicer, Data, Volume Rendering, Models.
 +
**Audience: End-users
 +
**Based on Slicer 4.9
 +
**Compatible with Slicer 4.10.1
 +
**The [http://slicer.kitware.com/midas3/download/?items=330421,1 3DVisualization dataset] contains an MR scan and a series of 3D models of the brain.
 +
 
 +
| align="right" |
 +
[[Image:20180426_DataLoadingAndVisualizationTutorial.png|right|200px|]]
 +
[[Image:Slicer4DataLoading_tutorial.png|right|200px|]]
 +
|}
 +
 
 +
==DICOM==
 +
{| width="100%"
 +
|
 +
*The [https://spujol.github.io/SlicerDICOMTutorial/ DICOM and Slicer] tutorial provides an introduction to the DICOM standard and shows how to load and visualize DICOM datasets in 3D Slicer version 5.0.
 
*Author: Sonia Pujol, Ph.D.
 
*Author: Sonia Pujol, Ph.D.
−
*Modules: Welcome to Slicer, Sample Data, Models.
+
*Modules: DICOM, Volumes
 +
*Based on: 3D Slicer version 5.0/4.11
 +
*The [https://spujol.github.io/SlicerDICOMTutorial/ 3D Slicer DICOM Tutorial Data] contains a torso-CT and a breast MRI.
 +
| align="right" |
 +
[[Image:SlicerAndDICOM.png|right|250px|]]
 +
|}
 +
 
 +
{| width="100%"
 +
|
 +
*The [https://www.dropbox.com/s/8pm5mty2c0zwmyk/3DVisualizationDICOM_Slicer4.10_SoniaPujol.pdf?dl=0 3D Visualization of DICOM images]  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., 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 4.8
 +
*Compatible with 3D Slicer version 4.10
 +
*The [[Media:3DVisualization DICOM images part1.zip| 3DVisualizationDICOM_part1]] and [[Media:3DVisualization DICOM images part2.zip| 3DVisualizationDICOM_part2]] datasets contain a series of MR and CT scans, and 3D models of the brain, lung and liver.
 +
| align="right" |
 +
[[Image:Slicer4RSNA_2.png|right|250px|]]
 +
|}
 +
 
 +
==Open Anatomy Browser==
 +
{| width="100%"
 +
|
 +
[[Image:OABrowser.png|right|250px|]]
 +
 
 +
*The [https://www.dropbox.com/s/f2641iu27hif8p4/OpenAnatomyTutorial_SoniaPujol-MikeHalle.pdf?dl=0 Open Anatomy Browser]  tutorial is an introduction to the OABrowser technology for viewing and interacting with atlases.
 +
*Author: Sonia Pujol, Ph.D., Mike Halle, Ph.D.
 
*Audience: End-users
 
*Audience: End-users
−
*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.
 
−
|align="right"|
 
−
[[Image:Slicer4DataLoading_tutorial.png|right|250px|]]
 
 
|}
 
|}
  
 
=Tutorials for software developers=
 
=Tutorials for software developers=
  
−
== Slicer4 Programming Tutorial ==
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==PerkLab's Slicer bootcamp training materials==
−
{|width="100%"
+
{| width="100%"
 +
|
 +
*The [http://perk.cs.queensu.ca/ Laboratory for Percutaneous Surgery at Queen's University] has made available training material of its internal yearly bootcamp, covering topics, such as 3D Slicer overview, basic visualization, segmentation, registration, scripting and module development, surgical navigation, DICOM, reproducible medical image computing research methodology, version control, and research project management.
 +
**[https://github.com/PerkLab/PerkLabBootcamp/blob/master/Doc/day3_2_SlicerProgramming.pptx?raw=true Scripting and module development tutorial]
 +
**[https://github.com/PerkLab/PerkLabBootcamp/tree/master/Doc All other tutorials]
 +
*Author: Andras Lasso, Csaba Pinter, Tamas Ungi, Csaba Pinter, Matthew Holden, Kyle Sunderland
 +
*Audience: Developers, Users
 +
*Based on: 3D Slicer version 4.10
 +
| align="right" |
 +
[[Image:PerkLabSlicerProgrammingTutorial.png|right|250px|]]
 +
|}
 +
 
 +
==Slicer Programming Tutorial==
 +
{| width="100%"
 
|
 
|
−
*The [https://1drv.ms/b/s!Arm_AFxB9yqHsIUKNqVboYvm4sgd4w Hello Python Programming tutorial] course guides through the integration of a python module in Slicer4.  
+
*The [https://spujol.github.io/SlicerProgrammingTutorial/ Slicer Programming tutorial] guides through the integration of a python module in Slicer. It provides an introduction to the Python Console and the Qt Widget toolkit in 3D Slicer.
 
*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 4.5
+
*Based on: 3D Slicer version 5.0/4.11
−
*The [https://1drv.ms/u/s!Arm_AFxB9yqHsIR2N_9krtTHTsTo1Q HelloPython dataset] contains sample data set (MR scan of the brain) and complete Python module examples.
+
| align="right" |
−
|align="right"|
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[[Image:SlicerProgrammingTutorial.png|right|250px|]]
−
[[Image:HelloPythonTutorial.png|right|250px|]]
 
 
|}
 
|}
  
−
For additional Python scripts examples, please visit the [[Documentation/{{documentation/version}}/ScriptRepository|Script Repository page]]
+
==Slicer script repository==
 +
 
 +
For additional Python scripts examples, please visit the [https://slicer.readthedocs.io/en/latest/developer_guide/script_repository.html Script repository].
  
 
==Developing and contributing extensions for 3D Slicer==
 
==Developing and contributing extensions for 3D Slicer==
−
{|width="100%"
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{| width="100%"
 
|
 
|
−
*The [http://goo.gl/IP4cdg Developing and contributing extensions for 3D Slicer tutorial ] is an introduction to the internals of 3D Slicer and the process of contributing a 3D Slicer extension.
+
*The [http://goo.gl/IP4cdg Developing and contributing extensions for 3D Slicer tutorial] is an introduction to the internals of 3D Slicer and the process of contributing a 3D Slicer extension.
 
*Authors: Andrey Fedorov, Jean-Christophe Fillion-Robin, Steve Pieper
 
*Authors: Andrey Fedorov, Jean-Christophe Fillion-Robin, Steve Pieper
 
*Audience: Developers
 
*Audience: Developers
 
*Based on: 3D Slicer version 4.4
 
*Based on: 3D Slicer version 4.4
−
|align="right"|
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| align="right" |
 
[[Image:Contributing3DSlicerExtension.png|right|250px|]]
 
[[Image:Contributing3DSlicerExtension.png|right|250px|]]
 
|}
 
|}
  
−
=Specific functions=
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=Segmentation=
 +
{| width="100%"
 +
|
 +
*Segmentation for 3D printing: shows how to use the Segment Editor module for combining CAD designed parts with patient-specific models.
 +
**'''[https://discourse.slicer.org/t/new-video-tutorial-for-segment-editor-lumbar-spine-segmentation-for-3d-printing/700 Video tutorial]'''. Author: Hillary Lia.
 +
**'''[[Documentation/{{documentation/version}}/Training#Segmentation_for_3D_printing|Segmentation for 3D printing Step-by-step tutorial]]'''. Author: Csaba Pinter, MSc
 +
**Audience: Users and developers interested in segmentation and 3D printing
 +
**Dataset: [[:File:BasePiece.zip|Phantom base STL model]] Source: [http://perk-software.cs.queensu.ca/plus/doc/nightly/modelcatalog/ PerkLab].
 +
**Based on: 3D Slicer version 4.7
 +
| align="right" |[[Image:20170717_3DPrintingTutorialYoutube.PNG|280px]]
 +
|---
 +
|
 +
*'''[https://www.youtube.com/watch?v=BJoIexIvtGo Video tutorial: Whole heart segmentation from cardiac CT]''' shows how to use the Segment Editor module for segmenting heart ventricles, atria, and great vessels from cardiac CT volumes.
 +
**Author: Andras Lasso, PhD
 +
**Audience: Users who need to segment heart structures, for example for visualization, quantification, or simulation.
 +
**[http://slicer.kitware.com/midas3/download/bitstream/738905/CTA-cardio2.nrrd Sample data set]
 +
**Based on: 3D Slicer version 4.8
 +
| align="right" |[[Image:WholeHeartSegYoutube.png|280px]]
 +
|---
 +
|
 +
*'''[https://www.youtube.com/watch?v=0at15gjk-Ns Video tutorial: Femur and pelvis segmentation from CT]''' shows how to use the Segment Editor module for segmenting pelvis and femur from CT volumes.
 +
**Author: Andras Lasso, PhD
 +
**Audience: Users who need to segment bones in CT images for visualization, quantification, or simulation.
 +
**Sample data set: https://wiki.cancerimagingarchive.net/display/Public/TCGA-PRAD (Subject TCGA-VP-A878)
 +
**Based on: 3D Slicer version 4.8
 +
| align="right" |[[Image:FemurSegmentationYoutube.png|280px]]
 +
|---
 +
|
 +
*'''[https://lassoan.github.io/SlicerSegmentationRecipes/ Slicer Segmentation Recipes]''' provide step-by-step description of useful segmentation techniques.
 +
** Segmentation tutorials for common tasks, such as skin surface extraction, craniotomy (splitting segments), sorta segmentation, cerebral vessel segmentation by subtraction, segmentation on arbitrarily oriented slices, skull stripping.
 +
| align="right" |[[Image:SegmentationRecipes.png|280px]]
 +
|---
 +
|
 +
*'''[https://spujol.github.io/SkullStrippingTutorial/ The Skull Stripping tutorial]''' shows how to perform skull-stripping in CT and MR data.
 +
**Author: Sonia Pujol, PhD, Andras Lasso, PhD, Ron Kikinis, MD
 +
**Audience: Users interested in brain segmentation
 +
**Based on: 3D Slicer version 4.11
 +
| align="right" |[[Image:SkullStripping.png|280px]]
 +
|}
 +
 
