Training:Slicer4 Tutorials - Revision history

Spujol at 13:23, 27 March 2018

2018-03-27T13:23:16Z

Spujol at 13:22, 27 March 2018

2018-03-27T13:22:08Z

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Spujol: Created page with "( Page under construction) =Introduction: Slicer 4Tutorials= *This page contains "How to" tutorials with matched sample data sets. They demonstrate how to use the 3D Slicer v..."

2018-03-27T12:53:23Z

Created page with "( Page under construction) =Introduction: Slicer 4Tutorials= *This page contains "How to" tutorials with matched sample data sets. They demonstrate how to use the 3D Slicer v..."

New page

( Page under construction)
=Introduction: Slicer 4Tutorials=
*This page contains "How to" tutorials with matched sample data sets. They demonstrate how to use the 3D Slicer version 4 release to accomplish certain tasks.
*For tutorials for other versions of Slicer, please visit the [[Training| Slicer training portal]].
*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.]'''

__TOC__

=General Introduction=

==Slicer Welcome Tutorial==
{|width="100%"
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*The [[media:SlicerWelcome-tutorial_Slicer4.5.pdf|SlicerWelcome tutorial]] is an introduction to Slicer based on the Welcome module.
*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 4.6
|align="right"|
[[image:SlicerWelcome-image.png|250px|SlicerWelcome tutorial]]
|}

==Slicer4Minute Tutorial==
{|width="100%"
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*The [[media:Slicer4.5minute_SoniaPujol.pdf|Slicer4Minute tutorial]] is a brief introduction to the advanced 3D visualization capabilities of Slicer 4.5.
*Author: Sonia Pujol, Ph.D.
*Audience: First time users who want to discover Slicer in 4 minutes.
*Modules: Welcome to Slicer, Models
*Based on: 3D Slicer version 4.5
*The [[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]]
|}

==Slicer4 Data Loading and 3D Visualization ==
{|width="100%"
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*The [[Media:3DDataLoadingandVisualization_Slicer4.5_SoniaPujol.pdf | Data loading and 3D visualization]] course guides through the basics of loading and viewing volumes and 3D models in Slicer4 .
*Author: Sonia Pujol, Ph.D.
*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] contains an MR scan and a series of 3D models of the brain.
|align="right"|
[[Image:Slicer4DataLoading_tutorial.png|right|250px|]]
|}

=Tutorials for software developers=

== Slicer4 Programming Tutorial ==
{|width="100%"
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*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.
*Audience: Developers
*Based on: 3D Slicer version 4.7
*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"|
[[Image:HelloPythonTutorial.png|right|250px|]]
|}

For additional Python scripts examples, please visit the [[Documentation/{{documentation/version}}/ScriptRepository|Script Repository page]]

==Developing and contributing extensions for 3D Slicer==
{|width="100%"
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*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
*Based on: 3D Slicer version 4.4
|align="right"|
[[Image:Contributing3DSlicerExtension.png|right|250px|]]
|}

=Specific functions=

==Slicer4 Diffusion Tensor Imaging Tutorial ==
{|width="100%"
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*Please visit [http://dmri.slicer.org/docs/ dmri.slicer.org/docs] for the latest documentation of SlicerDMRI.
*The [[Media:DiffusionMRIanalysisTutorial_Slicer4.5_SoniaPujol.pdf |Diffusion Tensor Imaging Tutorial]] course guides through the basics of loading Diffusion Weighted images in Slicer, estimating tensors and generating fiber tracts.
*Author: Sonia Pujol, Ph.D.
*Audience: End-users and developers
*Modules: Data, Volumes, DWI to DTI Estimation, Diffusion Tensor Scalar Measurements, Editor, Markups,Tractography Label Map Seeding, Tractography Interactive Seeding
*Based on: 3D Slicer version 4.5
*The [[media:Dti tutorial data.zip|DTI dataset]] contains an MR Diffusion Weighted Imaging scan of the brain.
|align="right"|
[[Image:Slicer4DTI Tutorial.png|right|250px|]]
|}

