<noinclude>{{documentation/versioncheck}}</noinclude>
__TOC__

=Introduction: Slicer {{documentation/version}} Tutorials=
*This page contains "How to" tutorials with matched sample data sets. They demonstrate how to use the 3D Slicer environment (version {{documentation/version}} release) to accomplish certain tasks.
*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 an overview of Slicer and its abilities please see [http://www.slicer.org/publications/item/view/2219 3D Slicer as an Image Computing Platform for the Quantitative Imaging Network].
*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.]'''.

=General Introduction=

==Slicer Welcome Tutorial==
{|width="100%"
|
*The [[media:SlicerWelcome-tutorial_SoniaPujol.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 Slicer.
|align="right"|
[[image:SlicerWelcome-image.png|250px|SlicerWelcome tutorial]]
|}

==Slicer4Minute Tutorial==
{|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.
*Author: Sonia Pujol, Ph.D.
*Audience: First time users who want to discover Slicer in 4 minutes.
*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%"
|
*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 .
*Author: Sonia Pujol, Ph.D.
*Audience: End-users
*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=

== Slicer4 Programming Tutorial ==
{|width="100%"
|
*The [[Media:Slicer4_ProgrammingTutorial_SPujol-SPieper.pdf | Hello Python Programming tutorial]] course guides through the integration of a python module in Slicer4.
*Author: Sonia Pujol, Ph.D., Steve Pieper, Ph.D.
*Audience: Developers
*The [[Media:HelloPythonSlicer4.zip‎| HelloPython dataset]] contains three Python files and an MR scan of the brain.
|align="right"|
[[Image:HelloPythonTutorial.png|right|250px|]]
|}

=Specific functions=

==Slicer4 Diffusion Tensor Imaging Tutorial ==
{|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.
*Author: Sonia Pujol, Ph.D.
*Audience: End-users and developers
*The [[Media:DiffusionMRI_tutorialData.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%"
|
*The [[Media:NeurosurgicalPlanning_SoniaPujol.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 presented: Main GUI, add data, interactive editor, tractography interactive seeding, tractography display.
*The [[Media:WhiteMatterExplorationData.zip| White Matter Exploration datasets]] contains a single tensor Diffusion Tensor data set of a patient with a brain tumor.
|align="right"|
[[Image:NeurosurgicalPlanningTutorial.png|right|250px|]]
|}

==Slicer4 3D Visualization of DICOM images for Radiology Applications==
{|width="100%"
|
*The [[Media:3DVisualizationDICOM_RadiologyApplications_SoniaPujol_RSNA2012.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.
*The [[Media:3Dvisualization_DICOM_Data-RSNA2012-Part1.zip | Slicer4RSNAdataset1]] and [[Media:3Dvisualization_DICOM_Data-RSNA2012-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==
{|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.
*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.
*Audience: Radiologists and users of Slicer who need a more comprehensive overview over Slicer4 quantitative imaging capabilities.
*The [[media:PETCTFusion-TutorialData.zip| PETCTFusion]] and [[media:ChangeTracker2011.zip|Change Tracker]] datasets contain a series of MR, CT and PET data.
|align="right"|
[[Image:Slicer4_QuantitativeImaging.png|right|250px|]]
|}
=Summer 2013 Tutorial contest=

==Cardiac MRI Toolkit==
{|width="100%"
|
*[[Media:Cardiac MRI Toolkit Tutorial Summer2013.pdf|Cardiac MRI Toolkit]]
*Authors: Salma Bengali, Josh Cates, SCI, Utah
*Dataset: [[Media:Cardiac_MRI_Toolkit_Tutorial_Data.zip|Cardiac MRI Toolkit Tutorial Dataset]]
|align="right"|
[[Image:CMRToolkit_Tutorial_Image.png|250px]]
|}

==HelloCLI==
{|width="100%"
|
*[[Media:Hello_CLI_TutorialContestSummer2013.pdf|HelloCLI]]
*Authors: Nadya Shusharina, Greg Sharp, MGH, Boston
*Dataset: [[Media:Hello_CLI_TutorialContestSummer2013.zip‎|HelloCLI Dataset]]