 +
 
 +
=Image Phenotyping=
 +
{| width="100%"
 +
|
 +
*Based on: 3D Slicer version 4.10
 +
*The [https://spujol.github.io/ImagePhenotypingTutorial/ Image Phenotyping tutorial] is an introduction to brain tumor segmentation and image phenotyping using the Slicer Radiomics extension.
 +
*Authors: Sonia Pujol, Ph.D.
 +
*Audience: Clinical researchers
 +
*Dataset: [https://www.dropbox.com/s/hdlduw6oqnf2n72/Meningioma.nrrd?dl=0 Meningioma dataset]
 +
| align="right" |[[File:ImagePhenotyping.png|250px]]
 +
 
 +
|}
 +
 
 +
=Registration=
  
−
==Slicer4 Diffusion Tensor Imaging Tutorial ==
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==Slicer4 Image Registration==
−
{|width="100%"
+
 
 +
{| width="100%"
 
|
 
|
−
*The [https://github.com/SlicerDMRI/slicerdmri.github.io/raw/master/docs/tutorials/DiffusionMRIanalysis.pdf Diffusion Tensor Imaging Tutorial] course guides through the basics of loading Diffusion Weighted images in Slicer, estimating tensors and generating fiber tracts.  
+
*The [https://www.dropbox.com/s/chrugp2j2as5gop/ImageRegistration_Slicer4.8_SoniaPujol.pdf?dl=0 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: [[Media:RegistrationData.zip| 3D Slicer Registration Data]]
 +
| align="right" |[[File:registration_Slicer4.png|250px]]
 +
|}
 +
 
 +
*Based on: 3D Slicer version 4.8; Compatible with Slicer 4.10
 +
 
 +
{| width="100%"
 +
|
 +
*The [https://spujol.github.io/3DSlicerTutorial-Registration Brain Tumor Registration] is a video-based tutorial that shows how to register two MRI datasets in a brain tumor case for surgical resection follow-up.
 +
*Authors: Sonia Pujol, Ph.D., Dominik Meier, Ph.D.
 +
*Audience: Users and developers interested in image registration
 +
*Dataset: [[Special:FilePath/RegLib C37 Data.zip| Registration Library Case #37]]
 +
| align="right" |[[File:RigidRegistration.jpg|250px]]
 +
|}
 +
 
 +
*Based on: 3D Slicer version 4.10
 +
 
 +
==Slicer Registration Case Library==
 +
{| width="100%"
 +
|
 +
*The ''[[Documentation/{{documentation/version}}/Registration/RegistrationLibrary|Slicer Registration Case Library]]'' provides real-life example cases of using the Slicer registration tools. They include pre-computed dataset and step-by-step instructions for users to follow.
 +
 
 +
:Author: Dominik Meier, Ph.D.
 +
:Audience:  users interested learning/applying Slicer image registration technology
 +
| align="right" |[[Image:RegLib_table.png|250px|link=https://www.slicer.org/wiki/Documentation/{{documentation/version}}/Registration/RegistrationLibrary]]
 +
|}
 +
 
 +
=Slicer Extensions=
 +
==Slicer4 Diffusion Tensor Imaging Tutorial==
 +
{| width="100%"
 +
|
 +
*The [https://spujol.github.io/SlicerDiffusionMRITutorial Diffusion MRI Tutorial] is an introduction to 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
−
*Modules: Data, Volumes, DWI to DTI Estimation, Diffusion Tensor Scalar Measurements, Editor, Markups,Tractography Label Map Seeding, Tractography Interactive Seeding
+
*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
+
*Based on: 3D Slicer version 4.8; Compatible with Slicer version 4.10.2
−
*The [[media:Dti tutorial data.zip|DTI dataset]] contains an MR Diffusion Weighted Imaging scan of the brain.
+
*The [https://www.dropbox.com/s/gba2zsn276x43up/SlicerDiffusionMRITutorialData.zip?dl=1 Slicer Diffusion MRI Tutorial dataset] contains an MR Diffusion Weighted Imaging scan of the brain.
−
|align="right"|
+
*Please visit [http://dmri.slicer.org/docs/ dmri.slicer.org/docs] for the latest documentation of SlicerDMRI.
 +
| align="right" |
 
[[Image:Slicer4DTI Tutorial.png|right|250px|]]
 
[[Image:Slicer4DTI Tutorial.png|right|250px|]]
 
|}
 
|}
  
 
==Slicer4 Neurosurgical Planning Tutorial==
 
==Slicer4 Neurosurgical Planning Tutorial==
−
{|width="100%"
+
{| width="100%"
 
|
 
|
−
*The [https://github.com/SlicerDMRI/slicerdmri.github.io/raw/master/docs/tutorials/WhiteMatterExplorationTutorial.pdf Neurosurgical Planning tutorial] course guides through the generation of fiber tracts in the vicinity of a tumor.
+
*The [https://spujol.github.io/NeurosurgicalPlanningTutorial/ Neurosurgical Planning tutorial] course guides end-users 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: Clinicians and Clinical Researchers
−
*Modules: Volumes, Editor, Tractography Label Map Seeding, Tractography Interactive Seeding
+
*Modules: Segment Editor, Tractography
−
*Based on: 3D Slicer version 4.5
+
*Based on 3D Slicer version 4.10
−
*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 dataset]] contains a Diffusion Weighted Imaging scan of a brain tumor patient.
−
|align="right"|
+
| align="right" |
 
[[Image:NeurosurgicalPlanningTutorial.png|right|250px|link=http://vimeo.com/67336069]]
 
[[Image:NeurosurgicalPlanningTutorial.png|right|250px|link=http://vimeo.com/67336069]]
−
|}
 
−
 
−
==Slicer4 3D Visualization of DICOM images for Radiology Applications==
 
−
{|width="100%"
 
−
|
 
−
*The [[Media:3DSlicer_Dicom_RSNA2015_SoniaPujol.pdf |3D Visualization of DICOM images for Radiology Applications]]  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., 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 [[Media:3DVisualization_DICOM_images_part1.zip‎  | 3DVisualizationDICOM_part1]] and [[Media:3DVisualization_DICOM_images_part2.zip | 3DVisualizationDICOM_part2]] datasets contain a series of MR and CT scans, and 3D models of the brain, lung and liver.
 
−
|align="right"|
 
−
[[Image:Slicer4RSNA_2.png|right|250px|]]
 
 
|}
 
|}
  
 
==Slicer4 Quantitative Imaging tutorial==
 
==Slicer4 Quantitative Imaging tutorial==
−
{|width="100%"
+
{| width="100%"
 
|
 
|
−
*The [[media:QuantitativeImaging_Slicer4.5.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:QuantitativeImaging Slicer4.5.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: Sonia Pujol, Ph.D., Katarzyna Macura, M.D., Ron Kikinis, M.D.
 
*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.
 