==Slicer4 Neurosurgical Planning Tutorial==
{|width="100%"
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*Please visit [http://dmri.slicer.org/docs/ dmri.slicer.org/docs] for the latest documentation of SlicerDMRI.
*The [http://dmri.slicer.org/tutorials/Slicer-4.8/WhiteMatterExplorationTutorial.pdf Neurosurgical Planning tutorial] course guides through the generation of fiber tracts in the vicinity of a tumor.
*Author: Sonia Pujol, Ph.D., Ron Kikinis, M.D.
*Audience: End-users and developers
*Modules: Volumes, Editor, Tractography Label Map Seeding, Tractography Interactive Seeding
*Based on: 3D Slicer version 4.6
*The [[Media:WhiteMatterExplorationData.zip| White Matter Exploration dataset]] contains a Diffusion Weighted Imaging scan of brain tumor patient.
|align="right"|
[[Image:NeurosurgicalPlanningTutorial.png|right|250px|link=http://vimeo.com/67336069]]
|}

==Slicer4 3D Visualization of DICOM images for Radiology Applications==
{|width="100%"
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*The [[Media:3DSlicer_Dicom_RSNA2015_SoniaPujol.pdf |3D Visualization of DICOM images for Radiology Applications]] course guides through 3D data loading and visualization of DICOM images for Radiology Applications in Slicer4.
*Author: Sonia Pujol, Ph.D., Kitt Shaffer, M.D., Ph.D., Ron Kikinis, M.D.
*Audience: Radiologists and users of Slicer who need a more comprehensive overview over Slicer4 visualization capabilities.
*Modules: DICOM, Volumes, Volume Rendering, Models.
*Based on: 3D Slicer version 4.5
*The [[Media:3DVisualization_DICOM_images_part1.zip‎ | 3DVisualizationDICOM_part1]] and [[Media:3DVisualization_DICOM_images_part2.zip | 3DVisualizationDICOM_part2]] datasets contain a series of MR and CT scans, and 3D models of the brain, lung and liver.
|align="right"|
[[Image:Slicer4RSNA_2.png|right|250px|]]
|}

==Slicer4 Quantitative Imaging tutorial==
{|width="100%"
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*The [[media:QuantitativeImaging_Slicer4.5.pdf‎ | Slicer4 Quantitative Imaging tutorial]] guides through the use for Slicer for quantifying small volumetric changes in slow-growing tumors, and for calculating Standardized Uptake Value (SUV) from PET/CT data.
*Authors: Sonia Pujol, Ph.D., Katarzyna Macura, M.D., Ron Kikinis, M.D.
*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 [[media:QuantitativeImaging.zip‎| Quantitative Imaging dataset]] contains a series of MR and PET/CT data.
|align="right"|
[[Image:Slicer4_QuantitativeImaging.png|right|250px|]]
|}

== Slicer4 IGT ==
{|width="100%"
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*[http://www.slicerigt.org/wp/user-tutorial/ 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: [https://onedrive.live.com/redir?resid=7230D4DEC6058018!2937&authkey=!AGQkSCZOwjVYXw8&ithint=folder%2cpptx Slicer-IGT datasets]
|align="right"|
[[Image:SlicetIGT.png|right|150px|]]
|}

== Slicer4 Image Segmentation ==

{|width="100%"
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* 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
** 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]]
|}

== Slicer4 Image Registration ==

{|width="100%"
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*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.
* 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 4.5
See [[Documentation/{{documentation/version}}/Registration/RegistrationLibrary|the Registration Library for worked out registration examples with data]].

==Slicer4 Radiation Therapy Tutorial ==

{|width="100%"
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* The [https://github.com/SlicerRt/SlicerRtDoc/raw/master/tutorials/SlicerRT_WorldCongress_TutorialIGRT.pdf SlicerRT tutorial] is an introduction to the Radiation Therapy functionalities of Slicer.
* Author: Csaba Pinter, Andras Lasso, An Wang, Gregory C. Sharp, David Jaffray, Gabor Fichtinger.
* Dataset: [http://slicer.kitware.com/midas3/download/item/205404/SlicerRT_WorldCongress_TutorialIGRT_Dataset.zip download] from MIDAS server
* Based on Slicer 4.7
|align="right"|

|}

== Other ==

Additional (non-curated) videos-based demonstrations using 3D Slicer are accessible on [http://www.youtube.com/results?search_query=3d+slicer&sm=3 You Tube].