==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"|
[[]]
|}

==DTIPrep==
{|width="100%"
|
*[[Media:DTIPrep_TutorialContestSummer2013.pdf|DTIPrep]]
*Authors: Dave Welch, SINAPSE, IOWA
*Dataset: [[Media:DTIPrepData_TutorialContestSummer2013.zip|DTIPrep Dataset]]

=Summer 2012 Tutorial contest=

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

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

==Dose accumulation for adaptive radiation therapy==
{|width="100%"
|
*[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:Wang-DoseAccumulationforAdaptiveRadiationTherapy TutorialContestSummer2012-fig1.png|250px]]
|}

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

==OpenIGTLink==
{|width="100%"
|
*[http://wiki.slicer.org/slicerWiki/images/f/f1/OpenIGTLinkTutorial_Slicer4.1.0_JunichiTokuda_Apr2012.pdf OpenIGTLink]
*Authors: Junichi Tokuda, BWH
|align="right"|
[[Image:OpenIGTLink-Tracking.png|250px]]
|}

=Additional resources =

{|width="100%"
|
*Title: [https://wiki.cancerimagingarchive.net/display/Public/Hands-on+Tutorial+-+Using+3D+Slicer+with+the+Prostate-Diagnosis+data Visualizing Prostate-Diagnosis images and segmentations] tutorial from [http://cancerimagingarchive.net/about-archive.html The Cancer Imaging Archive (TCIA)].
* Author: Justin Kirby
*Audience: Novice 3D Slicer users interested in visualizing prostate segmentations hosted on TCIA.
*Summary: 3D Slicer was used to generate NRRD segmentations of the following prostate components: prostate gland boundary; internal capsule; central gland, peripheral zone; seminal vesicles; urethra; cancer – dominant nodule; neurovascular bundle; penile bulb; ejaculatory duct; veru-montanum; rectum. These segmentations are currently available for [https://wiki.cancerimagingarchive.net/display/Public/Prostate-Diagnosis 5 subjects from TCIA’s Prostate-Diagnosis image collection]. The [http://www.slicer.org/slicerWiki/index.php/File:ProstateDx-01-0006-1.zip archive] contains both the DICOM images and the NRRD file for one of the 5 available subjects.
|align="right"|[[Image:NCIA-prostate.png|250px]]
|-
|
* 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]]
|-
|
*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]]
|-
|
*The ''[http://na-mic.org/Wiki/index.php/Projects:RegistrationDocumentation:RegLibTable 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 Banner.png|250px]]
|}

= External Resources =

== Using the Editor ==

This set of tutorials about the use of slicer in paleontology is very well written and provides step-by-step instructions. Even though it covers slicer version 3.4, many of the concepts and techniques have applicability to the new version and to any 3D imaging field:

* [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]

== User Contributions ==
See the [[Documentation/{{documentation/version}}/Training/UserContributions|User Contributions Page]] for more content.

Documentation/4.2/Training

2013-08-21T17:02:57Z

Pamin27: /* Cardiac MRI Toolkit */

<noinclude>{{documentation/versioncheck}}</noinclude>
__TOC__

=Introduction: Slicer {{documentation/version}} Tutorials=
*This page contains "How to" tutorials with matched sample data sets. They demonstrate how to use the 3D Slicer environment (version {{documentation/version}} release) to accomplish certain tasks.
*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 an overview of Slicer and its abilities please see [http://www.slicer.org/publications/item/view/2219 3D Slicer as an Image Computing Platform for the Quantitative Imaging Network].
*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.]'''.