*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
 
*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
−
*The [[media:QuantitativeImaging.zip‎| Quantitative Imaging dataset]]  contains a series of MR and PET/CT data.
+
*The [[Media:QuantitativeImaging.zip| Quantitative Imaging dataset]]  contains a series of MR and PET/CT data.
−
|align="right"|
+
| align="right" |
 
[[Image:Slicer4_QuantitativeImaging.png|right|250px|]]
 
[[Image:Slicer4_QuantitativeImaging.png|right|250px|]]
 
|}
 
|}
  
−
== Slicer4 IGT ==
+
==Slicer4 IGT==
−
{|width="100%"
+
{| width="100%"
 
|
 
|
 
*[http://www.slicerigt.org/wp/user-tutorial/ Slicer IGT tutorials]
 
*[http://www.slicerigt.org/wp/user-tutorial/ Slicer IGT tutorials]
Line 141: Line 292:
 
*Modules: SlicerIGT Extension
 
*Modules: SlicerIGT Extension
 
*Based on: Slicer4.3.1-2014.09.14
 
*Based on: Slicer4.3.1-2014.09.14
−
*Data: [https://onedrive.live.com/redir?resid=7230D4DEC6058018!2937&authkey=!AGQkSCZOwjVYXw8&ithint=folder%2cpptx Slicer-IGT datasets]
+
*Data: [https://onedrive.live.com/redir?resid=7230D4DEC6058018!2937&authkey=!AGQkSCZOwjVYXw8&ithint=folder%2cpptx Slicer-IGT datasets]
−
|align="right"|
+
| align="right" |
 
[[Image:SlicetIGT.png|right|150px|]]
 
[[Image:SlicetIGT.png|right|150px|]]
 
|}
 
|}
  
−
== Slicer4 3D Printing ==
 
  
−
{|width="100%"
+
==Slicer4 Radiation Therapy Tutorial==
 +
 
 +
{| width="100%"
 
|
 
|
−
* The video tutorial [https://youtu.be/Uht6Fwtr9hE Segmenting a CT for 3D Printing of a Lumbar Phantom] shows how to use the Segment Editor of 3D Slicer for 3D printing using Slicer 4.7.
+
*The [https://github.com/SlicerRt/SlicerRtDoc/raw/master/tutorials/SlicerRT_WorldCongress_TutorialIGRT.pdf SlicerRT tutorial] is an introduction to the Radiation Therapy functionalities of Slicer.
−
** Author: Hillary Lia
+
*Author: Csaba Pinter, Andras Lasso, An Wang, Gregory C. Sharp, David Jaffray, Gabor Fichtinger.
−
** Audience: Users and developers interested in 3D printing
+
*Dataset: [http://slicer.kitware.com/midas3/download/item/205404/SlicerRT_WorldCongress_TutorialIGRT_Dataset.zip download] from MIDAS server
−
* The [https://www.slicer.org/wiki/Documentation/4.6/Training#Segmentation_for_3D_printing Segmentation for 3D printing] shows how to use the Segment Editor of 3D Slicer for 3D printing using Slicer 4.6.
+
*Based on Slicer 4.7
−
** Author: Csaba Pinter, MSc
+
| align="right" |
−
** Audience: Users and developers interested in 3D printing
+
[[Image:SlicerRTUseCaseImage.png|right|150px|]]
−
* This ''Slicer 4.3 [https://www.youtube.com/watch?v=MKLWzD0PiIc 3D printing tutorial]''  shows how to prepare 3D Slicer data for 3D printing using legacy Editor module.
 
−
** Authors: Nabgha Farhat, MSc
 
−
** Audience: Users and developers interested in 3D printing
 
−
|align="right"|[[Image:20170717_3DPrintingTutorialYoutube.PNG|280px]]
 
 
|}
 
|}
  
−
== Slicer4 Image Registration ==
+
==Slicer Pathology==
 +
{| width="100%"
 +
|
 +
*The [[Documentation/{{documentation/version}}/Extensions/SlicerPathology|Slicer Pathology Tutorial]] describes how to use the corresponding tools for automatic and semi-automatic pathology image segmentation.
 +
*Author: Erich Bremer (Stonybrook), Andriy Fedorov (Brigham and Women’s Hospital)
 +
*Dataset:  Available directly with the Slicer Pathology Slicer extension.
 +
| align="right" |
 +
[[File:SlicerPathologyScreenShot8.png | 200px]].
 +
|}
  
−
{|width="100%"
+
==SPHARM-PDM==
 +
{| width="100%"
 
|
 
|
−
*The [https://www.slicer.org/slicerWiki/index.php/File:RegistrationTutorial_3DSlicer4.5_spujol.pdf Registration tutorial] shows how to perform intra- and inter-subject registration within Slicer.
+
*The [https://www.nitrc.org/docman/view.php/308/1982/SPHARM-PDM_Tutorial_July2015.pdf SPHARM-PDM Tutorial] describes how to use SPHARM-PDM and ShapePopulationViewer Slicer extensions to respectively compute point-based models using a parametric boundary description for the computing of Shape Analysis and perform the quality control between the different models.
−
* Authors: Sonia Pujol, Ph.D., Dominik Meier, Ph.D., Ron Kikinis, M.D.
+
*Author: Jonathan Perdomo (UNC), Beatriz Paniagua (Kitware Inc.)
−
* Audience: Users and developers interested in image registration
+
*Dataset: [https://www.nitrc.org/docman/view.php/308/1981/SPHARM_Tutorial_Data_July2015.zip Tutorial Data]
−
* Dataset: [[Media:RegistrationData.zip| 3D Slicer Registration Data]]
+
| align="right" |
−
|align="right"|[[File:registration_Slicer4.png|250px]]
+
[[File:SlicerWinterProjectWeek2017-SPHARM-PDM.png | 200px]].
 
|}
 
|}
−
*Based on: 3D Slicer version 4.5
 
−
See [[Documentation/{{documentation/version}}/Registration/RegistrationLibrary|the Registration Library for worked out registration examples with data]].
 
  
−
== Fast GrowCut ==
+
==Fiber Bundle Volume Measurement==
−
 
+
{| width="100%"
−
{|width="100%"
 
 
|
 
|
−
* The [[media:FastGrowCutTutorial.pdf |Fast GrowCut tutorial]]  shows how to perform a segmentation using the Fast GrowCut effect in Slicer.
+
*The [http://www.na-mic.org/Wiki/images/5/57/Fiber_Bundle_Volume_Measurement.pptx Fiber Bundle Volume Measurement Tutorial] aim is to calculate the volume of the fiber bundle that passes through the Corpus Callosum(CC). Following this tutorial, you’ll be able to (1) convert fiber bundles to label map and (2) calculate volume measurements from the fiber bundles.
−
* Authors: Hillary Lia
+
*Author: Shun Gong (Shanghai Changzheng Hospital, China)
−
* Audience: Users interested in segmentation
+
*Dataset: [http://www.na-mic.org/Wiki/images/4/4c/FiberVolume_data.zip Tutorial data]: The following data are provided: Baseline image, Down sampled whole brain tractography (conducted as in the [[Documentation/{{documentation/version}}/Training#Slicer4_Diffusion_Tensor_Imaging_Tutorial|DWI tutorial]] and down-sampled to about 10000 fibers using Tractography Display module), Corpus callosum label map (drawn as in the [[Documentation/{{documentation/version}}/Training#Slicer4_Diffusion_Tensor_Imaging_Tutorial|DWI tutorial]]).
−
|align="right"|[[File:FastGrowCutLogo.png|200px]]
+
| align="right" |
 +
[[File:SlicerWinterProjectWeek2017-FiberBundleVolumeMeasurements.png | 200px]].
 
|}
 
|}
  
−
==Slicer4 Radiation Therapy Tutorial ==
+
==Slicer4 Lung CT Analyzer==
−
** The [https://app.assembla.com/spaces/slicerrt/subversion/source/HEAD/trunk/SlicerRt/doc/tutorials/SlicerRT_TutorialIGRT_4.7.pdf?_format=raw SlicerRT tutorial] is an introduction to the Radiation Therapy functionalities of Slicer.
+
{| width="100%"
−
** Author: Csaba Pinter, Andras Lasso, An Wang, Gregory C. Sharp, David Jaffray, Gabor Fichtinger.  
+
|
−
** Dataset: [http://slicer.kitware.com/midas3/download/item/205404/SlicerRT_WorldCongress_TutorialIGRT_Dataset.zip download] from MIDAS server
+
*The [https://github.com/rbumm/SlicerLungCTAnalyzer LungCTAnalyzer tutorial] and the [https://www.youtube.com/watch?v=fpLxm7uAvZQ LungCTAnalyzer video-based demo] show how to visualize and quantify infiltration, emphysema and collapsed lung areas in CT datasets acquired on COVID-19 patients.
−
**Based on Slicer 4.7
+
*Authors: Rudolph Bumm, MD, Andras Lasso, PhD.
 +
*Audience: End-users
 +
*Modules: LungCTSegmenter, LungCTAnalyzer
 +
*Based on: 3D Slicer version 5.0 (4.11)
 +
| align="right" |
 +
[[Image:LungCTAnalyzer.png|right|250px|]]
  
