Difference between revisions of "Documentation/Nightly/Training"

From Slicer Wiki
Jump to: navigation, search
Tag: 2017 source edit
 
(154 intermediate revisions by 11 users not shown)
Line 1: Line 1:
−
<noinclude>{{documentation/versioncheck}}</noinclude>
+
=Introduction: Slicer Tutorials=
−
__TOC__
 
  
 +
*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 "reference manual" style documentation, please see the [https://slicer.readthedocs.io/en/latest/ Slicer manual on ReadTheDocs].
 +
*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.]'''
  
−
=Introduction: Slicer {{documentation/version}} 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 [[Training| Slicer training portal]].
  
−
*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.
+
__TOC__
−
*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 questions related to the Slicer4 Compendium, please send an e-mail to '''[http://www.na-mic.org/Wiki/index.php/User:SPujol Sonia Pujol, Ph.D]'''
 
  
−
{{documentation/banner|text=Some of these tutorials are based on older releases of 3D Slicer. The concepts are still useful but bear in mind that some interface elements and features will be different in updated versions.}}
+
=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==
−
{|width="100%"
+
{| width="100%"
 
|
 
|
−
*The [[media:SlicerWelcome-tutorial_SoniaPujol.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 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
−
*Based on: 3D Slicer version 4.0
+
*Modules: Welcome to Slicer, Sample Data
−
|align="right"|
+
*Based on 3D Slicer 4.8
 +
*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==
−
{|width="100%"
+
{| width="100%"
 
|
 
|
−
*The [[media:Slicer4minute-tutorial_SoniaPujol-mj.pdf|Slicer4Minute tutorial]] is a brief introduction to the advanced 3D visualization capabilities of Slicer 4.0.
+
*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
−
*Based on: 3D Slicer version 4.0
+
*Modules: Welcome to Slicer, Models
−
*The [[media:Slicer4minute.zip|Slicer4Minute dataset]] contains an MR scan of the brain and 3D reconstructions of the anatomy
+
*Based on Slicer version 4.8
−
|align="right"|
+
*Compatible with Slicer 4.10.1
 +
*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 ==
+
=3D Visualization=
−
{|width="100%"
+
==Data Loading and 3D Visualization==
 +
{| width="100%"
 
|
 
|
−
*The [[Media:DataLoadingAndVisualizationSlicer4.1_SoniaPujol.pdf | Data loading and 3D visualization]] course guides through the basics of loading and viewing volumes and 3D models in Slicer4 .  
+
*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: 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 4.1
+
 
−
*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 ==
+
==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 [[Media: Slicer4_ProgrammingTutorial_SPujol-SPieper_slicer4.4.pdf‎| 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
 +
*Based on: 3D Slicer version 5.0/4.11
 +
| align="right" |
 +
[[Image:SlicerProgrammingTutorial.png|right|250px|]]
 +
|}
 +
 +
==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==
 +
{| 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.
 +
*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
−
*The [[Media:HelloPython_Slicer4.4| HelloPython dataset]] contains three Python files and an MR scan of the brain.
+
| align="right" |
−
|align="right"|
+
[[Image:Contributing3DSlicerExtension.png|right|250px|]]
−
[[Image:HelloPythonTutorial.png|right|250px|]]
+
|}
 +
 
 +
=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]]
 +
 
 
|}
 
|}
  
−
=Specific functions=
+
=Registration=
  
−
==Slicer4 Diffusion Tensor Imaging Tutorial ==
+
==Slicer4 Image Registration==
−
{|width="100%"
+
 
 +
{| width="100%"
 
|
 
|
−
*The [[Media:DiffusionTensorImaging_Slicer4.1_SoniaPujol.pdf | Diffusion Tensor Imaging Tutorial]] course guides through the basics of loading Diffusion Weighted images in Slicer, estimating tensors and generating fiber tracts.  
+
*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
−
*Based on: 3D Slicer version 4.1
+
*Modules: Data, Volumes, DWI to DTI Estimation, Diffusion Tensor Scalar Measurements, Editor, Markups, Tractography Label Map Seeding, Tractography Interactive Seeding
−
*The [[Media:DiffusionMRI_tutorialData.zip |DTI dataset]] contains an MR Diffusion Weighted Imaging scan of the brain.
+
*Based on: 3D Slicer version 4.8; Compatible with Slicer version 4.10.2
−
|align="right"|
+
*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.
 +
*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 [[Media:NeurosurgicalPlanning_SoniaPujol.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
−
*Based on: 3D Slicer version 4.1
+
*Modules: Segment Editor, Tractography
−
*The [[Media:WhiteMatterExplorationData.zip| White Matter Exploration datasets]] contains a Diffusion Weighted Imaging scan of brain tumor patient.
+
*Based on 3D Slicer version 4.10
−
|align="right"|
+
*The [[Media:WhiteMatterExplorationData.zip| White Matter Exploration dataset]] contains a Diffusion Weighted Imaging scan of a brain tumor patient.
 +
| 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:3DVisualizationDICOMforRadiologyApplications_SoniaPujol_KittShaffer_RSNA2011.pdf | Slicer4RSNA]] course guides through 3D data loading and visualization of DICOM images for Radiology Applications in Slicer4.
 