=General Introduction=

==Slicer Welcome Tutorial==
{|width="100%"
|
*The [[media:SlicerWelcome-tutorial_SoniaPujol.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 Slicer.
|align="right"|
[[image:SlicerWelcome-image.png|250px|SlicerWelcome tutorial]]
|}

==Slicer4Minute Tutorial==
{|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.
*Author: Sonia Pujol, Ph.D.
*Audience: First time users who want to discover Slicer in 4 minutes.
*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%"
|
*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 .
*Author: Sonia Pujol, Ph.D.
*Audience: End-users
*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=

== Slicer4 Programming Tutorial ==
{|width="100%"
|
*The [[Media:Slicer4_ProgrammingTutorial_SPujol-SPieper.pdf | Hello Python Programming tutorial]] course guides through the integration of a python module in Slicer4.
*Author: Sonia Pujol, Ph.D., Steve Pieper, Ph.D.
*Audience: Developers
*The [[Media:HelloPythonSlicer4.zip‎| HelloPython dataset]] contains three Python files and an MR scan of the brain.
|align="right"|
[[Image:HelloPythonTutorial.png|right|250px|]]
|}

=Specific functions=

==Slicer4 Diffusion Tensor Imaging Tutorial ==
{|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.
*Author: Sonia Pujol, Ph.D.
*Audience: End-users and developers
*The [[Media:DiffusionMRI_tutorialData.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%"
|
*The [[Media:NeurosurgicalPlanning_SoniaPujol.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 presented: Main GUI, add data, interactive editor, tractography interactive seeding, tractography display.
*The [[Media:WhiteMatterExplorationData.zip| White Matter Exploration datasets]] contains a single tensor Diffusion Tensor data set of a patient with a brain tumor.
|align="right"|
[[Image:NeurosurgicalPlanningTutorial.png|right|250px|]]
|}

==Slicer4 3D Visualization of DICOM images for Radiology Applications==
{|width="100%"
|
*The [[Media:3DVisualizationDICOM_RadiologyApplications_SoniaPujol_RSNA2012.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.
*The [[Media:3Dvisualization_DICOM_Data-RSNA2012-Part1.zip | Slicer4RSNAdataset1]] and [[Media:3Dvisualization_DICOM_Data-RSNA2012-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==
{|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.
*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.
*Audience: Radiologists and users of Slicer who need a more comprehensive overview over Slicer4 quantitative imaging capabilities.
*The [[media:PETCTFusion-TutorialData.zip| PETCTFusion]] and [[media:ChangeTracker2011.zip|Change Tracker]] datasets contain a series of MR, CT and PET data.
|align="right"|
[[Image:Slicer4_QuantitativeImaging.png|right|250px|]]
|}
=Summer 2013 Tutorial contest=

==Cardiac MRI Toolkit==
{|width="100%"
|
*[[Media:Cardiac MRI Toolkit Tutorial Summer2013.pdf|Cardiac MRI Toolkit]]
*Authors: Salma Bengali, Josh Cates, SCI, Utah
*Dataset: [[Media:Cardiac_MRI_Toolkit_Tutorial_Data.zip|Cardiac MRI Toolkit Tutorial Dataset]]
|align="right"|
[[Image:CMRToolkit_Tutorial_Image.png|250px]]
|}

==HelloCLI==
{|width="100%"
|
*[[Media:Hello_CLI_TutorialContestSummer2013.pdf|HelloCLI]]
*Authors: Nadya Shusharina, Greg Sharp, MGH, Boston
*Dataset: [[Media:Hello_CLI_TutorialContestSummer2013.zip‎|HelloCLI Dataset]]

==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%"
|
*[[Media:DTIPrep_TutorialContestSummer2013.pdf|DTIPrep]]
*Authors: Dave Welch, SINAPSE, IOWA
*Dataset: [[Media:DTIPrepData_TutorialContestSummer2013.zip|DTIPrep Dataset]]

=Summer 2012 Tutorial contest=

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

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

==Dose accumulation for adaptive radiation therapy==
{|width="100%"
|
*[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:Wang-DoseAccumulationforAdaptiveRadiationTherapy TutorialContestSummer2012-fig1.png|250px]]
|}

