Difference between revisions of "Documentation/4.6/Training"
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− | *The [http://www.na-mic.org/Wiki/images/a/a6/SegmentationFor3DPrinting_TutorialContestWinter2017.pdf Segmentation for 3D printing Tutorial] | + | *The [http://www.na-mic.org/Wiki/images/a/a6/SegmentationFor3DPrinting_TutorialContestWinter2017.pdf Segmentation for 3D printing Tutorial] is an introduction to the new [[Documentation/{{documentation/version}}/Modules/SegmentEditor|Segment Editor]] module of Slicer. |
*Author: Csaba Pinter (Queen's University, Canada) | *Author: Csaba Pinter (Queen's University, Canada) | ||
*Dataset: [http://www.na-mic.org/Wiki/images/1/1e/BasePiece.stl Phantom base STL model] Source: [http://perk-software.cs.queensu.ca/plus/doc/nightly/modelcatalog/ PerkLab]. | *Dataset: [http://www.na-mic.org/Wiki/images/1/1e/BasePiece.stl Phantom base STL model] Source: [http://perk-software.cs.queensu.ca/plus/doc/nightly/modelcatalog/ PerkLab]. | ||
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− | *The [[Documentation/{{documentation/version}}/Extensions/SlicerPathology|Slicer Pathology Tutorial]] describes how to use the | + | *The [[Documentation/{{documentation/version}}/Extensions/SlicerPathology|Slicer Pathology Tutorial]] describes how to use the automated and semi-automated segmentation tools of the Slicer Pathology Extension. |
*Author: Erich Bremer (Stonybrook), Andriy Fedorov (Brigham and Women’s Hospital) | *Author: Erich Bremer (Stonybrook), Andriy Fedorov (Brigham and Women’s Hospital) | ||
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[[File:SlicerPathologyScreenShot8.png | 200px]]. | [[File:SlicerPathologyScreenShot8.png | 200px]]. | ||
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− | *The [https://www.na-mic.org/Wiki/index.php/File:SimpleDiffusionGradientInformationExtractorTutorial_Chauvin_Jan2017.pdf Simple Multi-shell Diffusion Gradients Information Extractor Tutorial] describes how to use a simple Python script for parsing multi-shell sensitizing gradients information from | + | *The [https://www.na-mic.org/Wiki/index.php/File:SimpleDiffusionGradientInformationExtractorTutorial_Chauvin_Jan2017.pdf Simple Multi-shell Diffusion Gradients Information Extractor Tutorial] describes how to use a simple Python script for parsing multi-shell sensitizing gradients information from diffusion MRI datasets in Nifti file. |
*Author: Laurent Chauvin (ETS Montreal) | *Author: Laurent Chauvin (ETS Montreal) | ||
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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 | + | *The [https://www.nitrc.org/docman/view.php/308/1982/SPHARM-PDM_Tutorial_July2015.pdf SPHARM-PDM Tutorial] describes how to use the SPHARM-PDM and ShapePopulationViewer Slicer extensions to compute point-based models for Shape Analysis and perform quality control of the different models. |
*Author: Jonathan Perdomo (UNC), Beatriz Paniagua (Kitware Inc.) | *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] | *Dataset: [https://www.nitrc.org/docman/view.php/308/1981/SPHARM_Tutorial_Data_July2015.zip Tutorial Data] | ||
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− | *The [https://www.na-mic.org/Wiki/index.php/File:ROSIGTLTutorial. | + | *The [https://www.na-mic.org/Wiki/index.php/File:ROSIGTLTutorial.pdf Integration of Robot Operating System (ROS) and 3D Slicer using OpenIGTLink Tutorial] is an introduction to the software architecture of surgical robot systems. The tutorial provides hands-on experience on the integration of software and hardware for medical robotics applications. |
*Author: Junichi Tokuda (Brigham and Women’s Hospital) | *Author: Junichi Tokuda (Brigham and Women’s Hospital) | ||
*Dataset: Not available. | *Dataset: Not available. | ||
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− | *The [ | + | *The [https://www.na-mic.org/Wiki/index.php/File:Fiber_Bundle_Volume_Measurement_TutorialContestWinter2017.pdf Fiber Bundle Volume Measurement Tutorial] shows how to calculate the volume of tractography reconstructions of white matter tracts. |
*Author: Shun Gong (Shanghai Changzheng Hospital, China) | *Author: Shun Gong (Shanghai Changzheng Hospital, China) | ||
− | *Dataset: [http://www.na-mic.org/Wiki/images/4/4c/FiberVolume_data.zip Tutorial data] | + | *Dataset: [http://www.na-mic.org/Wiki/images/4/4c/FiberVolume_data.zip Tutorial data] |
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[[File:SlicerWinterProjectWeek2017-FiberBundleVolumeMeasurements.png | 200px]]. | [[File:SlicerWinterProjectWeek2017-FiberBundleVolumeMeasurements.png | 200px]]. | ||
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==Winter 2016 Tutorial contest== | ==Winter 2016 Tutorial contest== |
Revision as of 19:35, 22 February 2017
Home < Documentation < 4.6 < Training
For the latest Slicer documentation, visit the read-the-docs. |
Introduction: Slicer 4.6 Tutorials
- The 3D Slicer compendium is a collection of hands-on tutorials with anonymized sample data sets. The tutorials demonstrate how to use the 3D Slicer software platform (version 4.6 release) to accomplish certain tasks.