−
*Author: Sonia Pujol, Ph.D., Kitt Shaffer, M.D., Ph.D.
 
−
*Audience: Radiologists and users of Slicer who need a more comprehensive overview over Slicer4 visualization capabilities.
 
−
*Based on: 3D Slicer version 4.0
 
−
*The [[Media:3DVisualizationData RSNA2011 part1.zip | Slicer4RSNAdataset1]] and [[Media:3DVisualizationData RSNA2011 part2.zip | Slicer4RSNAdataset2]] contain a series of MR and CT scans, and 3D models of the brain, lung and liver.
 
−
|align="right"|
 
−
[[Image:Slicer4RSNA_2.png|right|250px|]]
 
 
|}
 
|}
  
 
==Slicer4 Quantitative Imaging tutorial==
 
==Slicer4 Quantitative Imaging tutorial==
−
{|width="100%"
+
{| width="100%"
 
|
 
|
−
*The [[media:Slicer4QuantitativeImaging.pdf| Slicer4 Quantitative Imaging tutorial]] guides through the use for Slicer for quantifying small volumetric changes in slow-growing tumors, and for calculating Standardized Uptake Value (SUV) from PET/CT data.
+
*The [[Media: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: Jeffrey Yap, Ph.D., Ron Kikinis, M.D., Randy Gollub, M.D., Ph.D., Wendy Plesniak, Ph.D., Nicole Aucoin, B.Sc., Sonia Pujol, Ph.D., Valerie Humblet, Ph.D., Andriy Fedorov, Ph.D., Kilian Poh, Ph.D., Ender Konugolu, Ph.D.
+
*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.
−
*Based on: 3D Slicer version 4.0
+
*Modules: Data, Volumes, Models, Change Tracker, PET Standard Uptake Value Computation
−
*The [[media:PETCTFusion-TutorialData.zip| PETCTFusion]] and [[media:ChangeTracker2011.zip|Change Tracker]] datasets contain a series of MR, CT and PET data.
+
*Based on: 3D Slicer version 4.5
−
|align="right"|
+
*The [[Media:QuantitativeImaging.zip| Quantitative Imaging dataset]] contains a series of MR and PET/CT data.
 +
| align="right" |
 
[[Image:Slicer4_QuantitativeImaging.png|right|250px|]]
 
[[Image:Slicer4_QuantitativeImaging.png|right|250px|]]
 
|}
 
|}
  
−
== Slicer4 3D Printing ==
+
==Slicer4 IGT==
−
{|width="100%"
+
{| width="100%"
 
|
 
|
−
* This ''Slicer 4.3 [https://www.youtube.com/watch?v=MKLWzD0PiIc 3D printing tutorial]''  shows how to prepare 3D Slicer data for 3D printing.
+
*[http://www.slicerigt.org/wp/user-tutorial/ Slicer IGT tutorials]
−
* Authors: Nabgha Farhat, MSc
+
*Authors: Tamas Ungi, M.D, Ph.D., Junichi Tokuda, Ph.D.
−
* Audience: Users and developers interested in 3D printing
+
*Audience: End-users interested in using Slicer for real-time navigated procedures. E.g. navigated needle insertions or other minimally invasive medical procedures.
−
|align="right"|[[Image:3DPrinting_tutorial.png|250px]]
+
*Modules: SlicerIGT Extension
 +
*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]
 +
| align="right" |
 +
[[Image:SlicetIGT.png|right|150px|]]
 
|}
 
|}
−
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].
 