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

==OpenIGTLink==
{|width="100%"
|
*[http://wiki.slicer.org/slicerWiki/images/f/f1/OpenIGTLinkTutorial_Slicer4.1.0_JunichiTokuda_Apr2012.pdf OpenIGTLink]
*Authors: Junichi Tokuda, BWH
|align="right"|
[[Image:OpenIGTLink-Tracking.png|250px]]
|}

=Additional resources =

{|width="100%"
|
*Title: [https://wiki.cancerimagingarchive.net/display/Public/Hands-on+Tutorial+-+Using+3D+Slicer+with+the+Prostate-Diagnosis+data Visualizing Prostate-Diagnosis images and segmentations] tutorial from [http://cancerimagingarchive.net/about-archive.html The Cancer Imaging Archive (TCIA)].
* Author: Justin Kirby
*Audience: Novice 3D Slicer users interested in visualizing prostate segmentations hosted on TCIA.
*Summary: 3D Slicer was used to generate NRRD segmentations of the following prostate components: prostate gland boundary; internal capsule; central gland, peripheral zone; seminal vesicles; urethra; cancer – dominant nodule; neurovascular bundle; penile bulb; ejaculatory duct; veru-montanum; rectum. These segmentations are currently available for [https://wiki.cancerimagingarchive.net/display/Public/Prostate-Diagnosis 5 subjects from TCIA’s Prostate-Diagnosis image collection]. The [http://www.slicer.org/slicerWiki/index.php/File:ProstateDx-01-0006-1.zip archive] contains both the DICOM images and the NRRD file for one of the 5 available subjects.
|align="right"|[[Image:NCIA-prostate.png|250px]]
|-
|
* 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]]
|-
|
*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]]
|-
|
*The ''[http://na-mic.org/Wiki/index.php/Projects:RegistrationDocumentation:RegLibTable 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 Banner.png|250px]]
|}

= External Resources =

== Using the Editor ==

This set of tutorials about the use of slicer in paleontology is very well written and provides step-by-step instructions. Even though it covers slicer version 3.4, many of the concepts and techniques have applicability to the new version and to any 3D imaging field:

* [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]

== User Contributions ==
See the [[Documentation/{{documentation/version}}/Training/UserContributions|User Contributions Page]] for more content.

Pamin27:

Documentation/4.2/Training

2013-08-20T19:18:55Z

Pamin27: /* Summer 2012 Tutorial contest */

<noinclude>{{documentation/versioncheck}}</noinclude>
__TOC__

=Introduction: Slicer {{documentation/version}} Tutorials=
*This page contains "How to" tutorials with matched sample data sets. They demonstrate how to use the 3D Slicer environment (version {{documentation/version}} release) to accomplish certain tasks.
*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 an overview of Slicer and its abilities please see [http://www.slicer.org/publications/item/view/2219 3D Slicer as an Image Computing Platform for the Quantitative Imaging Network].
*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.]'''.

=General Introduction=

==Slicer Welcome Tutorial==
{|width="100%"
|
*The [[media:SlicerWelcome-tutorial_SoniaPujol.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 Slicer.
|align="right"|
[[image:SlicerWelcome-image.png|250px|SlicerWelcome tutorial]]
|}

==Slicer4Minute Tutorial==
{|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.
*Author: Sonia Pujol, Ph.D.
*Audience: First time users who want to discover Slicer in 4 minutes.
*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%"
|
*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 .
*Author: Sonia Pujol, Ph.D.
*Audience: End-users
*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=

== Slicer4 Programming Tutorial ==
{|width="100%"
|
*The [[Media:Slicer4_ProgrammingTutorial_SPujol-SPieper.pdf | Hello Python Programming tutorial]] course guides through the integration of a python module in Slicer4.
*Author: Sonia Pujol, Ph.D., Steve Pieper, Ph.D.
*Audience: Developers
*The [[Media:HelloPythonSlicer4.zip‎| HelloPython dataset]] contains three Python files and an MR scan of the brain.
|align="right"|
[[Image:HelloPythonTutorial.png|right|250px|]]
|}

=Specific functions=

==Slicer4 Diffusion Tensor Imaging Tutorial ==
{|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.
*Author: Sonia Pujol, Ph.D.
*Audience: End-users and developers
*The [[Media:DiffusionMRI_tutorialData.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%"
|
*The [[Media:NeurosurgicalPlanning_SoniaPujol.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 presented: Main GUI, add data, interactive editor, tractography interactive seeding, tractography display.
*The [[Media:WhiteMatterExplorationData.zip| White Matter Exploration datasets]] contains a single tensor Diffusion Tensor data set of a patient with a brain tumor.
|align="right"|
[[Image:NeurosurgicalPlanningTutorial.png|right|250px|]]
|}

==Slicer4 3D Visualization of DICOM images for Radiology Applications==
{|width="100%"
|
*The [[Media:3DVisualizationDICOM_RadiologyApplications_SoniaPujol_RSNA2012.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.
*The [[Media:3Dvisualization_DICOM_Data-RSNA2012-Part1.zip | Slicer4RSNAdataset1]] and [[Media:3Dvisualization_DICOM_Data-RSNA2012-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==
{|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.
*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.
*Audience: Radiologists and users of Slicer who need a more comprehensive overview over Slicer4 quantitative imaging capabilities.
*The [[media:PETCTFusion-TutorialData.zip| PETCTFusion]] and [[media:ChangeTracker2011.zip|Change Tracker]] datasets contain a series of MR, CT and PET data.
|align="right"|
[[Image:Slicer4_QuantitativeImaging.png|right|250px|]]
|}

=Summer 2013 Tutorial contest=

=Summer 2012 Tutorial contest=

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

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

==Dose accumulation for adaptive radiation therapy==
{|width="100%"
|
*[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:Wang-DoseAccumulationforAdaptiveRadiationTherapy TutorialContestSummer2012-fig1.png|250px]]
|}

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

==OpenIGTLink==
{|width="100%"
|
*[http://wiki.slicer.org/slicerWiki/images/f/f1/OpenIGTLinkTutorial_Slicer4.1.0_JunichiTokuda_Apr2012.pdf OpenIGTLink]
*Authors: Junichi Tokuda, BWH
|align="right"|
[[Image:OpenIGTLink-Tracking.png|250px]]
|}

=Additional resources =

{|width="100%"
|
*Title: [https://wiki.cancerimagingarchive.net/display/Public/Hands-on+Tutorial+-+Using+3D+Slicer+with+the+Prostate-Diagnosis+data Visualizing Prostate-Diagnosis images and segmentations] tutorial from [http://cancerimagingarchive.net/about-archive.html The Cancer Imaging Archive (TCIA)].
* Author: Justin Kirby
*Audience: Novice 3D Slicer users interested in visualizing prostate segmentations hosted on TCIA.
*Summary: 3D Slicer was used to generate NRRD segmentations of the following prostate components: prostate gland boundary; internal capsule; central gland, peripheral zone; seminal vesicles; urethra; cancer – dominant nodule; neurovascular bundle; penile bulb; ejaculatory duct; veru-montanum; rectum. These segmentations are currently available for [https://wiki.cancerimagingarchive.net/display/Public/Prostate-Diagnosis 5 subjects from TCIA’s Prostate-Diagnosis image collection]. The [http://www.slicer.org/slicerWiki/index.php/File:ProstateDx-01-0006-1.zip archive] contains both the DICOM images and the NRRD file for one of the 5 available subjects.
|align="right"|[[Image:NCIA-prostate.png|250px]]
|-
|
* 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]]
|-
|
*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]]
|-
|
*The ''[http://na-mic.org/Wiki/index.php/Projects:RegistrationDocumentation:RegLibTable 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 Banner.png|250px]]
|}

= External Resources =

== Using the Editor ==

This set of tutorials about the use of slicer in paleontology is very well written and provides step-by-step instructions. Even though it covers slicer version 3.4, many of the concepts and techniques have applicability to the new version and to any 3D imaging field:

* [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]

== User Contributions ==
See the [[Documentation/{{documentation/version}}/Training/UserContributions|User Contributions Page]] for more content.