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*For tutorials for other versions of Slicer, please visit the [[Training| Slicer training portal]].
 
*For tutorials for other versions of Slicer, please visit the [[Training| Slicer training portal]].
 
*For "reference manual" style documentation, please visit the [[Documentation/{{documentation/version}}|Slicer {{documentation/version}} documentation page]]
 
*For "reference manual" style documentation, please visit the [[Documentation/{{documentation/version}}|Slicer {{documentation/version}} documentation page]]
*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]'''
+
*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. The concepts are still useful but bear in mind that some interface elements and features will be different in updated versions.
+
* Some of these tutorials are based on older releases of 3D Slicer and are being upgraded to Slicer4.10. The concepts are still useful but some interface elements and features may be different in updated versions.
  
 
__TOC__
 
__TOC__
 +
 +
=Quick Start Guide =
 +
 +
==Downloading and Installing Slicer==
 +
{|width="100%"
 +
|
 +
*The [https://www.dropbox.com/s/gtir3x6e007snkx/QuickStartGuide_3DSlicer_SoniaPujol.pdf?dl=0| Quick Start Guide] shows how to install and start 3D Slicer
 +
*Author: Sonia Pujol, Ph.D.
 +
*Based on: 3D Slicer version 4.8
 +
|align="right"|
 +
[[image:QuickStart_image.png|250px|SlicerWelcome tutorial]]
 +
|}
  
 
=General Introduction=
 
=General Introduction=
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{|width="100%"
 
{|width="100%"
 
|
 
|
*The [[media:SlicerWelcome-tutorial_Slicer4.5.pdf|SlicerWelcome tutorial]] is an introduction to Slicer based on the Welcome module.
+
*The [https://www.dropbox.com/s/vn8sqlof2kag2kk/SlicerWelcome-tutorial_Slicer4.8_SoniaPujol.pdf?dl=0] 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 4.5
+
*Based on: 3D Slicer version 4.8
 
|align="right"|
 
|align="right"|
 
[[image:SlicerWelcome-image.png|250px|SlicerWelcome tutorial]]
 
[[image:SlicerWelcome-image.png|250px|SlicerWelcome tutorial]]
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{|width="100%"
 
{|width="100%"
 
|
 
|
*The [[media:Slicer4.5minute_SoniaPujol.pdf|Slicer4Minute tutorial]]  is a brief introduction to the advanced 3D visualization capabilities of Slicer 4.0.
+
*The [https://www.dropbox.com/s/9jfsyhhgude5hf1/Slicer4.8minute_SoniaPujol.pdf?dl=0| Slicer4 Minute Tutorial]  is a brief introduction to the advanced 3D visualization capabilities of Slicer 4.8.
 
*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
+
*Based on: 3D Slicer version 4.8
 
*The [[media:Slicer4minute.zip|Slicer4Minute dataset]] contains an MR scan of the brain and 3D reconstructions of the anatomy
 
*The [[media:Slicer4minute.zip|Slicer4Minute dataset]] contains an MR scan of the brain and 3D reconstructions of the anatomy
 
|align="right"|
 
|align="right"|
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|}
 
|}
  
 +
=3D Visualization=
 
==Slicer4 Data Loading and 3D Visualization ==
 
==Slicer4 Data Loading and 3D Visualization ==
 
{|width="100%"
 
{|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 .  
+
 
*Author: Sonia Pujol, Ph.D.
+
* Slicer 4.10
*Modules: Welcome to Slicer, Sample Data, Models.
+
** 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.
*Audience: End-users
+
** Author: Csaba Pinter
*Based on: 3D Slicer version 4.5
+
** Modules: Welcome to Slicer, Data, Volume Rendering, Models.
*The [[Media:3DVisualizationData.zip | 3DVisualization dataset]] contain an MR scan and a series of 3D models of the brain.
+
** Audience: End-users
 +
** Based on: 3D Slicer version 4.10
 +
** The [http://slicer.kitware.com/midas3/download/?items=330421,1 3DVisualization dataset] contain an MR scan and a series of 3D models of the brain.
 +
 