= 3D Slicer Tutorial contests=

==Winter 2017 Tutorial contest==

===Segmentation for 3D printing===
{|width="100%"
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*The [https://github.com/SlicerRt/SlicerRtDoc/raw/master/tutorials/SegmentationFor3DPrinting_TutorialContestWinter2017.pdf Segmentation for 3D printing Tutorial] ([https://github.com/SlicerRt/SlicerRtDoc/raw/master/tutorials/SegmentationFor3DPrinting_TutorialContestWinter2017.pptx pptx]) is an introduction to the new [[Documentation/{{documentation/version}}/Modules/SegmentEditor|Segment Editor]] module, demonstrated through the popular topic of 3D printing.
*Author: Csaba Pinter (Queen's University, Canada)
* [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"|
[[File:SlicerWinterProjectWeek2017-Segmentation-for-3d-printing.png | 200px]].
|}

===Slicer Pathology===
{|width="100%"
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*The [[Documentation/{{documentation/version}}/Extensions/SlicerPathology|Slicer Pathology Tutorial]] describes how to use the corresponding tools for automatic and semi-automatic pathology image segmentation.
*Author: Erich Bremer (Stonybrook), Andriy Fedorov (Brigham and Women’s Hospital)
*Dataset: Available directly with the Slicer Pathology Slicer extension.
|align="right"|
[[File:SlicerPathologyScreenShot8.png | 200px]].
|}

===Simple Python Tool for Quality Control of DWI data===
{|width="100%"
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*The [http://www.na-mic.org/Wiki/images/3/3a/SimpleDiffusionGradientInformationExtractorTutorial_Chauvin_Jan2017.pptx Simple Multi-shell Diffusion Gradients Information Extractor Tutorial] describes how to use a simple Python script for parsing multi-shell sensitizing gradients information from nifti file format (separated bvecs, bvals files).
*Author: Laurent Chauvin (ETS Montreal)
*Dataset: Not available.
|align="right"|
[[File:SlicerWinterProjectWeek2017-SimpleDiffusionGradientInformationExtractorTutorial.png | 200px]].
|}

===SPHARM-PDM===
{|width="100%"
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*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]].
|}

===Integration of Robot Operating System (ROS) and 3D Slicer using OpenIGTLink===
{|width="100%"
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*The [https://www.na-mic.org/Wiki/images/a/ab/ROSIGTLTutorial_Tokuda_Jan2017.pptx Integration of Robot Operating System (ROS) and 3D Slicer using OpenIGTLink Tutorial] describes the software architecture of surgical robot systems and allows to acquire hands-on experience of software-hardware integration for medical robotics.
*Author: Junichi Tokuda (Brigham and Women’s Hospital)
*Dataset: Not available.
|align="right"|
[[File:SlicerWinterProjectWeek2017-Integration-ROS-3DSlicer-OpenIGTLink.png | 200px]].
|}

===Fiber Bundle Volume Measurement===
{|width="100%"
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*The [http://www.na-mic.org/Wiki/images/5/57/Fiber_Bundle_Volume_Measurement.pptx Fiber Bundle Volume Measurement Tutorial] aim is to calculate the volume of the fiber bundle that passes through the Corpus Callosum(CC). Following this tutorial, you’ll be able to (1) convert fiber bundles to label map and (2) calculate volume measurements from the fiber bundles.
*Author: Shun Gong (Shanghai Changzheng Hospital, China)
*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]].
|}

==Winter 2016 Tutorial contest==

===Subject Hierarchy===
{|width="100%"
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*The [http://wiki.na-mic.org/Wiki/images/2/27/SubjectHierarchy.TutorialContestWinter2016.pdf Subject Hierarchy] tutorial demonstrates the basic usage and potential of Slicer’s data manager module Subject Hierarchy using a two-timepoint radiotherapy phantom dataset.
*Author: Csaba Pinter, Queen's University, Canada
*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.
|align="right"|
[[File:SubjectHierarchyTutorial.png | 200px]].
|}

===Fiber Bundle Selection and Scalar Measurements===
{|width="100%"
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*The [https://github.com/SlicerDMRI/slicerdmri.github.io/raw/master/docs/tutorials/FiberBundleSelectionAndScalarMeasurement.pdf Fiber Bundle Selection and Scalar Measurements] tutorial guides through the use of the Diffusion Bundle Selection module and the Fiber Tract Scalar Measurement module for diffusion MRI tractography data analysis.
*Author: Fan Zhang, University of Sydney Australia and Brigham and Women's Hospital
*Dataset: [[media:FiberBundleSelectionAndScalarMeasurement_TutorialContestWinter2016.zip| Fiber Bundle Selection And Scalar Measurement Tutorial Dataset]]
|align="right"|
[[File:FiberBundleSelectionAndScalarMeasurement_TutorialContestWinter2016_Snapshot.png|200px]]
|}

