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| − | =Introduction: Slicer {{documentation/version}} Tutorials= | + | =Community-contributed modules= |
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| − | *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. | + | ==Segmentation== |
| − | *For tutorials for other versions of Slicer, please visit the [[Training| Slicer training portal]].
| + | * FillRoi: Use this module to fill a ROI with a constant value. It can be used after an automatic segmentation for removing certain regions of a scalar or labelmap volume. |
| − | *For "reference manual" style documentation, please visit the [[Documentation/{{documentation/version}}|Slicer {{documentation/version}} documentation page]]
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| − | *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]'''
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| | + | ==Registration== |
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| − | =General Introduction= | + | ==Quantification== |
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| − | ==Slicer Welcome Tutorial== | + | =Community-contributed examples= |
| − | {|width="100%"
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| − | *The [[media:SlicerWelcome-tutorial_SoniaPujol.pdf|SlicerWelcome tutorial]] is an introduction to Slicer based on the Welcome module.
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| − | *Author: Sonia Pujol, Ph.D.
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| − | *Audience: First time users who want a general introduction to the software.
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| − | [[image:SlicerWelcome-image.png|250px|SlicerWelcome tutorial]]
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| − | |}
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| − | ==Slicer4Minute Tutorial== | + | ==Capture== |
| − | {|width="100%"
| + | * ScreenCapture: Capture the full Slicer screen into a file |
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| + | * Rotating3dViewCapture: Capture a video of the scene rotating in the 3D view |
| − | *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.
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| − | *Audience: First time users who want to discover Slicer in 4 minutes.
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| − | *The [[media:Slicer4minute.zip|Slicer4Minute dataset]] contains an MR scan of the brain and 3D reconstructions of the anatomy
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| − | [[image:Slicer4minute-image.png|250px|right|Slicer4Minute tutorial]]
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| − | |}
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| − | ==Slicer4 Data Loading and 3D Visualization ==
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| − | {|width="100%"
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| − | *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 .
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| − | *Author: Sonia Pujol, Ph.D.
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| − | *Audience: End-users
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| − | *The [[Media:3DVisualizationData.zip | 3DVisualization dataset]] contain an MR scan and a series of 3D models of the brain.
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| − | [[Image:Slicer4DataLoading_tutorial.png|right|250px|]]
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| − | |}
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| − | =Tutorials for software developers=
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| − | == Slicer4 Programming Tutorial ==
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| − | {|width="100%"
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| − | *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.
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| − | *Audience: Developers
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| − | *The [[Media:HelloPythonSlicer4.zip| HelloPython dataset]] contains three Python files and an MR scan of the brain.
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| − | [[Image:HelloPythonTutorial.png|right|250px|]]
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| − | |}
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| − | =Specific functions=
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| − | ==Slicer4 Diffusion Tensor Imaging Tutorial ==
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| − | {|width="100%"
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| − | *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.
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| − | *Author: Sonia Pujol, Ph.D.
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| − | *Audience: End-users and developers
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| − | *The [[Media:DiffusionMRI_tutorialData.zip |DTI dataset]] contains an MR Diffusion Weighted Imaging scan of the brain.
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| − | |align="right"|
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| − | [[Image:Slicer4DTI Tutorial.png|right|250px|]]
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| − | |}
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| − | ==Slicer4 Neurosurgical Planning Tutorial==
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| − | {|width="100%"
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| − | *The [[Media:NeurosurgicalPlanning_SoniaPujol.pdf | Neurosurgical Planning tutorial]] course guides through the generation of fiber tracts in the vicinity of a tumor.
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| − | *Author: Sonia Pujol, Ph.D., Ron Kikinis, M.D.
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| − | *Audience: End-users and developers
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| − | *The [[Media:WhiteMatterExplorationData.zip| White Matter Exploration datasets]] contains a Diffusion Weighted Imaging scan of brain tumor patient.
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| − | |align="right"|
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| − | [[Image:NeurosurgicalPlanningTutorial.png|right|250px|link=http://vimeo.com/67336069]]
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| − | |}
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| − | ==Slicer4 3D Visualization of DICOM images for Radiology Applications==
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| − | {|width="100%"
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| − | *The [[Media:3DVisualizationDICOMforRadiologyApplications_SoniaPujol_KittShaffer_RSNA2011.pdf | Slicer4RSNA]] course guides through 3D data loading and visualization of DICOM images for Radiology Applications in Slicer4.
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| − | *Author: Sonia Pujol, Ph.D., Kitt Shaffer, M.D., Ph.D.
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| − | *Audience: Radiologists and users of Slicer who need a more comprehensive overview over Slicer4 visualization capabilities.
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| − | *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.
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| − | |align="right"|
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| − | [[Image:Slicer4RSNA_2.png|right|250px|]]
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| − | |}
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| − | ==Slicer4 Quantitative Imaging tutorial==
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| − | {|width="100%"
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| − | *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.
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| − | *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.