 +
* Slicer 4.5
 +
** 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 Slicer 4.5.  
 +
** Author: Sonia Pujol, Ph.D.
 +
** Modules: Welcome to Slicer, Sample Data, Models.
 +
** Audience: End-users
 +
** Based on: 3D Slicer version 4.5
 +
** The [http://slicer.kitware.com/midas3/download/?items=330421,1 3DVisualization dataset] contain an MR scan and a series of 3D models of the brain.
 
|align="right"|
 
|align="right"|
 +
[[Image:20180426_DataLoadingAndVisualizationTutorial.png|right|250px|]]
 
[[Image:Slicer4DataLoading_tutorial.png|right|250px|]]
 
[[Image:Slicer4DataLoading_tutorial.png|right|250px|]]
 
|}
 
|}
 +
 +
==Slicer4 3D Visualization of DICOM images for Radiology Applications==
 +
{|width="100%"
 +
|
 +
*The [https://www.dropbox.com/s/9jcjpl33qfh5pi6/3DVisualizationDICOM_Slicer4.8_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
 +
*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|]]
 +
|}
 +
 +
  
 
=Tutorials for software developers=
 
=Tutorials for software developers=
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{|width="100%"
 
{|width="100%"
 
|
 
|
*The [[Media:Slicer4_ProgrammingTutorial_Slicer4.5.pdf | Hello Python Programming tutorial]]course guides through the integration of a python module in Slicer4.  
+
*The [https://www.dropbox.com/s/wrhrvvmplosiis1/Slicer4_ProgrammingTutorial_SPujol-SPieper_Nightly.pdf?dl=0# Slicer Programming tutorial] guides through the integration of a python module in Slicer4.  
 
*Author: Sonia Pujol, Ph.D., Steve Pieper, Ph.D.
 
*Author: Sonia Pujol, Ph.D., Steve Pieper, Ph.D.
 
*Audience: Developers
 
*Audience: Developers
*Based on: 3D Slicer version 4.5
+
*Based on: 3D Slicer version 4.7
*The [[Media:HelloPython_Slicer4.4.zip| HelloPython dataset]] contains three Python files and an MR scan of the brain.
+
*The [https://www.dropbox.com/s/6yxu8qepmvywk0n/HelloPython_Nightly.zip?dl=0 HelloPython dataset] contains sample data set (MR scan of the brain) and complete Python module examples.
 
|align="right"|
 
|align="right"|
 
[[Image:HelloPythonTutorial.png|right|250px|]]
 
[[Image:HelloPythonTutorial.png|right|250px|]]
 
|}
 
|}
 +
 +
== PerkLab's Slicer bootcamp training materials ==
 +
{|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 script repository ==
  
 
For additional Python scripts examples, please visit the [[Documentation/{{documentation/version}}/ScriptRepository|Script Repository page]]
 
For additional Python scripts examples, please visit the [[Documentation/{{documentation/version}}/ScriptRepository|Script Repository page]]
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|}
 
|}
  
=Specific functions=
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=Segmentation=
 +
== Slicer4 Image 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://youtu.be/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.
 +
** Sample data set: http://slicer.kitware.com/midas3/download/bitstream/738905/CTA-cardio2.nrrd
 +
** Based on: 3D Slicer version 4.8
 +
|align="right"|[[Image:WholeHeartSegYoutube.png|280px]]
 +
|---
 +
|
 +
* '''[https://youtu.be/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]
 +
|}
 +
 +
=Registration=
 +
 +
== Slicer4 Image Registration ==
 +
 +
{|width="100%"
 +
|
 +
*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
 +
 +
 +
== 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 ==
 
==Slicer4 Diffusion Tensor Imaging Tutorial ==
 
{|width="100%"
 
{|width="100%"
 
|
 
|
*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.  
+
*Please visit [http://dmri.slicer.org/docs/ dmri.slicer.org/docs] for the latest documentation of SlicerDMRI.
 +
*The [https://www.dropbox.com/s/m7rzeblbdzr49bc/DiffusionMRIAnalysis_Slicer4.8_SoniaPujol.pdf?dl=0| Diffusion Tensor Imaging]  course 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
 
*The [[media:Dti tutorial data.zip|DTI dataset]] contains an MR Diffusion Weighted Imaging scan of the brain.
 
