Difference between revisions of "Documentation/4.10/Training"
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*For tutorials for other versions of Slicer, please visit the [[Training| Slicer training portal]]. | *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 "reference manual" style documentation, please visit the [[Documentation/{{documentation/version}}|Slicer {{documentation/version}} documentation page]] | ||
− | *For questions related to the | + | *For questions related to 3D Slicer training materials and to the organization of 3D Slicer training workshops, please send an e-mail to '''[http://www.na-mic.org/Wiki/index.php/User:SPujol Sonia Pujol, Ph.D., Director of Training and Education of 3D Slicer.]''' |
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*The [https://www.dropbox.com/s/gtir3x6e007snkx/QuickStartGuide_3DSlicer_SoniaPujol.pdf?dl=0| Quick Start Guide] shows how to install and start 3D Slicer | *The [https://www.dropbox.com/s/gtir3x6e007snkx/QuickStartGuide_3DSlicer_SoniaPujol.pdf?dl=0| Quick Start Guide] shows how to install and start 3D Slicer | ||
*Author: Sonia Pujol, Ph.D. | *Author: Sonia Pujol, Ph.D. | ||
− | *Based on | + | *Based on 3D Slicer 4.8 |
+ | *Compatible with 3D Slicer 4.10.1 | ||
|align="right"| | |align="right"| | ||
[[image:QuickStart_image.png|250px|SlicerWelcome tutorial]] | [[image:QuickStart_image.png|250px|SlicerWelcome tutorial]] | ||
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*Audience: First-time users who want a general introduction to the software | *Audience: First-time users who want a general introduction to the software | ||
*Modules: Welcome to Slicer, Sample Data | *Modules: Welcome to Slicer, Sample Data | ||
− | *Based on | + | *Based on 3D Slicer 4.8 |
+ | *Compatible with Slicer 4.10.1 | ||
|align="right"| | |align="right"| | ||
[[image:SlicerWelcome-image.png|250px|SlicerWelcome tutorial]] | [[image:SlicerWelcome-image.png|250px|SlicerWelcome tutorial]] | ||
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{|width="100%" | {|width="100%" | ||
| | | | ||
− | *The [https://www.dropbox.com/s/ | + | *The [https://www.dropbox.com/s/v3lyivwgdoro7yn/Slicer4.10minute_SoniaPujol.pdf?dl=0| Slicer4 Minute Tutorial] is a brief introduction to the advanced 3D visualization capabilities of Slicer. |
*Author: Sonia Pujol, Ph.D. | *Author: Sonia Pujol, Ph.D. | ||
*Audience: First-time users who want to discover Slicer in 4 minutes | *Audience: First-time users who want to discover Slicer in 4 minutes | ||
*Modules: Welcome to Slicer, Models | *Modules: Welcome to Slicer, Models | ||
− | *Based on | + | *Based on Slicer version 4.8 |
+ | *Compatible with Slicer 4.10.1 | ||
*The [[media:Slicer4minute.zip|Slicer4Minute dataset]] contains an MR scan of the brain and 3D reconstructions of the anatomy | *The [[media:Slicer4minute.zip|Slicer4Minute dataset]] contains an MR scan of the brain and 3D reconstructions of the anatomy | ||
|align="right"| | |align="right"| | ||
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** Modules: Welcome to Slicer, Data, Volume Rendering, Models. | ** Modules: Welcome to Slicer, Data, Volume Rendering, Models. | ||
** Audience: End-users | ** Audience: End-users | ||
− | ** Based on | + | ** Based on Slicer 4.9 |
+ | ** Compatible with Slicer 4.10.1 | ||
** The [http://slicer.kitware.com/midas3/download/?items=330421,1 3DVisualization dataset] contain an MR scan and a series of 3D models of the brain. | ** The [http://slicer.kitware.com/midas3/download/?items=330421,1 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|]] | [[Image:Slicer4DataLoading_tutorial.png|right|250px|]] | ||
|} | |} | ||
− | |||
==Slicer4 3D Visualization of DICOM images for Radiology Applications== | ==Slicer4 3D Visualization of DICOM images for Radiology Applications== | ||
{|width="100%" | {|width="100%" | ||
| | | | ||
− | *The [https://www.dropbox.com/s/ | + | *The [https://www.dropbox.com/s/8pm5mty2c0zwmyk/3DVisualizationDICOM_Slicer4.10_SoniaPujol.pdf?dl=0 3D Visualization of DICOM images] course guides through 3D data loading and visualization of DICOM images for Radiology Applications in Slicer4. |
*Author: Sonia Pujol, Ph.D., Kitt Shaffer, M.D., Ph.D., Ron Kikinis, M.D. | *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. | *Audience: Radiologists and users of Slicer who need a more comprehensive overview over Slicer4 visualization capabilities. | ||
*Modules: DICOM, Volumes, Volume Rendering, Models. | *Modules: DICOM, Volumes, Volume Rendering, Models. | ||
*Based on: 3D Slicer version 4.8 | *Based on: 3D Slicer version 4.8 | ||
+ | *Compatible with 3D Slicer version 4.10 | ||
*The [[Media:3DVisualization_DICOM_images_part1.zip | 3DVisualizationDICOM_part1]] and [[Media:3DVisualization_DICOM_images_part2.zip | 3DVisualizationDICOM_part2]] datasets contain a series of MR and CT scans, and 3D models of the brain, lung and liver. | *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"| | |align="right"| | ||