  
−
<br>
 
−
=Summer 2014 Tutorial contest=
 
  
−
==Cardiac Agatston Tutorial==
+
==Slicer4 Radiation Therapy Tutorial==
−
{|width="100%"
+
 
 +
{| width="100%"
 
|
 
|
−
*[http://wiki.na-mic.org/Wiki/index.php/File:TutorialContest_CardiacAgatstonScoring_2014.pdf| Cardiac Agatston Scoring Tutorial]
+
*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:   Jessica Forbes, Hans Johnson, University of Iowa
+
*Author: Csaba Pinter, Andras Lasso, An Wang, Gregory C. Sharp, David Jaffray, Gabor Fichtinger.
−
*Dataset: [http://wiki.na-mic.org/Wiki/index.php/File:CardiacAgatstonMeasures_TutorialContestSummer2014.zip|Cardiac Agatston Scoring Tutorial Dataset]
+
*Dataset: [http://slicer.kitware.com/midas3/download/item/205404/SlicerRT_WorldCongress_TutorialIGRT_Dataset.zip download] from MIDAS server
−
|align="right"|
+
*Based on Slicer 4.7
−
[[File:CardiacAgatstonMeasuresModuleScreenshot.jpg| 250px]]
+
| align="right" |
 +
[[Image:SlicerRTUseCaseImage.png|right|150px|]]
 
|}
 
|}
  
−
==CMR ToolkitLA workflow==
+
==Slicer Pathology==
−
{|width="100%"
+
{| width="100%"
 
|
 
|
−
*[http://wiki.na-mic.org/Wiki/index.php/File:CMRToolkitLAWorkflow_TutorialContestSummer2014.pdf |CMRToolkitLAWorkflow 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: Salma Bengali, Josh Cates, University of Utah
+
*Author: Erich Bremer (Stonybrook), Andriy Fedorov (Brigham and Women’s Hospital)
−
*Dataset:  [http://wiki.na-mic.org/Wiki/index.php/File:CMRToolkitLAWorkflowData_TutorialContestSummer2014.zip |CMRToolkitLAWorkflow Dataset]
+
*Dataset:  Available directly with the Slicer Pathology Slicer extension.
−
|align="right"|
+
| align="right" |
−
[[Image:Cli_icon.png|300px]]
+
[[File:SlicerPathologyScreenShot8.png | 200px]].
 
|}
 
|}
  
−
=Summer 2013 Tutorial contest=  
+
==SPHARM-PDM==
 +
{| 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.
 +
*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]
 +
| align="right" |
 +
[[File:SlicerWinterProjectWeek2017-SPHARM-PDM.png | 200px]].
 +
|}
  
−
==Cardiac MRI Toolkit==
+
==Fiber Bundle Volume Measurement==
−
{|width="100%"
+
{| width="100%"
 
|
 
|
−
*[[Media:Cardiac MRI Toolkit Tutorial Summer2013.pdf|Cardiac MRI Toolkit]]
+
*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, SCI, Utah
+
*Author: Shun Gong (Shanghai Changzheng Hospital, China)
−
*Dataset:  [[Media:Cardiac_MRI_Toolkit_Tutorial_Data.zip|Cardiac MRI Toolkit Tutorial 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:CMRToolkit_Tutorial_Image.png|250px]]
+
[[File:SlicerWinterProjectWeek2017-FiberBundleVolumeMeasurements.png | 200px]].
 
|}
 
|}
  
−
==HelloCLI==
+
==Slicer4 Lung CT Analyzer==
−
{|width="100%"
+
{| width="100%"
 
|
 
|
−
*[[Media:Hello_CLI_TutorialContestSummer2013.pdf|HelloCLI]]
+
*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.
−
*Authors:   Nadya Shusharina, Greg Sharp, MGH, Boston
+
*Authors: Rudolph Bumm, MD, Andras Lasso, PhD.
−
*Dataset: [[Media:Hello_CLI_TutorialContestSummer2013.zip‎|HelloCLI Dataset]]
+
*Audience: End-users
−
|align="right"|
+
*Modules: LungCTSegmenter, LungCTAnalyzer
−
[[Image:Cli_icon.png|300px]]
+
*Based on: 3D Slicer version 5.0 (4.11)
 +
| align="right" |
 +
[[Image:LungCTAnalyzer.png|right|250px|]]
 +
 
 
|}
 
|}
  
−
==SlicerRT==
+
=3D Slicer version 4.7 Tutorial Contest=
−
{|width="100%"
+
 
 +
For previous editions of the contest, please visit the [https://na-mic.org/wiki/Tutorial_Contests 3D Slicer Tutorial Contests page]
 +
 