===Plastimatch ===
{|width="100%"
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*The [http://www.na-mic.org/Wiki/images/5/5c/Plastimatch_TutorialContestWinter2016.pdf Plastimatch tutorial] guides through registration and wrapping of DICOM and DICOM-RT data using the Plastimatch extension of 3D Slicer.
*Author: Gregory Sharp, Massachusetts General Hospital
*Dataset: [http://www.na-mic.org/Wiki/index.php/File:Plastimatch_TutorialContestWinter2016.zip Plastimatch Tutorial Dataset]
|align="right"|
[[File:PlastimatchTutorial_Winter2016Contest.png|200px]]
|}

===UKF ===
{|width="100%"
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*The [https://github.com/SlicerDMRI/slicerdmri.github.io/raw/master/docs/tutorials/UKFTractography.pdf UKF tutorial] guides through the use of the Unscented Kalman Filter (UKF) tractography module.
*Author: Pegah Kahali, Brigham and Women's Hopital
*Dataset: [http://www.na-mic.org/Wiki/index.php/File:UKF-Tractography_TutorialContestWinter2016.zip UKF tutorial Dataset]
|align="right"|
[[File:UKF_Winter2016.png|200px]]
|}

==Summer 2014 Tutorial contest==

===Cardiac Agatston Tutorial===
{|width="100%"
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*[http://wiki.na-mic.org/Wiki/index.php/File:TutorialContest_CardiacAgatstonScoring_2014.pdf Cardiac Agatston Scoring Tutorial]
*Authors: Jessica Forbes, Hans Johnson, University of Iowa
*Dataset: [http://wiki.na-mic.org/Wiki/index.php/File:CardiacAgatstonMeasures_TutorialContestSummer2014.zip Cardiac Agatston Scoring Tutorial Dataset]
|align="right"|
[[File:CardiacAgatstonMeasuresModuleScreenshot.jpg| 250px]]
|}

===CMR Toolkit LA workflow===
{|width="100%"
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*[http://wiki.na-mic.org/Wiki/index.php/File:CMRToolkitLAWorkflow_TutorialContestSummer2014.pdf CMR Toolkit LA Workflow Tutorial]
*Authors: Salma Bengali, Josh Cates, University of Utah
*Dataset: [http://wiki.na-mic.org/Wiki/index.php/File:CMRToolkitLAWorkflowData_TutorialContestSummer2014.zip CMRToolkitLAWorkflow Dataset]
|align="right"|
[[Image:Utah_SummerContest2014_tutorial.png|300px]]
|}

==Summer 2013 Tutorial contest==

===Cardiac MRI Toolkit===
{|width="100%"
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*[[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===
{|width="100%"
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*[[Media:Hello_CLI_TutorialContestSummer2013.pdf|HelloCLI]]
*Authors: Nadya Shusharina, Greg Sharp, MGH, Boston
*Dataset: [[Media:Hello_CLI_TutorialContestSummer2013.zip‎|HelloCLI Dataset]]
|align="right"|
[[Image:Cli_icon.png|300px]]
|}

===SlicerRT===
{|width="100%"
|
*[[Media:SlicerRT_TutorialContestSummer2013.pdf|SlicerRT Tutorial]]
*Authors: Csaba Pinter, Andras Lasso (Queen's), Kevin Wang (PMH, Toronto)
*Dataset: [[Media:CsabaPinter-SlicerRtTutorial_Namic2013June.zip|SlicerRT Dataset]]
|align="right"|
[[Image:667px-SlicerRT_0.10_IsocenterShiftingEvaluation.png|250px]]
|}

===DTIPrep===
{|width="100%"
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*[[Media:DTIPrep_TutorialContestSummer2013.pdf|DTIPrep]]
*Authors: Dave Welch, SINAPSE, IOWA
*Dataset: [[Media:DTIPrepData_TutorialContestSummer2013.zip|DTIPrep Dataset]]
|align="right"|
[[Image:DTIPrep-tutorial.png|250px]]
|}