[[Image:Slicer4RSNA_2.png|right|250px|]] | [[Image:Slicer4RSNA_2.png|right|250px|]] | ||
|} | |} | ||
+ | ==Open Anatomy Browser == | ||
+ | {|width="100%" | ||
+ | | | ||
+ | [[Image:OABrowser.png|right|250px|]] | ||
+ | *The [https://www.dropbox.com/s/f2641iu27hif8p4/OpenAnatomyTutorial_SoniaPujol-MikeHalle.pdf?dl=0 Open Anatomy Browser] tutorial is an introduction to the OABrowser technology for viewing and interacting with atlases. | ||
+ | *Author: Sonia Pujol, Ph.D., Mike Halle, Ph.D. | ||
+ | *Audience: End-users | ||
− | + | |} | |
− | |||
=Tutorials for software developers= | =Tutorials for software developers= | ||
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* Authors: Sonia Pujol, Ph.D., Dominik Meier, Ph.D., Ron Kikinis, M.D. | * Authors: Sonia Pujol, Ph.D., Dominik Meier, Ph.D., Ron Kikinis, M.D. | ||
* Audience: Users and developers interested in image registration | * Audience: Users and developers interested in image registration | ||
− | * Dataset: [[Media:RegistrationData.zip| 3D Slicer Registration Data]] | + | * Dataset: [[Media:RegistrationData.zip | 3D Slicer Registration Data]] |
|align="right"|[[File:registration_Slicer4.png|250px]] | |align="right"|[[File:registration_Slicer4.png|250px]] | ||
|} | |} | ||
− | *Based on: 3D Slicer version 4.8 | + | *Based on: 3D Slicer version 4.8; Compatible with Slicer 4.10 |
− | + | {|width="100%" | |
+ | | | ||
+ | *The [https://spujol.github.io/3DSlicerTutorial-Registration Brain Tumor Registration] is a video-based tutorial that shows how to register two MRI datasets in a brain tumor case for surgical resection follow-up. | ||
+ | * Authors: Sonia Pujol, Ph.D., Dominik Meier, Ph.D. | ||
+ | * Audience: Users and developers interested in image registration | ||
+ | * Dataset: [[Media:RegLib_C37_Data.zip | Registration Library Case #37]] | ||
+ | |align="right"|[[File:RigidRegistration.jpg|250px]] | ||
+ | |} | ||
+ | *Based on: 3D Slicer version 4.10 | ||
== Slicer Registration Case Library== | == Slicer Registration Case Library== | ||
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|align="right"|[[Image:RegLib_table.png|250px|link=http://wiki.slicer.org/slicerWiki/index.php/Documentation/{{documentation/version}}/Registration/RegistrationLibrary]] | |align="right"|[[Image:RegLib_table.png|250px|link=http://wiki.slicer.org/slicerWiki/index.php/Documentation/{{documentation/version}}/Registration/RegistrationLibrary]] | ||
|} | |} | ||
+ | |||
+ | == Image Phenotyping== | ||
+ | {|width="100%" | ||
+ | | | ||
+ | *Based on: 3D Slicer version 4.10 | ||
+ | *The [https://www.dropbox.com/s/lg417kr754fo6ji/ImagePhenotypingTutorial_SoniaPujol.pdf?dl=0 Image Phenotyping tutorial] is an introduction to image phenotyping using the Slicer Radiomics extension.. | ||
+ | * Authors: Sonia Pujol, Ph.D. | ||
+ | * Audience: Clinical researchers | ||
+ | * Dataset: [https://www.dropbox.com/s/hdlduw6oqnf2n72/Meningioma.nrrd?dl=0 Meningioma dataset] | ||
+ | |align="right"|[[File:ImagePhenotyping.png|250px]] | ||
+ | |||
+ | |} | ||
+ | |||
=Slicer Extensions= | =Slicer Extensions= | ||
==Slicer4 Diffusion Tensor Imaging Tutorial == | ==Slicer4 Diffusion Tensor Imaging Tutorial == | ||
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{|width="100%" | {|width="100%" | ||
| | | | ||
− | *The [https:// | + | *The [https://spujol.github.io/NeurosurgicalPlanningTutorial/ Neurosurgical Planning tutorial] course guides end-users through the generation of fiber tracts in the vicinity of a tumor. |
*Author: Sonia Pujol, Ph.D., Ron Kikinis, M.D. | *Author: Sonia Pujol, Ph.D., Ron Kikinis, M.D. | ||
− | *Audience: | + | *Audience: Clinicians and Clinical Researchers |
− | *Modules: | + | *Modules: Segment Editor, Tractography |
− | *Based on | + | *Based on 3D Slicer version 4.10 |
− | + | *The [[Media:WhiteMatterExplorationData.zip| White Matter Exploration dataset]] contains a Diffusion Weighted Imaging scan of a brain tumor patient. | |
− | *The [[Media:WhiteMatterExplorationData.zip| White Matter Exploration dataset]] contains a Diffusion Weighted Imaging scan of | ||
|align="right"| | |align="right"| | ||
[[Image:NeurosurgicalPlanningTutorial.png|right|250px|link=http://vimeo.com/67336069]] | [[Image:NeurosurgicalPlanningTutorial.png|right|250px|link=http://vimeo.com/67336069]] | ||
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| style="width:25%" | [[Image:Femurmodel.png|right|250px|]] [https://www.youtube.com/watch?v=0at15gjk-Ns Creating a femur model from CT volume using 3D Slicer - Author: Nabgha Farhat ] | | style="width:25%" | [[Image:Femurmodel.png|right|250px|]] [https://www.youtube.com/watch?v=0at15gjk-Ns Creating a femur model from CT volume using 3D Slicer - Author: Nabgha Farhat ] | ||