 +
===Segmentation for 3D printing===
 +
{| width="100%"
 
|
 
|
−
*[[Media:SlicerRT_TutorialContestSummer2013.pdf|SlicerRT Tutorial]]
+
*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:   Csaba Pinter, Andras Lasso (Queen's), Kevin Wang (PMH, Toronto)
+
*Author: Csaba Pinter (Queen's University, Canada)
−
*Dataset: [[Media:CsabaPinter-SlicerRtTutorial_Namic2013June.zip|SlicerRT Dataset]]  
+
*[https://www.youtube.com/watch?v=Uht6Fwtr9hE Narrated video version on YouTube].
−
|align="right"|
+
*Dataset: [[:File:BasePiece.zip|Phantom base STL model]] Source: [http://perk-software.cs.queensu.ca/plus/doc/nightly/modelcatalog/ PerkLab].
−
[[Image:667px-SlicerRT_0.10_IsocenterShiftingEvaluation.png|250px]]
+
| align="right" |
 +
[[File:SlicerWinterProjectWeek2017-Segmentation-for-3d-printing.png | 200px]].
 
|}
 
|}
  
−
==DTIPrep==
+
===Slicer Pathology===
−
{|width="100%"
+
{| width="100%"
 
|
 
|
−
*[[Media:DTIPrep_TutorialContestSummer2013.pdf|DTIPrep]]
+
*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:   Dave Welch, SINAPSE, IOWA
+
*Author: Erich Bremer (Stonybrook), Andriy Fedorov (Brigham and Women’s Hospital)
−
*Dataset:  [[Media:DTIPrepData_TutorialContestSummer2013.zip|DTIPrep Dataset]]
+
*Dataset:  Available directly with the Slicer Pathology Slicer extension.
−
|align="right"|
+
| align="right" |
−
[[Image:DTIPrep-tutorial.png|250px]]
+
[[File:SlicerPathologyScreenShot8.png | 200px]].
 
|}
 
|}
  
−
=Summer 2012 Tutorial contest (under construction)=  
+
===Simple Python Tool for Quality Control of DWI data===
−
 
+
{| width="100%"
−
==Automatic Left Atrial Scar Segmenter ==
 
−
{|width="100%"
 
 
|
 
|
−
*[http://wiki.na-mic.org/Wiki/index.php/CARMA-LA-Scar_TutorialContestSummer2012 Automatic Left Atrial Scar Segmenter]
+
*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: Greg Gardner, Josh Cates, SCI, Utah
+
*Author: Laurent Chauvin (ETS Montreal)
−
*Dataset: [http://wiki.na-mic.org/Wiki/index.php/File:CARMA-LA-Scar_TutorialContestSummer2012.zip CARMA-LA-Scar data]
+
*Dataset: Not available.
−
|align="right"|
+
| align="right" |
 +
[[File:SlicerWinterProjectWeek2017-SimpleDiffusionGradientInformationExtractorTutorial.png | 200px]].
 
|}
 
|}
  
−
==Qualitative and quantitative comparison of  two RT dose distributions==
+
===SPHARM-PDM===
−
{|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.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:  James Shackleford, Nadya Shusharina, Greg Sharp, MGH
+
*Author: Jonathan Perdomo (UNC), Beatriz Paniagua (Kitware Inc.)
−
|align="right"|
+
*Dataset:  [https://www.nitrc.org/docman/view.php/308/1981/SPHARM_Tutorial_Data_July2015.zip Tutorial Data]
 +
| align="right" |
 +
[[File:SlicerWinterProjectWeek2017-SPHARM-PDM.png | 200px]].
 
|}
 
|}
  
−
==Dose accumulation for adaptive radiation therapy==
+
===Integration of Robot Operating System (ROS) and 3D Slicer using OpenIGTLink===
−
{|width="100%"
+
{| width="100%"
 
|
 
|
−
*[http://www.na-mic.org/Wiki/index.php/File:DoseAccumulationforAdaptiveRadiationTherapy_TutorialContestSummer2012.pdf Dose accumulation for adaptive radiation therapy]
+
*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.
−
*Authors:  Kevin Wang, Csaba Pinter, Andras Lasso, PMH, Queen's
+
*Author: Junichi Tokuda (Brigham and Women’s Hospital)
−
|align="right"|
+
*Dataset:  Not available.
 +
| align="right" |
 +
[[File:SlicerWinterProjectWeek2017-Integration-ROS-3DSlicer-OpenIGTLink.png | 200px]].
 
|}
 
|}
  
−
==WebGL Export==
+
===Fiber Bundle Volume Measurement===
−
{|width="100%"
+
{| width="100%"
 
|
 
|
−
*[http://www.na-mic.org/Wiki/index.php/File:WebGLExport_TutorialContestSummer2012.pdf  WebdGLExport]
+
*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:  Nicolas Rannou, Daniel Haehn, Children's Hospital
+
*Author: Shun Gong (Shanghai Changzheng Hospital, China)
−
|align="right"|
+
*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:SlicerWinterProjectWeek2017-FiberBundleVolumeMeasurements.png | 200px]].
 
|}
 
|}
  
−
==OpenIGTLink==
+
=YouTube videos=
−
{|width="100%"
+
{| 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]
−
*[http://wiki.slicer.org/slicerWiki/images/f/f1/OpenIGTLinkTutorial_Slicer4.1.0_JunichiTokuda_Apr2012.pdf OpenIGTLink]
+
| 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]
−
*Authors: Junichi Tokuda, BWH
+
| style="width:33%" |[[Image:3DPrinting.png|right|250px|]] [https://www.youtube.com/watch?v=MKLWzD0PiIc Preparing data for 3D printing - Author: Nabgha Farhat]
−
|align="right"|
+
|}
 +
{| 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 resources =
+
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%"
+
 
 +
=Teams Contributions=
 +
{| width="100%"
 
|
 
|
−
* 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.
+
*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.
−
* Authors: Steve Pieper Ph.D.
+
*Authors: Steve Pieper Ph.D.
−
* Audience: First time users and developers interested in Slicer 4.1 new features.
+
*Audience: First time users and developers interested in Slicer 4.1 new features.
−
* Length: 0h20m
+
*Length: 0h20m
−
|align="right"|[[Image:Webinar-Slicer-4.1.png|250px]]
+
| 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.
 
*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.  
+
*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.
 
*Audience: First time users interested in a broad overview of Slicer’s features and tools.
 
*Length: 1h20m
 
*Length: 1h20m
−
|align="right"|[[Image:Webinar.png|250px]]
+
| align="right" |[[Image:Webinar.png|250px]]
−
|-
+
|}
 +
<br>
 +
----
 +
<br>
 +
==International resources==
 +
International resources in Chinese and in German are made available by the Slicer community.
 +
 
 +
==Resources in Chinese==
 +
{| width="100%"
 
|
 
|
−
*The ''[http://wiki.slicer.org/slicerWiki/index.php/Documentation/Nightly/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. There's also a [http://wiki.slicer.org/slicerWiki/index.php/Category:Documentation/Nightly/Modules/Registration ''Registration Portal page''] with additional resources and training material regarding image registration.
+
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: 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/Nightly/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]
 +
*[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]
 +
 
 +
The WeChat 3D Slicer Group in China offers a [https://spujol.github.io/SlicerTutorialsInChinese/ comprehensive list of tutorials in Chinese.]
 +
 
 +
<br />
 +
 
 +
| 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===
  
−
== Using the Editor ==
+
{| 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]]
 +
|}
  
−
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:
+
{| 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.
 +
| align="right" |[[Image:ChuRouen.png|180px]]
 +
|}
  
−
* [http://openpaleo.blogspot.com/2008/12/3d-slicer-tutorial.html Open Source Paleontologist: 3D Slicer: The Tutorial]
+
===Use case: Slicer in paleontology===
−
* [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-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-vi.html Open Source Paleontologist: 3D Slicer: The Tutorial Part VI]
 
  
−
== Team Contributions ==
+
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:
−
See the collection of videos on the [http://vimeo.com/album/2363361 Kitware vimeo album].
 
  
−
== User Contributions ==
+
*[http://openpaleo.blogspot.com/2008/12/3d-slicer-tutorial.html Open Source Paleontologist: 3D Slicer: The Tutorial]
−
See the [[Documentation/{{documentation/version}}/Training/UserContributions|User Contributions Page]] for more content.
+
*[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-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-vi.html Open Source Paleontologist: 3D Slicer: The Tutorial Part VI]

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:

Retrieved from "https://www.slicer.org/w/index.php?title=Documentation/Nightly/Training&oldid=64301"