== Summer 2012 Tutorial contest ==

===Automatic Left Atrial Scar Segmenter ===
{|width="100%"
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*[http://wiki.na-mic.org/Wiki/index.php/CARMA-LA-Scar_TutorialContestSummer2012 Automatic Left Atrial Scar Segmenter]
*Authors: Greg Gardner, Josh Cates, SCI, Utah
*Dataset: [http://wiki.na-mic.org/Wiki/index.php/File:CARMA-LA-Scar_TutorialContestSummer2012.zip CARMA-LA-Scar data]
|align="right"|
[[Image:Carma afib auto scar.png|250px]]
|}

===Qualitative and quantitative comparison of two RT dose distributions===
{|width="100%"
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*[http://www.na-mic.org/Wiki/index.php/File:PlastimatchDose_TutorialContestSummer2012.pdf Qualitative and quantitative comparison of two RT dose distributions]
*Authors: James Shackleford, Nadya Shusharina, Greg Sharp, MGH
|align="right"|
[[Image:PlastimatchDose.png|250px]]
|}

===Dose accumulation for adaptive radiation therapy===
{|width="100%"
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*[http://www.na-mic.org/Wiki/index.php/File:DoseAccumulationforAdaptiveRadiationTherapy_TutorialContestSummer2012.pdf Dose accumulation for adaptive radiation therapy]
*Authors: Kevin Wang, Csaba Pinter, Andras Lasso, PMH, Queen's
|align="right"|
[[Image:AdaptiveradiationTherapy.png|250px]]
|}

===WebGL Export===
{|width="100%"
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*[http://www.na-mic.org/Wiki/index.php/File:WebGLExport_TutorialContestSummer2012.pdf WebdGLExport]
*Authors: Nicolas Rannou, Daniel Haehn, Children's Hospital
|align="right"|
[[Image:WebGLExport.png|250px]]
|}

===OpenIGTLink===
{|width="100%"
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*[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 =
{|width="100%"
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* 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.
* Audience: First time users and developers interested in Slicer 4.1 new features.
* Length: 0h20m
|align="right"|[[Image:Webinar-Slicer-4.1.png|250px]]
|}
<br>
----
<br>
{|width="100%"
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*This ''Intro to Slicer 4.0 [http://vimeo.com/37671358 webinar]'' provides an introduction to 3DSlicer, and demonstrates core functionalities such as loading, visualizing and saving data. Basic processing tools, including manual registration, manual segmentation and tractography tools are also highlighted. This webinar is a general overview. For in depth information see the modules above and the documentation pages.
*Authors: Julien Finet, M.S., Steve Pieper, Ph.D., Jean-Christophe Fillion-Robin, M.S.
*Audience: First time users interested in a broad overview of Slicer’s features and tools.
*Length: 1h20m
|align="right"|[[Image:Webinar.png|250px]]
|}
<br>
----
<br>
{|width="100%"
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*The ''[[Documentation/{{documentation/version}}/Registration/RegistrationLibrary|Slicer Registration Case Library]]'' provides many real-life example cases of using the Slicer registration tools. They include the dataset and step-by-step instructions to follow and try yourself.
:Author: Dominik Meier, Ph.D.
:Audience: users interested learning/applying Slicer image registration technology
|align="right"|[[Image:RegLib_table.png|250px|link=http://wiki.slicer.org/slicerWiki/index.php/Documentation/{{documentation/version}}/Registration/RegistrationLibrary]]
|}

= External Resources =

== Resources for Chinese users ==

{|width="100%"
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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.

* [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]

* [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]]
|}

== 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]]
|}

=== 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:

* [http://openpaleo.blogspot.com/2008/12/3d-slicer-tutorial.html Open Source Paleontologist: 3D Slicer: The Tutorial]
* [http://openpaleo.blogspot.com/2008/12/3d-slicer-tutorial-part-ii.html Open Source Paleontologist: 3D Slicer: The Tutorial Part II]
* [http://openpaleo.blogspot.com/2008/12/3d-slicer-tutorial-part-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 ==
See the collection of videos on the [http://vimeo.com/album/2363361 Kitware vimeo album].

== User Contributions ==
[http://www.youtube.com/results?search_query=3d+slicer&sm=3 YouTube videos about 3D Slicer]

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 ==Winter 2017 Tutorial contest==
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+===Segmentation for 3D printing (Winter 2017 Tutorial contest)===
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 [[File:SlicerWinterProjectWeek2017-Segmentation-for-3d-printing.png | 200px]].
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 ==Summer 2014 Tutorial contest==
 ===CMR Toolkit LA workflow===