−
== Other ==
+
|}
  
−
Additional (non-curated) videos-based demonstrations using 3D Slicer are accessible on  [http://www.youtube.com/results?search_query=3d+slicer&sm=3 You Tube].
+
=3D Slicer version 4.7 Tutorial Contest=
  
−
= 3D Slicer Tutorial contests=
+
For previous editions of the contest, please visit the [https://na-mic.org/wiki/Tutorial_Contests 3D Slicer Tutorial Contests page]
−
 
 
−
==Winter 2017 Tutorial contest==
 
  
 
===Segmentation for 3D printing===
 
===Segmentation for 3D printing===
−
{|width="100%"
+
{| width="100%"
 
|
 
|
−
*The [https://www.assembla.com/spaces/slicerrt/documents/bmRQGEzzur54v-dmr6CpXy/download/bmRQGEzzur54v-dmr6CpXy Segmentation for 3D printing Tutorial] is an introduction to the new [[Documentation/{{documentation/version}}/Modules/SegmentEditor|Segment Editor]] module, demonstrated through the popular topic of 3D printing.  
+
*The [https://github.com/SlicerRt/SlicerRtDoc/raw/master/tutorials/SegmentationFor3DPrinting_TutorialContestWinter2017.pdf Segmentation for 3D printing Tutorial] ([https://github.com/SlicerRt/SlicerRtDoc/raw/master/tutorials/SegmentationFor3DPrinting_TutorialContestWinter2017.pptx pptx]) is an introduction to the new [[Documentation/{{documentation/version}}/Modules/SegmentEditor|Segment Editor]] module, demonstrated through the popular topic of 3D printing.
 
*Author: Csaba Pinter (Queen's University, Canada)
 
*Author: Csaba Pinter (Queen's University, Canada)
 +
*[https://www.youtube.com/watch?v=Uht6Fwtr9hE Narrated video version on YouTube].
 
*Dataset: [[:File:BasePiece.zip|Phantom base STL model]] Source: [http://perk-software.cs.queensu.ca/plus/doc/nightly/modelcatalog/ PerkLab].
 
*Dataset: [[:File:BasePiece.zip|Phantom base STL model]] Source: [http://perk-software.cs.queensu.ca/plus/doc/nightly/modelcatalog/ PerkLab].
−
|align="right"|
+
| align="right" |
 
[[File:SlicerWinterProjectWeek2017-Segmentation-for-3d-printing.png | 200px]].  
 
[[File:SlicerWinterProjectWeek2017-Segmentation-for-3d-printing.png | 200px]].  
 
|}
 
|}
  
 
===Slicer Pathology===
 
===Slicer Pathology===
−
{|width="100%"
+
{| width="100%"
 
|
 
|
 
*The [[Documentation/{{documentation/version}}/Extensions/SlicerPathology|Slicer Pathology Tutorial]] describes how to use the corresponding tools for automatic and semi-automatic pathology image segmentation.
 
*The [[Documentation/{{documentation/version}}/Extensions/SlicerPathology|Slicer Pathology Tutorial]] describes how to use the corresponding tools for automatic and semi-automatic pathology image segmentation.
 
*Author: Erich Bremer (Stonybrook), Andriy Fedorov (Brigham and Women’s Hospital)
 
*Author: Erich Bremer (Stonybrook), Andriy Fedorov (Brigham and Women’s Hospital)
 
*Dataset:  Available directly with the Slicer Pathology Slicer extension.
 
*Dataset:  Available directly with the Slicer Pathology Slicer extension.
−
|align="right"|
+
| align="right" |
 
[[File:SlicerPathologyScreenShot8.png | 200px]].  
 
[[File:SlicerPathologyScreenShot8.png | 200px]].  
 
|}
 
|}
  
 
===Simple Python Tool for Quality Control of DWI data===
 
===Simple Python Tool for Quality Control of DWI data===
−
{|width="100%"
+
{| width="100%"
 
|
 
|
 
*The [http://www.na-mic.org/Wiki/images/3/3a/SimpleDiffusionGradientInformationExtractorTutorial_Chauvin_Jan2017.pptx Simple Multi-shell Diffusion Gradients Information Extractor Tutorial] describes how to use a simple Python script for parsing multi-shell sensitizing gradients information from nifti file format (separated bvecs, bvals files).
 
*The [http://www.na-mic.org/Wiki/images/3/3a/SimpleDiffusionGradientInformationExtractorTutorial_Chauvin_Jan2017.pptx Simple Multi-shell Diffusion Gradients Information Extractor Tutorial] describes how to use a simple Python script for parsing multi-shell sensitizing gradients information from nifti file format (separated bvecs, bvals files).
 
*Author: Laurent Chauvin (ETS Montreal)
 
*Author: Laurent Chauvin (ETS Montreal)
 
*Dataset:  Not available.
 
*Dataset:  Not available.
−
|align="right"|
+
| align="right" |
 
[[File:SlicerWinterProjectWeek2017-SimpleDiffusionGradientInformationExtractorTutorial.png | 200px]].  
 
[[File:SlicerWinterProjectWeek2017-SimpleDiffusionGradientInformationExtractorTutorial.png | 200px]].  
 
|}
 
|}
  
 
===SPHARM-PDM===
 
===SPHARM-PDM===
−
{|width="100%"
+
{| width="100%"
 
|
 
|
 
*The [https://www.nitrc.org/docman/view.php/308/1982/SPHARM-PDM_Tutorial_July2015.pdf SPHARM-PDM Tutorial] describes how to use SPHARM-PDM and ShapePopulationViewer Slicer extensions to respectively compute point-based models using a parametric boundary description for the computing of Shape Analysis and perform the quality control between the different models.
 
*The [https://www.nitrc.org/docman/view.php/308/1982/SPHARM-PDM_Tutorial_July2015.pdf SPHARM-PDM Tutorial] describes how to use SPHARM-PDM and ShapePopulationViewer Slicer extensions to respectively compute point-based models using a parametric boundary description for the computing of Shape Analysis and perform the quality control between the different models.
 
*Author: Jonathan Perdomo (UNC), Beatriz Paniagua (Kitware Inc.)
 
*Author: Jonathan Perdomo (UNC), Beatriz Paniagua (Kitware Inc.)
 
*Dataset:  [https://www.nitrc.org/docman/view.php/308/1981/SPHARM_Tutorial_Data_July2015.zip Tutorial Data]
 
*Dataset:  [https://www.nitrc.org/docman/view.php/308/1981/SPHARM_Tutorial_Data_July2015.zip Tutorial Data]
−
|align="right"|
+
| align="right" |
 
[[File:SlicerWinterProjectWeek2017-SPHARM-PDM.png | 200px]].  
 
[[File:SlicerWinterProjectWeek2017-SPHARM-PDM.png | 200px]].  
 
|}
 
|}
  
 
===Integration of Robot Operating System (ROS) and 3D Slicer using OpenIGTLink===
 
===Integration of Robot Operating System (ROS) and 3D Slicer using OpenIGTLink===
−
{|width="100%"
+
{| width="100%"
 
|
 
|
 
*The [https://www.na-mic.org/Wiki/images/a/ab/ROSIGTLTutorial_Tokuda_Jan2017.pptx Integration of Robot Operating System (ROS) and 3D Slicer using OpenIGTLink Tutorial] describes the software architecture of surgical robot systems and allows to acquire hands-on experience of software-hardware integration for medical robotics.
 
*The [https://www.na-mic.org/Wiki/images/a/ab/ROSIGTLTutorial_Tokuda_Jan2017.pptx Integration of Robot Operating System (ROS) and 3D Slicer using OpenIGTLink Tutorial] describes the software architecture of surgical robot systems and allows to acquire hands-on experience of software-hardware integration for medical robotics.
 
*Author: Junichi Tokuda (Brigham and Women’s Hospital)
 
*Author: Junichi Tokuda (Brigham and Women’s Hospital)
 
*Dataset:  Not available.
 
*Dataset:  Not available.
−
|align="right"|
+
| align="right" |
 
[[File:SlicerWinterProjectWeek2017-Integration-ROS-3DSlicer-OpenIGTLink.png | 200px]].  
 