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| − | *Audience: Radiologists and users of Slicer who need a more comprehensive overview over Slicer4 quantitative imaging capabilities.
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| − | *The [[media:PETCTFusion-TutorialData.zip| PETCTFusion]] and [[media:ChangeTracker2011.zip|Change Tracker]] datasets contain a series of MR, CT and PET data.
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| − | |align="right"|
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| − | [[Image:Slicer4_QuantitativeImaging.png|right|250px|]]
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| − | |}
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| − | =Summer 2012 Tutorial contest (under construction)=
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| − | ==Automatic Left Atrial Scar Segmenter ==
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| − | {|width="100%"
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| − | *[http://wiki.na-mic.org/Wiki/index.php/CARMA-LA-Scar_TutorialContestSummer2012 Automatic Left Atrial Scar Segmenter]
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| − | *Authors: Greg Gardner, Josh Cates, SCI, Utah
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| − | *Dataset: [http://wiki.na-mic.org/Wiki/index.php/File:CARMA-LA-Scar_TutorialContestSummer2012.zip CARMA-LA-Scar data]
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| − | |}
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| − | ==Qualitative and quantitative comparison of two RT dose distributions==
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| − | {|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]
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| − | *Authors: James Shackleford, Nadya Shusharina, Greg Sharp, MGH
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| − | |}
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| − | ==Dose accumulation for adaptive radiation therapy==
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| − | {|width="100%"
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| − | *[http://www.na-mic.org/Wiki/index.php/File:DoseAccumulationforAdaptiveRadiationTherapy_TutorialContestSummer2012.pdf Dose accumulation for adaptive radiation therapy]
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| − | *Authors: Kevin Wang, Csaba Pinter, Andras Lasso, PMH, Queen's
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| − | |align="right"|
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| − | |}
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| − | ==WebGL Export==
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| − | {|width="100%"
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| − | *[http://www.na-mic.org/Wiki/index.php/File:WebGLExport_TutorialContestSummer2012.pdf WebdGLExport]
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| − | *Authors: Nicolas Rannou, Daniel Haehn, Children's Hospital
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| − | |}
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| − | ==OpenIGTLink==
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| − | {|width="100%"
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| − | *[http://wiki.slicer.org/slicerWiki/images/f/f1/OpenIGTLinkTutorial_Slicer4.1.0_JunichiTokuda_Apr2012.pdf OpenIGTLink]
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| − | *Authors: Junichi Tokuda, BWH
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| − | |align="right"|
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| − | |}
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| − | =Additional resources =
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| − | {|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.
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| − | * Authors: Steve Pieper Ph.D.
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| − | * Audience: First time users and developers interested in Slicer 4.1 new features.
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| − | * Length: 0h20m
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| − | |align="right"|[[Image:Webinar-Slicer-4.1.png|250px]]
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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.
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| − | *Authors: Julien Finet, M.S., Steve Pieper, Ph.D., Jean-Christophe Fillion-Robin, M.S.
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| − | *Audience: First time users interested in a broad overview of Slicer’s features and tools.
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| − | *Length: 1h20m
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| − | |align="right"|[[Image:Webinar.png|250px]]
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| − | *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.
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| − | :Author: Dominik Meier, Ph.D.
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| − | :Audience: users interested learning/applying Slicer image registration technology
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| − | |align="right"|[[Image:RegLib Banner.png|250px]]
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| − | |}
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| − | = External Resources =
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| − | == Using the Editor ==
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| − | This set of tutorials about the use of slicer in paleontology is very well written and provides step-by-step instructions. Even though it covers slicer version 3.4, many of the concepts and techniques have applicability to the new version and to any 3D imaging field:
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| − | * [http://openpaleo.blogspot.com/2008/12/3d-slicer-tutorial.html Open Source Paleontologist: 3D Slicer: The Tutorial]
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| − | * [http://openpaleo.blogspot.com/2008/12/3d-slicer-tutorial-part-ii.html Open Source Paleontologist: 3D Slicer: The Tutorial Part II]
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| − | * [http://openpaleo.blogspot.com/2008/12/3d-slicer-tutorial-part-iii.html Open Source Paleontologist: 3D Slicer: The Tutorial Part III]
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| − | * [http://openpaleo.blogspot.com/2008/12/3d-slicer-tutorial-part-iv.html Open Source Paleontologist: 3D Slicer: The Tutorial Part IV]
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| − | * [http://openpaleo.blogspot.com/2009/03/3d-slicer-tutorial-part-v.html Open Source Paleontologist: 3D Slicer: The Tutorial Part V]
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| − | * [http://openpaleo.blogspot.com/2009/03/3d-slicer-tutorial-part-vi.html Open Source Paleontologist: 3D Slicer: The Tutorial Part VI]
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| − | == Team Contributions ==
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| − | See the collection of videos on the [http://vimeo.com/album/2363361 Kitware vimeo album].
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| − | == User Contributions ==
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| − | See the [[Documentation/{{documentation/version}}/Training/UserContributions|User Contributions Page]] for more content.
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