*The [[media:Dti tutorial data.zip|DTI dataset]] contains an MR Diffusion Weighted Imaging scan of the brain.
 
|align="right"|
 
|align="right"|
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{|width="100%"
 
{|width="100%"
 
|
 
|
*The [[media:WhiteMatterExplorationTutorial_SoniaPujol_Slicer4.5.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|]]
 
 
|}
 
|}
  
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|}
 
|}
  
== Slicer4 3D Printing ==
 
  
{|width="100%"
+
==Slicer4 Radiation Therapy Tutorial ==
|
 
* This ''Slicer 4.3 [https://www.youtube.com/watch?v=MKLWzD0PiIc 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
 
|align="right"|[[Image:3DPrinting_tutorial.png|250px]]
 
|}
 
 
 
== Slicer4 Image Registration ==
 
  
 
{|width="100%"
 
{|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://github.com/SlicerRt/SlicerRtDoc/raw/master/tutorials/SlicerRT_WorldCongress_TutorialIGRT.pdf SlicerRT tutorial] is an introduction to the Radiation Therapy functionalities of Slicer.
* Authors: Sonia Pujol, Ph.D., Dominik Meier, Ph.D., Ron Kikinis, M.D.
+
* Author: Csaba Pinter, Andras Lasso, An Wang, Gregory C. Sharp, David Jaffray, Gabor Fichtinger.  
* Audience: Users and developers interested in image registration
+
* Dataset: [http://slicer.kitware.com/midas3/download/item/205404/SlicerRT_WorldCongress_TutorialIGRT_Dataset.zip download] from MIDAS server
* Dataset: [[Media:RegistrationData.zip| 3D Slicer Registration Data]]
+
* Based on Slicer 4.7
|align="right"|[[File:registration_Slicer4.png|250px]]
+
|align="right"|
 +
<!-- [[Image:TUTORIAL-IMAGE-HERE.png|right|150px|]] -->
 
|}
 
|}
*Based on: 3D Slicer version 4.5
 
See [[Documentation/{{documentation/version}}/Registration/RegistrationLibrary|the Registration Library for worked out registration examples with data]].
 
  
==Subject Hierarchy==
 
  
 +
==Slicer Pathology==
 
{|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.
+
*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: Csaba Pinter, Queen's University, Canada
+
*Author: Erich Bremer (Stonybrook), Andriy Fedorov (Brigham and Women’s Hospital)
*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.
+
*Dataset:  Available directly with the Slicer Pathology Slicer extension.
 
|align="right"|
 
|align="right"|
[[File:SubjectHierarchyTutorial.png | 200px]].  
+
[[File:SlicerPathologyScreenShot8.png | 200px]].  
 
|}
 
|}
  
== Fast GrowCut ==
+
==SPHARM-PDM==
 
 
 
{|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 [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: Hillary Lia
+
*Author: Jonathan Perdomo (UNC), Beatriz Paniagua (Kitware Inc.)
* Audience: Users interested in segmentation
+
*Dataset:  [https://www.nitrc.org/docman/view.php/308/1981/SPHARM_Tutorial_Data_July2015.zip Tutorial Data]
|align="right"|[[File:FastGrowCutLogo.png|200px]]
 
|}
 
 
 
 
 
== 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].
 
 
 
=Summer 2014 Tutorial contest=
 
 
 
==Cardiac Agatston Tutorial==
 
{|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"|
 
|align="right"|
[[File:CardiacAgatstonMeasuresModuleScreenshot.jpg| 250px]]
+
[[File:SlicerWinterProjectWeek2017-SPHARM-PDM.png | 200px]].
 
|}
 
|}
  
==CMR Toolkit LA workflow==
+
==Fiber Bundle Volume Measurement==
 
{|width="100%"
 