[[File:SlicerWinterProjectWeek2017-Integration-ROS-3DSlicer-OpenIGTLink.png | 200px]].  
 
|}
 
|}
  
 
===Fiber Bundle Volume Measurement===
 
===Fiber Bundle Volume Measurement===
−
{|width="100%"
+
{| width="100%"
 
|
 
|
 
*The [http://www.na-mic.org/Wiki/images/5/57/Fiber_Bundle_Volume_Measurement.pptx Fiber Bundle Volume Measurement Tutorial] aim is to calculate the volume of the fiber bundle that passes through the Corpus Callosum(CC). Following this tutorial, you’ll be able to (1) convert fiber bundles to label map and (2) calculate volume measurements from the fiber bundles.
 
*The [http://www.na-mic.org/Wiki/images/5/57/Fiber_Bundle_Volume_Measurement.pptx Fiber Bundle Volume Measurement Tutorial] aim is to calculate the volume of the fiber bundle that passes through the Corpus Callosum(CC). Following this tutorial, you’ll be able to (1) convert fiber bundles to label map and (2) calculate volume measurements from the fiber bundles.
 
*Author: Shun Gong (Shanghai Changzheng Hospital, China)
 
*Author: Shun Gong (Shanghai Changzheng Hospital, China)
 
*Dataset:  [http://www.na-mic.org/Wiki/images/4/4c/FiberVolume_data.zip Tutorial data]: The following data are provided: Baseline image, Down sampled whole brain tractography (conducted as in the [[Documentation/{{documentation/version}}/Training#Slicer4_Diffusion_Tensor_Imaging_Tutorial|DWI tutorial]] and down-sampled to about 10000 fibers using Tractography Display module), Corpus callosum label map (drawn as in the [[Documentation/{{documentation/version}}/Training#Slicer4_Diffusion_Tensor_Imaging_Tutorial|DWI tutorial]]).
 
*Dataset:  [http://www.na-mic.org/Wiki/images/4/4c/FiberVolume_data.zip Tutorial data]: The following data are provided: Baseline image, Down sampled whole brain tractography (conducted as in the [[Documentation/{{documentation/version}}/Training#Slicer4_Diffusion_Tensor_Imaging_Tutorial|DWI tutorial]] and down-sampled to about 10000 fibers using Tractography Display module), Corpus callosum label map (drawn as in the [[Documentation/{{documentation/version}}/Training#Slicer4_Diffusion_Tensor_Imaging_Tutorial|DWI tutorial]]).
−
|align="right"|
+
| align="right" |
 
[[File:SlicerWinterProjectWeek2017-FiberBundleVolumeMeasurements.png | 200px]].  
 
[[File:SlicerWinterProjectWeek2017-FiberBundleVolumeMeasurements.png | 200px]].  
 
|}
 
|}
  
−
==Winter 2016 Tutorial contest==
+
=YouTube videos=
 +
{| border="1" cellpadding="5" width="1200px"
 +
| style="width:33%" |[[Image:Verterbra.png|right|250px|]] [https://www.youtube.com/watch?v=Uht6Fwtr9hE How to segment multiple vertebrae in spine CT for 3D printing - Author: Hillary Lia]
 +
| style="width:33%" |[[Image:Femurmodel.png|right|250px|]] [https://www.youtube.com/watch?v=0at15gjk-Ns Creating a femur model from CT volume using 3D Slicer - Author: PerkLab]
 +
| style="width:33%" |[[Image:3DPrinting.png|right|250px|]] [https://www.youtube.com/watch?v=MKLWzD0PiIc Preparing data for 3D printing - Author: Nabgha Farhat]
 +
|}
 +
{| border="1" cellpadding="5" width="1200px" |
 +
| style="width:25%" |[[Image:DICOM2.png|right|250px|]] [https://www.youtube.com/watch?v=nzWf4xHy1BM& How to export CT and segmentation data to DICOM- Author: Andras Lasso, Csaba Pinter]
 +
| style="width:25%" |[[Image:LocalThresholdEffect.png|right|250px|]] [https://www.youtube.com/watch?time_continue=26&v=cevlMLyhfK8&feature=emb_logo Local Threshold Effect - Author: Kyle Sunderland]
 +
| style="width:25%" |[[Image:VMTKCenterlines.png|right|250px|]] [https://www.youtube.com/watch?v=yi07mjr3JeU SlicerVMTK centerline extraction (Slicer 4.11)- Author: Andras Lasso]
 +
| style="width:25%" |[[Image:MONAILabel.png|right|250px|]] [https://www.youtube.com/watch?v=PmD8umlcpF4 MONAI Label(Slicer 4.11)- Author: Andres Diaz-Pinto]
 +
|}
 +
 
 +
Additional [http://www.youtube.com/results?search_query=3d+slicer&sm=3 non-curated videos-based demonstrations using 3D Slicer are accessible on YouTube].
  
−
===Subject Hierarchy===
+
=Teams Contributions=
−
{|width="100%"
+
{| width="100%"
 
|
 
|
−
*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.
+
*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.
−
*Author: Csaba Pinter, Queen's University, Canada
+
*Authors: Steve Pieper Ph.D.
−
*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.
+
*Audience: First time users and developers interested in Slicer 4.1 new features.
−
|align="right"|
+
*Length: 0h20m
−
[[File:SubjectHierarchyTutorial.png | 200px]].
+
| align="right" |[[Image:Webinar-Slicer-4.1.png|250px]]
 
|}
 
|}
−
 
+
<br>
−
===Fiber Bundle Selection and Scalar Measurements===
+
----
−
{|width="100%"
+
<br>
 +
{| width="100%"
 
|
 
|
−
*The [https://github.com/SlicerDMRI/slicerdmri.github.io/raw/master/docs/tutorials/FiberBundleSelectionAndScalarMeasurement.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.
+
*This ''Intro to Slicer 4.0 [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.
−
*Author: Fan Zhang, University of Sydney Australia and Brigham and Women's Hospital
+
*Authors: Julien Finet, M.S., Steve Pieper, Ph.D., Jean-Christophe Fillion-Robin, M.S.
−
*Dataset:  [[media:FiberBundleSelectionAndScalarMeasurement_TutorialContestWinter2016.zip| Fiber Bundle Selection And Scalar Measurement Tutorial Dataset]]
+
*Audience: First time users interested in a broad overview of Slicer’s features and tools.
−
|align="right"|
+
*Length: 1h20m
−
[[File:FiberBundleSelectionAndScalarMeasurement_TutorialContestWinter2016_Snapshot.png|200px]]
+
| align="right" |[[Image:Webinar.png|250px]]
 
|}
 
|}
 +
<br>
 +
----
 +
<br>
 +
==International resources==
 +
International resources in Chinese and in German are made available by the Slicer community.
  
−
===Plastimatch ===
+
==Resources in Chinese==
−
{|width="100%"
+
{| width="100%"
 
|
 
|
−
*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.
+
A 3D Slicer community on WeChat in China offers many tutorials and clinical examples in Chinese. Note that the images are of interest to non-Chinese speakers and Google Translate does a reasonable job of translating some of the text. The tutorials below are examples of Slicer tutorials in Chinese.
−
*Author: Gregory Sharp, Massachusetts General Hospital
 
−
*Dataset:  [http://www.na-mic.org/Wiki/index.php/File:Plastimatch_TutorialContestWinter2016.zip Plastimatch Tutorial Dataset]
 
−
|align="right"|
 
−
[[File:PlastimatchTutorial_Winter2016Contest.png|200px]]
 
−
|}
 
  
−
===UKF ===
+
*[https://mp.weixin.qq.com/s?__biz=MzI3MDY4ODA5Mw==&mid=2247486116&idx=1&sn=772e9d431ac32cbb73d08cf0e6bc219a&chksm=eacc0096ddbb89805d93ac4be181d1a35058031bac673d7a91b3b44dccee2bfd1d8461397635#rd Getting started 大脑前动脉远端动脉瘤手术夹闭治疗]
−
{|width="100%"
 
−
|
 
−
*The [https://github.com/SlicerDMRI/slicerdmri.github.io/raw/master/docs/tutorials/UKFTractography.pdf UKF tutorial] guides through the use of the Unscented Kalman Filter (UKF) tractography module.
 
−
*Author: Pegah Kahali, Brigham and Women's Hopital
 
−
*Dataset:  [http://www.na-mic.org/Wiki/index.php/File:UKF-Tractography_TutorialContestWinter2016.zip UKF tutorial Dataset]
 
−
|align="right"|
 
−
[[File:UKF_Winter2016.png|200px]]
 
−
|}
 
  
−
==Summer 2014 Tutorial contest==  
+
*[https://mp.weixin.qq.com/s?__biz=MzI3MDY4ODA5Mw==&mid=2247484787&idx=1&sn=1f6279bdccab168fc79b7275e9fe91ca&chksm=eacc0f41ddbb8657be92f617661133d87bb55a4ecf12f786e97a8b7d5249a05d11e0cd620c3f#rd distal anterior cerebral artery aneurysm 3D Slicer：漂亮得不像实力派]
  
−
===Cardiac Agatston Tutorial===
+
*[https://mp.weixin.qq.com/s?__biz=MzI3MDY4ODA5Mw==&mid=2247486360&idx=1&sn=f833b13a26f543aa9175419a03df7f52&chksm=eacc01aaddbb88bcb004773a4db8a9b3c7633d21cda3956f84b96515252eb861c5eb1e75a60b&mpshare=1&scene=24&srcid=0212LIfOkBRm9CvA7ImHCpRt#rd meningioma skull resection 脑膜瘤患者颅骨切除一期修补的3DSlicer方案]
−
{|width="100%"
 
−
|
 
−
*[http://wiki.na-mic.org/Wiki/index.php/File:TutorialContest_CardiacAgatstonScoring_2014.pdf  Cardiac Agatston Scoring Tutorial]
 
−
*Authors:  Jessica Forbes, Hans Johnson, University of Iowa
 
−
*Dataset:  [http://wiki.na-mic.org/Wiki/index.php/File:CardiacAgatstonMeasures_TutorialContestSummer2014.zip Cardiac Agatston Scoring Tutorial Dataset]
 
−
|align="right"|
 
−
[[File:CardiacAgatstonMeasuresModuleScreenshot.jpg| 250px]]
 
−
|}
 
  
−
===CMR Toolkit LA workflow===
+
*[https://mp.weixin.qq.com/s?__biz=MzI3MDY4ODA5Mw==&mid=2247486079&idx=1&sn=9b926dc398a408e3441082b9e0ffde61&chksm=eacc004dddbb895bf9b60f5f1bc443513196e4cb90a6caf6f348a4da7b7fc22eb658661aeb49&mpshare=1&scene=24&srcid=0212AFtT2Wq7K7bvkMGTdyih#rd Cerebral hemorrhage by forehead positioning method 脑出血经额手术定位法（五]
−
{|width="100%"
 
−
|
 
−
*[http://wiki.na-mic.org/Wiki/index.php/File:CMRToolkitLAWorkflow_TutorialContestSummer2014.pdf  CMR Toolkit LA Workflow Tutorial]
 
−
*Authors: Salma Bengali, Josh Cates, University of Utah
 
−
*Dataset:  [http://wiki.na-mic.org/Wiki/index.php/File:CMRToolkitLAWorkflowData_TutorialContestSummer2014.zip CMRToolkitLAWorkflow Dataset]
 
−
|align="right"|
 
−
[[Image:Utah_SummerContest2014_tutorial.png|300px]]
 
−
|}
 
  
−
==Summer 2013 Tutorial contest==
+
*[https://mp.weixin.qq.com/s?__biz=MzI3MDY4ODA5Mw==&mid=2247485356&idx=1&sn=044f5899b651b35994db00c32ab688ee&chksm=eacc0d9eddbb8488f16ff82bb1dda8456a4011790fed024781972d578783e67781443cf4a319&mpshare=1&scene=24&srcid=0212G45TadrPnX8tp9eaNXUs#rd Hematoma modeling 血肿建模的第11种方法]
  
−
===Cardiac MRI Toolkit===
+
*[https://mp.weixin.qq.com/s?__biz=MzI3MDY4ODA5Mw==&mid=2247486025&idx=1&sn=b281324893be4ab116d20826f1b426c3&chksm=eacc007bddbb896d9deb096f209278f40c0b52c6410a8a9ff3ce8c3697c99304f18eb678f11e&mpshare=1&scene=24&srcid=02125v1kxvIGmfkxx7mUZcCM#rd Mobile phone positioning and AR application 手机定位及AR应用的初步探索]
−
{|width="100%"
+
*[https://mp.weixin.qq.com/s?__biz=MzI3MDY4ODA5Mw==&mid=2247483658&idx=1&sn=ad08fe01c61d6999a36f2960b34287ec&chksm=eacc0b38ddbb822e60206afcf0bb67562432bb275463b20ad6ac7d243ccc1429afaa8f2177ea#rd 3D printing 如何用3D Slicer实现模型3D打印 束旭俊]
−
|
 
−
*[[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]]
 
−
|}
 
  
−
===HelloCLI===
+
The WeChat 3D Slicer Group in China offers a [https://spujol.github.io/SlicerTutorialsInChinese/ comprehensive list of tutorials in Chinese.]  
−
{|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===
+
<br />
−
{|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===
+
| align="right" |
−
{|width="100%"
+
[[image:Wechat-hemorage-2018-02-12.png|250px|Example WeChat tutorial slides]]
−
|
 
−
*[[Media:DTIPrep_TutorialContestSummer2013.pdf|DTIPrep]]
 
−
*Authors:    Dave Welch, SINAPSE, IOWA
 
−
*Dataset:  [[Media:DTIPrepData_TutorialContestSummer2013.zip|DTIPrep Dataset]]
 
−
|align="right"|
 
−
[[Image:DTIPrep-tutorial.png|250px]]
 
 
|}
 
|}
  
−
== Summer 2012 Tutorial contest ==  
+
==Resources in German==
  
−
===Automatic Left Atrial Scar Segmenter ===
+
*[https://www.youtube.com/watch?v=sl-00kGpuPk&list=PLJWCUXz3GeAfmYLiFcKus_c0jcsMnVsgb A series of four YouTube videos on python programming in Slicer] (German narration with English subtitles)
−
{|width="100%"
 
−
|
 
−
*[http://wiki.na-mic.org/Wiki/index.php/CARMA-LA-Scar_TutorialContestSummer2012 Automatic Left Atrial Scar Segmenter]
 
−
*Authors:  Greg Gardner, Josh Cates, SCI, Utah
 
−
*Dataset: [http://wiki.na-mic.org/Wiki/index.php/File:CARMA-LA-Scar_TutorialContestSummer2012.zip CARMA-LA-Scar data]
 
−
|align="right"|
 
−
[[Image:Carma afib auto scar.png|250px]]
 
−
|}
 
  
−
===Qualitative and quantitative comparison of  two RT dose distributions===
+
==Murat Maga's blog posts about using 3D Slicer for biology==
−
{|width="100%"
 
−
|
 
−
*[http://www.na-mic.org/Wiki/index.php/File:PlastimatchDose_TutorialContestSummer2012.pdf Qualitative and quantitative comparison of  two RT dose distributions]
 
−
*Authors:  James Shackleford, Nadya Shusharina, Greg Sharp, MGH
 
−
|align="right"|
 
−
[[Image:PlastimatchDose.png|250px]]
 
−
|}
 
  
−
===Dose accumulation for adaptive radiation therapy===
+
*[https://blogs.uw.edu/maga/2017/04/11/getting-started-with-3d-slicer-as-a-biologist/ Slicer for Biologists]
−
{|width="100%"
+
*[https://blogs.uw.edu/maga/2017/04/11/a-worked-example-getting-and-visualizing-data-from-digimorph/ Loading data from DigiMorph]
−
|
+
*[https://blogs.uw.edu/maga/2017/04/11/morphosource-data-and-dealing-with-dicom-series-in-slicer/ Fixing problem DICOM]
−
*[http://www.na-mic.org/Wiki/index.php/File:DoseAccumulationforAdaptiveRadiationTherapy_TutorialContestSummer2012.pdf Dose accumulation for adaptive radiation therapy]
+
*[https://blogs.uw.edu/maga/2017/04/12/scissors-tool-is-awesome/ Scissors tool is awesom]
−
*Authors:  Kevin Wang, Csaba Pinter, Andras Lasso, PMH, Queen's
+
−
|align="right"|
+
==Using the (legacy) Editor==
−
[[Image:AdaptiveradiationTherapy.png|250px]]
 
−
|}
 
  
−
===WebGL Export===
+
===Fast GrowCut===
−
{|width="100%"
 
−
|
 
−
*[http://www.na-mic.org/Wiki/index.php/File:WebGLExport_TutorialContestSummer2012.pdf  WebdGLExport]
 
−
*Authors:  Nicolas Rannou, Daniel Haehn, Children's Hospital
 
−
|align="right"|
 
−
[[Image:WebGLExport.png|250px]]
 
−
|}
 
  
−
===OpenIGTLink===
+
{| width="100%"
−
{|width="100%"
 
 
|
 
|
−
*[http://wiki.slicer.org/slicerWiki/images/f/f1/OpenIGTLinkTutorial_Slicer4.1.0_JunichiTokuda_Apr2012.pdf OpenIGTLink]
+
*The [[Media:FastGrowCutTutorial.pdf|Fast GrowCut tutorial]] shows how to perform a segmentation using the Fast GrowCut effect in Slicer.
−
*Authors: Junichi Tokuda, BWH
+
*Authors: Hillary Lia
−
|align="right"|
+
*Audience: Users interested in segmentation
−
[[Image:OpenIGTLink.png|250px]]
+
| align="right" |[[File:FastGrowCutLogo.png|200px]]
 
|}
 
|}
  
−
=Additional resources =
+
{| width="100%"
−
{|width="100%"
+
*'''[https://www.youtube.com/channel/UC8vxI0-dEWrw0_tBF-v8xGA/videos Video-based segmentation tutorials from CHU de Rouen (France)]
−
|
+
** Segmentation tutorials, including liver, wrist bones, lungs, kidneys, hips.
−
* 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.
+
| align="right" |[[Image:ChuRouen.png|180px]]
−
* Authors: Steve Pieper Ph.D.
 
−
* Audience: First time users and developers interested in Slicer 4.1 new features.
 
−
* Length: 0h20m
 
−
|align="right"|[[Image:Webinar-Slicer-4.1.png|250px]]
 
−
|}
 
−
<br>
 
−
----
 
−
<br>
 
−
{|width="100%"
 
−
|
 
−
*This ''Intro to Slicer 4.0 [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.
 
−
*Audience: First time users interested in a broad overview of Slicer’s features and tools.
 
−
*Length: 1h20m
 
−
|align="right"|[[Image:Webinar.png|250px]]
 
−
|}
 
−
<br>
 
−
----
 
−
<br>
 
−
{|width="100%"
 
−
|
 
−
*The ''[[Documentation/{{documentation/version}}/Registration/RegistrationLibrary|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
 
−
|align="right"|[[Image:RegLib_table.png|250px|link=http://wiki.slicer.org/slicerWiki/index.php/Documentation/{{documentation/version}}/Registration/RegistrationLibrary]]
 
 
|}
 
|}
  
−
= External Resources =
+
===Use case: Slicer in paleontology===
−
 
 
−
== Murat Maga's blog posts about using 3D Slicer for biology ==
 
−
 
 
−
* [https://blogs.uw.edu/maga/2017/04/11/getting-started-with-3d-slicer-as-a-biologist/ Slicer for Biologists]
 
−
* [https://blogs.uw.edu/maga/2017/04/11/a-worked-example-getting-and-visualizing-data-from-digimorph/ Loading data from DigiMorph]
 
−
* [https://blogs.uw.edu/maga/2017/04/11/morphosource-data-and-dealing-with-dicom-series-in-slicer/ Fixing problem DICOM]
 
−
* [https://blogs.uw.edu/maga/2017/04/12/scissors-tool-is-awesome/ Scissors tool is awesom]
 
−
 
−
== Using the (legacy) 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:
 
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.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-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-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/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-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]
+
*[http://openpaleo.blogspot.com/2009/03/3d-slicer-tutorial-part-vi.html Open Source Paleontologist: 3D Slicer: The Tutorial Part VI]
−
 
 
−
== Team Contributions ==
 
−
See the collection of videos on the [http://vimeo.com/album/2363361 Kitware vimeo album].
 
−
 
 
−
== User Contributions ==
 
−
See the [[Documentation/{{documentation/version}}/Training/UserContributions|User Contributions Page]] for more content.
 
−
 
 
−
[http://www.youtube.com/results?search_query=3d+slicer&sm=3 YouTube videos about 3D Slicer]
 

Latest revision as of 23:40, 22 November 2022

Home < Documentation < Nightly < Training

Introduction: Slicer Tutorials

  • Some of these tutorials are based on older releases of 3D Slicer and are being upgraded to Slicer 5.0. The concepts are still useful but some interface elements and features may be different in updated versions. For tutorials for older versions of Slicer, please visit the Slicer training portal.

Quick Start Guide

Downloading and Installing Slicer

  • The Quick Start Guide shows how to install and start 3D Slicer
  • Author: Sonia Pujol, Ph.D.
  • Based on 3D Slicer 5.0 / 4.11

SlicerWelcome tutorial

General Introduction

Slicer Welcome Tutorial

  • The Slicer Welcome tutorial is an introduction to Slicer.
  • 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 4.8
  • Compatible with Slicer 4.10.1

SlicerWelcome tutorial

Slicer4Minute Tutorial

  • The Slicer4 Minute Tutorial is a brief introduction to the advanced 3D visualization capabilities of Slicer.
  • Author: Sonia Pujol, Ph.D.
  • Audience: First-time users who want to discover Slicer in 4 minutes
  • Modules: Welcome to Slicer, Models
  • Based on Slicer version 4.8
  • Compatible with Slicer 4.10.1
  • The Slicer4Minute dataset contains an MR scan of the brain and 3D reconstructions of the anatomy
Slicer4Minute tutorial

3D Visualization

Data Loading and 3D Visualization


  • Slicer 4.10
    • The Data loading and visualization (pptx) course guides through the basics of loading and viewing volumes and 3D models in Slicer 4.10.
    • Author: Csaba Pinter
    • Modules: Welcome to Slicer, Data, Volume Rendering, Models.
    • Audience: End-users
    • Based on Slicer 4.9
    • Compatible with Slicer 4.10.1
    • The 3DVisualization dataset contains an MR scan and a series of 3D models of the brain.
20180426 DataLoadingAndVisualizationTutorial.png
Slicer4DataLoading tutorial.png

DICOM

  • The DICOM and Slicer tutorial provides an introduction to the DICOM standard and shows how to load and visualize DICOM datasets in 3D Slicer version 5.0.
  • Author: Sonia Pujol, Ph.D.
  • Modules: DICOM, Volumes
  • Based on: 3D Slicer version 5.0/4.11
  • The 3D Slicer DICOM Tutorial Data contains a torso-CT and a breast MRI.
SlicerAndDICOM.png
  • The 3D Visualization of DICOM images 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., 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 4.8
  • Compatible with 3D Slicer version 4.10
  • 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

Open Anatomy Browser

OABrowser.png
  • The Open Anatomy Browser tutorial is an introduction to the OABrowser technology for viewing and interacting with atlases.
  • Author: Sonia Pujol, Ph.D., Mike Halle, Ph.D.
  • Audience: End-users

Tutorials for software developers

PerkLab's Slicer bootcamp training materials

  • The Laboratory for Percutaneous Surgery at Queen's University has made available training material of its internal yearly bootcamp, covering topics, such as 3D Slicer overview, basic visualization, segmentation, registration, scripting and module development, surgical navigation, DICOM, reproducible medical image computing research methodology, version control, and research project management.
  • Author: Andras Lasso, Csaba Pinter, Tamas Ungi, Csaba Pinter, Matthew Holden, Kyle Sunderland
  • Audience: Developers, Users
  • Based on: 3D Slicer version 4.10
PerkLabSlicerProgrammingTutorial.png

Slicer Programming Tutorial

  • The Slicer Programming tutorial guides through the integration of a python module in Slicer. It provides an introduction to the Python Console and the Qt Widget toolkit in 3D Slicer.
  • Author: Sonia Pujol, Ph.D., Steve Pieper, Ph.D.
  • Audience: Developers
  • Based on: 3D Slicer version 5.0/4.11
SlicerProgrammingTutorial.png

Slicer script repository

For additional Python scripts examples, please visit the Script repository.

Developing and contributing extensions for 3D Slicer

Contributing3DSlicerExtension.png

Segmentation

20170717 3DPrintingTutorialYoutube.PNG
  • Video tutorial: Whole heart segmentation from cardiac CT shows how to use the Segment Editor module for segmenting heart ventricles, atria, and great vessels from cardiac CT volumes.
    • Author: Andras Lasso, PhD
    • Audience: Users who need to segment heart structures, for example for visualization, quantification, or simulation.
    • Sample data set
    • Based on: 3D Slicer version 4.8
 WholeHeartSegYoutube.png
FemurSegmentationYoutube.png
  • Slicer Segmentation Recipes provide step-by-step description of useful segmentation techniques.
    • Segmentation tutorials for common tasks, such as skin surface extraction, craniotomy (splitting segments), sorta segmentation, cerebral vessel segmentation by subtraction, segmentation on arbitrarily oriented slices, skull stripping.
 SegmentationRecipes.png
  • The Skull Stripping tutorial shows how to perform skull-stripping in CT and MR data.
    • Author: Sonia Pujol, PhD, Andras Lasso, PhD, Ron Kikinis, MD
    • Audience: Users interested in brain segmentation
    • Based on: 3D Slicer version 4.11
 SkullStripping.png


Image Phenotyping

  • Based on: 3D Slicer version 4.10
  • The Image Phenotyping tutorial is an introduction to brain tumor segmentation and image phenotyping using the Slicer Radiomics extension.
  • Authors: Sonia Pujol, Ph.D.
  • Audience: Clinical researchers
  • Dataset: Meningioma dataset
 ImagePhenotyping.png

Registration

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
  • Based on: 3D Slicer version 4.8; Compatible with Slicer 4.10
  • The Brain Tumor Registration is a video-based tutorial that shows how to register two MRI datasets in a brain tumor case for surgical resection follow-up.
  • Authors: Sonia Pujol, Ph.D., Dominik Meier, Ph.D.
  • Audience: Users and developers interested in image registration
  • Dataset: Registration Library Case #37
 RigidRegistration.jpg
  • Based on: 3D Slicer version 4.10

Slicer Registration Case Library

  • The Slicer Registration Case Library provides real-life example cases of using the Slicer registration tools. They include pre-computed dataset and step-by-step instructions for users to follow.
Author: Dominik Meier, Ph.D.
Audience: users interested learning/applying Slicer image registration technology
 RegLib table.png

Slicer Extensions

Slicer4 Diffusion Tensor Imaging Tutorial

  • The Diffusion MRI Tutorial is an introduction to 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 4.8; Compatible with Slicer version 4.10.2
  • The Slicer Diffusion MRI Tutorial dataset contains an MR Diffusion Weighted Imaging scan of the brain.
  • Please visit dmri.slicer.org/docs for the latest documentation of SlicerDMRI.
Slicer4DTI Tutorial.png

Slicer4 Neurosurgical Planning Tutorial

  • The Neurosurgical Planning tutorial course guides end-users through the generation of fiber tracts in the vicinity of a tumor.
  • Author: Sonia Pujol, Ph.D., Ron Kikinis, M.D.
  • Audience: Clinicians and Clinical Researchers
  • Modules: Segment Editor, Tractography
  • Based on 3D Slicer version 4.10
  • The White Matter Exploration dataset contains a Diffusion Weighted Imaging scan of a brain tumor patient.
NeurosurgicalPlanningTutorial.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.
Slicer4 QuantitativeImaging.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 Radiation Therapy Tutorial

  • The SlicerRT tutorial is an introduction to the Radiation Therapy functionalities of Slicer.
  • Author: Csaba Pinter, Andras Lasso, An Wang, Gregory C. Sharp, David Jaffray, Gabor Fichtinger.
  • Dataset: download from MIDAS server
  • Based on Slicer 4.7
SlicerRTUseCaseImage.png

Slicer Pathology

  • The Slicer Pathology Tutorial describes how to use the corresponding tools for automatic and semi-automatic pathology image segmentation.
  • Author: Erich Bremer (Stonybrook), Andriy Fedorov (Brigham and Women’s Hospital)
  • Dataset: Available directly with the Slicer Pathology Slicer extension.

SlicerPathologyScreenShot8.png.

SPHARM-PDM

  • The SPHARM-PDM Tutorial describes how to use SPHARM-PDM and ShapePopulationViewer Slicer extensions to respectively compute point-based models using a parametric boundary description for the computing of Shape Analysis and perform the quality control between the different models.
  • Author: Jonathan Perdomo (UNC), Beatriz Paniagua (Kitware Inc.)
  • Dataset: Tutorial Data

SlicerWinterProjectWeek2017-SPHARM-PDM.png.

Fiber Bundle Volume Measurement

  • The Fiber Bundle Volume Measurement Tutorial aim is to calculate the volume of the fiber bundle that passes through the Corpus Callosum(CC). Following this tutorial, you’ll be able to (1) convert fiber bundles to label map and (2) calculate volume measurements from the fiber bundles.
  • Author: Shun Gong (Shanghai Changzheng Hospital, China)
  • Dataset: Tutorial data: The following data are provided: Baseline image, Down sampled whole brain tractography (conducted as in the DWI tutorial and down-sampled to about 10000 fibers using Tractography Display module), Corpus callosum label map (drawn as in the DWI tutorial).

SlicerWinterProjectWeek2017-FiberBundleVolumeMeasurements.png.

Slicer4 Lung CT Analyzer

  • The LungCTAnalyzer tutorial and the LungCTAnalyzer video-based demo show how to visualize and quantify infiltration, emphysema and collapsed lung areas in CT datasets acquired on COVID-19 patients.
  • Authors: Rudolph Bumm, MD, Andras Lasso, PhD.
  • Audience: End-users
  • Modules: LungCTSegmenter, LungCTAnalyzer
  • Based on: 3D Slicer version 5.0 (4.11)
LungCTAnalyzer.png

3D Slicer version 4.7 Tutorial Contest

For previous editions of the contest, please visit the 3D Slicer Tutorial Contests page

Segmentation for 3D printing

SlicerWinterProjectWeek2017-Segmentation-for-3d-printing.png.

Slicer Pathology

  • The Slicer Pathology Tutorial describes how to use the corresponding tools for automatic and semi-automatic pathology image segmentation.
  • Author: Erich Bremer (Stonybrook), Andriy Fedorov (Brigham and Women’s Hospital)
  • Dataset: Available directly with the Slicer Pathology Slicer extension.

SlicerPathologyScreenShot8.png.

Simple Python Tool for Quality Control of DWI data

SlicerWinterProjectWeek2017-SimpleDiffusionGradientInformationExtractorTutorial.png.

SPHARM-PDM

  • The SPHARM-PDM Tutorial describes how to use SPHARM-PDM and ShapePopulationViewer Slicer extensions to respectively compute point-based models using a parametric boundary description for the computing of Shape Analysis and perform the quality control between the different models.
  • Author: Jonathan Perdomo (UNC), Beatriz Paniagua (Kitware Inc.)
  • Dataset: Tutorial Data

SlicerWinterProjectWeek2017-SPHARM-PDM.png.

Integration of Robot Operating System (ROS) and 3D Slicer using OpenIGTLink

SlicerWinterProjectWeek2017-Integration-ROS-3DSlicer-OpenIGTLink.png.

Fiber Bundle Volume Measurement

  • The Fiber Bundle Volume Measurement Tutorial aim is to calculate the volume of the fiber bundle that passes through the Corpus Callosum(CC). Following this tutorial, you’ll be able to (1) convert fiber bundles to label map and (2) calculate volume measurements from the fiber bundles.
  • Author: Shun Gong (Shanghai Changzheng Hospital, China)
  • Dataset: Tutorial data: The following data are provided: Baseline image, Down sampled whole brain tractography (conducted as in the DWI tutorial and down-sampled to about 10000 fibers using Tractography Display module), Corpus callosum label map (drawn as in the DWI tutorial).

SlicerWinterProjectWeek2017-FiberBundleVolumeMeasurements.png.

YouTube videos

Verterbra.png
How to segment multiple vertebrae in spine CT for 3D printing - Author: Hillary Lia
Femurmodel.png
Creating a femur model from CT volume using 3D Slicer - Author: PerkLab
3DPrinting.png
Preparing data for 3D printing - Author: Nabgha Farhat
DICOM2.png
How to export CT and segmentation data to DICOM- Author: Andras Lasso, Csaba Pinter
LocalThresholdEffect.png
Local Threshold Effect - Author: Kyle Sunderland
VMTKCenterlines.png
SlicerVMTK centerline extraction (Slicer 4.11)- Author: Andras Lasso
MONAILabel.png
MONAI Label(Slicer 4.11)- Author: Andres Diaz-Pinto

Additional non-curated videos-based demonstrations using 3D Slicer are accessible on YouTube.

Teams Contributions

  • 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



International resources

International resources in Chinese and in German are made available by the Slicer community.

Resources in Chinese

A 3D Slicer community on WeChat in China offers many tutorials and clinical examples in Chinese. Note that the images are of interest to non-Chinese speakers and Google Translate does a reasonable job of translating some of the text. The tutorials below are examples of Slicer tutorials in Chinese.

The WeChat 3D Slicer Group in China offers a comprehensive list of tutorials in Chinese.


Example WeChat tutorial slides

Resources in German

Murat Maga's blog posts about using 3D Slicer for biology

Using the (legacy) Editor

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
ChuRouen.png

Use case: Slicer in paleontology

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:

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