| style="width:25%" | [[Image:3DPrinting.png|right|250px|]] [https://www.youtube.com/watch?v=MKLWzD0PiIc Preparing data for 3D printing - Author: PerkLab ] | | style="width:25%" | [[Image:3DPrinting.png|right|250px|]] [https://www.youtube.com/watch?v=MKLWzD0PiIc Preparing data for 3D printing - Author: PerkLab ] | ||
− | |||
| style="width:25%" | [[Image:DICOM2.png|right|250px|]] [https://www.youtube.com/watch?v=nzWf4xHy1BM& How to export CT and segmentation data to DICOM- Author: Andras Lasso, Csaba Pinter] | | style="width:25%" | [[Image:DICOM2.png|right|250px|]] [https://www.youtube.com/watch?v=nzWf4xHy1BM& How to export CT and segmentation data to DICOM- Author: Andras Lasso, Csaba Pinter] | ||
|- | |- |
Revision as of 20:51, 23 April 2019
Home < Documentation < 4.10 < Training
For the latest Slicer documentation, visit the read-the-docs. |
Introduction: Slicer 4.10 Tutorials
- This page contains "How to" tutorials with matched sample data sets. They demonstrate how to use the 3D Slicer environment (version 4.10 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 4.10 documentation page
- For questions related to 3D Slicer training materials and to the organization of 3D Slicer training workshops, please send an e-mail to Sonia Pujol, Ph.D., Director of Training and Education of 3D Slicer.
- Some of these tutorials are based on older releases of 3D Slicer and are being upgraded to Slicer4.10. The concepts are still useful but some interface elements and features may be different in updated versions.
Contents
Quick Start Guide
Downloading and Installing Slicer
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General Introduction
Slicer Welcome Tutorial
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Slicer4Minute Tutorial
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3D Visualization
Slicer4 Data Loading and 3D Visualization
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Slicer4 3D Visualization of DICOM images for Radiology Applications
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Open Anatomy Browser
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Tutorials for software developers
Slicer4 Programming Tutorial
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PerkLab's Slicer bootcamp training materials
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Slicer script repository
For additional Python scripts examples, please visit the Script Repository page
Developing and contributing extensions for 3D Slicer
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Segmentation
Slicer4 Image Segmentation
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|
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Registration
Slicer4 Image Registration
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- Based on: 3D Slicer version 4.8; Compatible with Slicer 4.10
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- Based on: 3D Slicer version 4.10
Slicer Registration Case Library
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Image Phenotyping
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Slicer Extensions
Slicer4 Diffusion Tensor Imaging Tutorial
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Slicer4 Neurosurgical Planning Tutorial
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Slicer4 Quantitative Imaging tutorial
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Slicer4 IGT
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Slicer4 Radiation Therapy Tutorial
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Slicer Pathology
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SPHARM-PDM
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Fiber Bundle Volume Measurement
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3D Slicer version 4.7 Tutorial Contest
For previous editions of the contest, please visit the 3D Slicer Tutorial Contests page
Segmentation for 3D printing
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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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YouTube videos
Additional non-curated videos-based demonstrations using 3D Slicer are accessible on YouTube.
Teams Contributions
|
|
International resources
Resources in Chinese
A 3D Slicer community on WeChat in China offers many tutorials and clinical examples in Chinese. Note that the images are of interest to non-Chinese speakers and Google Translate does a reasonable job of translating some of the text. |
Resources in German
- A series of four YouTube videos on python programming in Slicer (German narration with English subtitles)
Murat Maga's blog posts about using 3D Slicer for biology
Using the (legacy) Editor
Fast GrowCut
|
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:
- 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