{|width="100%"
 
|
 
|
*[http://wiki.na-mic.org/Wiki/index.php/File:CMRToolkitLAWorkflow_TutorialContestSummer2014.pdf  CMR Toolkit LA Workflow Tutorial]
+
*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: Salma Bengali, Josh Cates, University of Utah
+
*Author: Shun Gong (Shanghai Changzheng Hospital, China)
*Dataset:  [http://wiki.na-mic.org/Wiki/index.php/File:CMRToolkitLAWorkflowData_TutorialContestSummer2014.zip CMRToolkitLAWorkflow Dataset]
+
*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"|
[[Image:Utah_SummerContest2014_tutorial.png|300px]]
+
[[File:SlicerWinterProjectWeek2017-FiberBundleVolumeMeasurements.png | 200px]].
 
|}
 
|}
  
=Summer 2013 Tutorial contest=  
+
= 3D Slicer version 4.7 Tutorial Contest=
  
==Cardiac MRI Toolkit==
+
For previous editions of the contest, please visit the [https://na-mic.org/wiki/Tutorial_Contests 3D Slicer Tutorial Contests page]
{|width="100%"
 
|
 
*[[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==
+
===Segmentation for 3D printing===
 
{|width="100%"
 
{|width="100%"
 
|
 
|
*[[Media:Hello_CLI_TutorialContestSummer2013.pdf|HelloCLI]]
+
*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.
*Authors:   Nadya Shusharina, Greg Sharp, MGH, Boston
+
*Author: Csaba Pinter (Queen's University, Canada)
*Dataset: [[Media:Hello_CLI_TutorialContestSummer2013.zip‎|HelloCLI Dataset]]
+
* [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].
 
|align="right"|
 
|align="right"|
[[Image:Cli_icon.png|300px]]
+
[[File:SlicerWinterProjectWeek2017-Segmentation-for-3d-printing.png | 200px]].
 
|}
 
|}
  
==SlicerRT==
+
===Slicer Pathology===
 
{|width="100%"
 
{|width="100%"
 
|
 
|
*[[Media:SlicerRT_TutorialContestSummer2013.pdf|SlicerRT Tutorial]]
+
*The [[Documentation/{{documentation/version}}/Extensions/SlicerPathology|Slicer Pathology Tutorial]] describes how to use the corresponding tools for automatic and semi-automatic pathology image segmentation.
*Authors:   Csaba Pinter, Andras Lasso (Queen's), Kevin Wang (PMH, Toronto)
+
*Author: Erich Bremer (Stonybrook), Andriy Fedorov (Brigham and Women’s Hospital)
*Dataset:  [[Media:CsabaPinter-SlicerRtTutorial_Namic2013June.zip|SlicerRT Dataset]]
+
*Dataset:  Available directly with the Slicer Pathology Slicer extension.
 
|align="right"|
 
|align="right"|
[[Image:667px-SlicerRT_0.10_IsocenterShiftingEvaluation.png|250px]]
+
[[File:SlicerPathologyScreenShot8.png | 200px]].
 
|}
 
|}
  
==DTIPrep==
+
===Simple Python Tool for Quality Control of DWI data===
 
{|width="100%"
 
{|width="100%"
 
|
 
|
*[[Media:DTIPrep_TutorialContestSummer2013.pdf|DTIPrep]]
+
*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).
*Authors:   Dave Welch, SINAPSE, IOWA
+
*Author: Laurent Chauvin (ETS Montreal)
*Dataset:  [[Media:DTIPrepData_TutorialContestSummer2013.zip|DTIPrep Dataset]]
+
*Dataset:  Not available.
 
|align="right"|
 
|align="right"|
[[Image:DTIPrep-tutorial.png|250px]]
+
[[File:SlicerWinterProjectWeek2017-SimpleDiffusionGradientInformationExtractorTutorial.png | 200px]].
 
|}
 
|}
  
= Summer 2012 Tutorial contest =  
+
===SPHARM-PDM===
 
 
==Automatic Left Atrial Scar Segmenter ==
 
 
{|width="100%"
 