- For tutorials for other versions of Slicer, please visit the Slicer training portal.
- For "reference manual" style documentation, please visit the Slicer 4.6 documentation page
- 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.
- For general questions related to the Slicer4 Training Compendium and to 3D Slicer training events, please send an e-mail to Sonia Pujol, Ph.D, Director of Training of 3D Slicer
Contents
- 1 Introduction: Slicer 4.6 Tutorials
- 2 General Introduction
- 3 Tutorials for Software Developers
- 4 Specific functions
- 4.1 Slicer4 Diffusion Tensor Imaging Tutorial
- 4.2 Slicer4 Neurosurgical Planning Tutorial
- 4.3 Slicer4 3D Visualization of DICOM Images for Radiology Applications
- 4.4 Slicer4 Quantitative Imaging Tutorial
- 4.5 Slicer4 IGT
- 4.6 Slicer4 3D Printing
- 4.7 Slicer4 Image Registration
- 4.8 Fast GrowCut
- 4.9 Other
- 5 3D Slicer Tutorial contests
- 6 Additional resources
- 7 External Resources
General Introduction
Slicer Welcome Tutorial
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Slicer4Minute Tutorial
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Slicer4 Data Loading and 3D Visualization
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Tutorials for Software Developers
Slicer4 Programming Tutorial
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For additional Python scripts examples, please visit the Script Repository page
Developing and Contributing Extensions for 3D Slicer
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Specific functions
Slicer4 Diffusion Tensor Imaging Tutorial
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Slicer4 Neurosurgical Planning Tutorial
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Slicer4 3D Visualization of DICOM Images for Radiology Applications
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Slicer4 Quantitative Imaging Tutorial
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Slicer4 IGT
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Slicer4 3D Printing
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Slicer4 Image Registration
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- Based on: 3D Slicer version 4.5
See the Registration Library for worked out registration examples with data.
Fast GrowCut
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Other
Additional (non-curated) videos-based demonstrations using 3D Slicer are accessible on You Tube.
3D Slicer Tutorial contests
Winter 2017 Tutorial contest
Segmentation for 3D printing
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Slicer Pathology
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Simple Python Tool for Quality Control of DWI data
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SPHARM-PDM
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Integration of Robot Operating System (ROS) and 3D Slicer using OpenIGTLink
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Fiber Bundle Volume Measurement
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Winter 2016 Tutorial contest
Subject Hierarchy
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Fiber Bundle Selection and Scalar Measurements
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Plastimatch
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UKF
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Summer 2014 Tutorial contest
Cardiac Agatston Tutorial
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CMR Toolkit LA workflow
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Summer 2013 Tutorial contest
Cardiac MRI Toolkit
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HelloCLI
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SlicerRT
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DTIPrep
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Summer 2012 Tutorial contest
Automatic Left Atrial Scar Segmenter
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Qualitative and Quantitative Comparison of Two RT Dose Distributions
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Dose Accumulation for Adaptive Radiation Therapy
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WebGL Export
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OpenIGTLink
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Additional resources
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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:
- Open Source Paleontologist: 3D Slicer: The Tutorial
- Open Source Paleontologist: 3D Slicer: The Tutorial Part II
- Open Source Paleontologist: 3D Slicer: The Tutorial Part III
- Open Source Paleontologist: 3D Slicer: The Tutorial Part IV
- Open Source Paleontologist: 3D Slicer: The Tutorial Part V
- Open Source Paleontologist: 3D Slicer: The Tutorial Part VI
Team Contributions
See the collection of videos on the Kitware vimeo album.
User Contributions
See the User Contributions Page for more content.