{|width="100%"
 
|
 
|
*[http://wiki.na-mic.org/Wiki/index.php/CARMA-LA-Scar_TutorialContestSummer2012 Automatic Left Atrial Scar Segmenter]  
+
*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: Greg Gardner, Josh Cates, SCI, Utah
+
*Author: Jonathan Perdomo (UNC), Beatriz Paniagua (Kitware Inc.)
*Dataset: [http://wiki.na-mic.org/Wiki/index.php/File:CARMA-LA-Scar_TutorialContestSummer2012.zip CARMA-LA-Scar data]
+
*Dataset: [https://www.nitrc.org/docman/view.php/308/1981/SPHARM_Tutorial_Data_July2015.zip Tutorial Data]
 
|align="right"|
 
|align="right"|
[[Image:Carma afib auto scar.png|250px]]
+
[[File:SlicerWinterProjectWeek2017-SPHARM-PDM.png | 200px]].
 
|}
 
|}
  
==Qualitative and quantitative comparison of  two RT dose distributions==
+
===Integration of Robot Operating System (ROS) and 3D Slicer using OpenIGTLink===
 
{|width="100%"
 
{|width="100%"
 
|
 
|
*[http://www.na-mic.org/Wiki/index.php/File:PlastimatchDose_TutorialContestSummer2012.pdf Qualitative and quantitative comparison of two RT dose distributions]
+
*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.
*AuthorsJames Shackleford, Nadya Shusharina, Greg Sharp, MGH
+
*Author: Junichi Tokuda (Brigham and Women’s Hospital)
 +
*DatasetNot available.
 
|align="right"|
 
|align="right"|
[[Image:PlastimatchDose.png|250px]]
+
[[File:SlicerWinterProjectWeek2017-Integration-ROS-3DSlicer-OpenIGTLink.png | 200px]].
 
|}
 
|}
  
==Dose accumulation for adaptive radiation therapy==
+
===Fiber Bundle Volume Measurement===
 
{|width="100%"
 
{|width="100%"
 
|
 
|
*[http://www.na-mic.org/Wiki/index.php/File:DoseAccumulationforAdaptiveRadiationTherapy_TutorialContestSummer2012.pdf Dose accumulation for adaptive radiation therapy]
+
*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.
*AuthorsKevin Wang, Csaba Pinter, Andras Lasso, PMH, Queen's
+
*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]]).
 
|align="right"|
 
|align="right"|
[[Image:AdaptiveradiationTherapy.png|250px]]
+
[[File:SlicerWinterProjectWeek2017-FiberBundleVolumeMeasurements.png | 200px]].
 
|}
 
|}
  
==WebGL Export==
+
=YouTube videos=
{|width="100%"
+
{| border="1" cellpadding="5" width="1200px"
|
+
| style="width:25%" | [[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]
*[http://www.na-mic.org/Wiki/index.php/File:WebGLExport_TutorialContestSummer2012.pdf  WebdGLExport]
+
| style="width:25%" | [[Image:Femurmodel.png|right|250px|]] [https://www.youtube.com/watch?v=0at15gjk-Ns Creating a femur model from CT volume using 3D Slicer - Author: Nabgha Farhat ]
*Authors: Nicolas Rannou, Daniel Haehn, Children's Hospital
+
| style="width:25%" | [[Image:3DPrinting.png|right|250px|]] [https://www.youtube.com/watch?v=MKLWzD0PiIc Preparing data for 3D printing - Author: PerkLab ]
|align="right"|
+
| style="width:25%" | [[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]
[[Image:WebGLExport.png|250px]]
+
| 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]
 +
|-
 
|}
 
|}
  
==OpenIGTLink==
+
Additional [http://www.youtube.com/results?search_query=3d+slicer&sm=3 non-curated videos-based demonstrations using 3D Slicer are accessible on YouTube].
{|width="100%"
 
|
 
*[http://wiki.slicer.org/slicerWiki/images/f/f1/OpenIGTLinkTutorial_Slicer4.1.0_JunichiTokuda_Apr2012.pdf OpenIGTLink]
 
*Authors:  Junichi Tokuda, BWH
 
|align="right"|
 
[[Image:OpenIGTLink.png|250px]]
 
|}
 
  
=Additional resources =
+
=Teams Contributions  =
 
{|width="100%"
 
{|width="100%"
 
|
 
|
Line 330: Line 386:
 
----
 
----
 
<br>
 
<br>
 +
== International resources==
 +
 +
==Resources in Chinese ==
 
{|width="100%"
 
{|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.
+
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.
:Author: Dominik Meier, Ph.D.
+
 
:Audience:  users interested learning/applying Slicer image registration technology
+
* [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]
|align="right"|[[Image:RegLib_table.png|250px|link=http://wiki.slicer.org/slicerWiki/index.php/Documentation/{{documentation/version}}/Registration/RegistrationLibrary]]
+
 
 +
* [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]
 +
 
 +
* [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]
 +
 
 +
* [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 ]
 +
 
 +
* [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]
 +
 
 +
* [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]
 +
 
 +
|align="right"|
 +
[[image:Wechat-hemorage-2018-02-12.png|250px|Example WeChat tutorial slides]]
 
|}
 
|}
  
= External Resources =
+
==Resources in German ==
 +
 
 +
* [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)
 +
 
 +
== 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 ==
 +
 
 +
=== Fast GrowCut ===
 +
 
 +
{|width="100%"
 +
|
 +
* The [[media:FastGrowCutTutorial.pdf |Fast GrowCut tutorial]]  shows how to perform a segmentation using the Fast GrowCut effect in Slicer.
 +
* Authors: Hillary Lia
 +
* Audience: Users interested in segmentation
 +
|align="right"|[[File:FastGrowCutLogo.png|200px]]
 +
|}
  
== Using the Editor ==
+
=== 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:
 
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:
Line 350: Line 442:
 
* [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 14:54, 27 November 2019

Home < Documentation < Nightly < Training

For the stable Slicer documentation, visit the 4.10 page.

Introduction: Slicer Nightly Tutorials


  • Some of these tutorials are based on older releases of 3D Slicer and are being upgraded to Slicer4.10. The concepts are still useful but some interface elements and features may be different in updated versions.

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 version 4.8

SlicerWelcome tutorial

General Introduction

Slicer Welcome Tutorial

  • The [1] 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 version 4.8

SlicerWelcome tutorial

Slicer4Minute Tutorial

  • The Slicer4 Minute Tutorial is a brief introduction to the advanced 3D visualization capabilities of Slicer 4.8.
  • 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 4.8
  • The Slicer4Minute dataset contains an MR scan of the brain and 3D reconstructions of the anatomy
Slicer4Minute tutorial

3D Visualization

Slicer4 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: 3D Slicer version 4.10
    • The 3DVisualization dataset contain an MR scan and a series of 3D models of the brain.
  • Slicer 4.5
    • The Data loading and 3D visualization course guides through the basics of loading and viewing volumes and 3D models in Slicer 4.5.
    • 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.
20180426 DataLoadingAndVisualizationTutorial.png
Slicer4DataLoading tutorial.png

Slicer4 3D Visualization of DICOM images for Radiology Applications

  • 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
  • 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


Tutorials for software developers

Slicer4 Programming Tutorial

  • The Slicer Programming tutorial 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 4.7
  • The HelloPython dataset contains sample data set (MR scan of the brain) and complete Python module examples.
HelloPythonTutorial.png

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 script repository

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

Developing and contributing extensions for 3D Slicer

Contributing3DSlicerExtension.png

Segmentation

Slicer4 Image Segmentation

20170717 3DPrintingTutorialYoutube.PNG
WholeHeartSegYoutube.png
FemurSegmentationYoutube.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


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

  • Please visit dmri.slicer.org/docs for the latest documentation of SlicerDMRI.
  • The Diffusion Tensor Imaging course 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
  • 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 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


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.

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: Nabgha Farhat
3DPrinting.png
Preparing data for 3D printing - Author: PerkLab
Verterbra.png
How to segment multiple vertebrae in spine CT for 3D printing - Author: Hillary Lia
DICOM2.png
How to export CT and segmentation data to DICOM- Author: Andras Lasso, Csaba Pinter

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

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.

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

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: