Difference between revisions of "Documentation/4.8/Training"
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− | * Some of these tutorials are based on older releases of 3D Slicer. | + | * Some of these tutorials are based on older releases of 3D Slicer, and are being upgraded to Slicer4.8. The concepts are still useful but bear in mind that some interface elements and features will be different in updated versions. |
__TOC__ | __TOC__ | ||
+ | |||
+ | =Quick Start Guide = | ||
+ | |||
+ | ==Downloading and Installing Slicer== | ||
+ | {|width="100%" | ||
+ | | | ||
+ | *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. | ||
+ | *Based on: 3D Slicer version 4.8 | ||
+ | |align="right"| | ||
+ | [[image:QuickStart_image.png|250px|SlicerWelcome tutorial]] | ||
+ | |} | ||
=General Introduction= | =General Introduction= | ||
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− | *The [ | + | *The [https://www.dropbox.com/s/vn8sqlof2kag2kk/SlicerWelcome-tutorial_Slicer4.8_SoniaPujol.pdf?dl=0| SlicerWelcome tutorial] is an introduction to Slicer based on the Welcome module. |
*Author: Sonia Pujol, Ph.D. | *Author: Sonia Pujol, Ph.D. | ||
*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: 3D Slicer version 4. | + | *Based on: 3D Slicer version 4.8 |
|align="right"| | |align="right"| | ||
[[image:SlicerWelcome-image.png|250px|SlicerWelcome tutorial]] | [[image:SlicerWelcome-image.png|250px|SlicerWelcome tutorial]] | ||
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− | *The [ | + | *The [https://www.dropbox.com/s/9jfsyhhgude5hf1/Slicer4.8minute_SoniaPujol.pdf?dl=0| Slicer4 Minute Tutorial] is a brief introduction to the advanced 3D visualization capabilities of Slicer 4.8. |
*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 3D Slicer version 4.8 |
*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 | ||
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− | *The [ | + | *The [https://www.dropbox.com/s/9jcjpl33qfh5pi6/3DVisualizationDICOM_Slicer4.8_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. | + | *Based on: 3D Slicer version 4.8 |
*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|]] | ||
|} | |} | ||
+ | |||
=Programming= | =Programming= | ||
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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. | * Segmentation for 3D printing: shows how to use the Segment Editor module for combining CAD designed parts with patient-specific models. | ||
− | |||
** '''[[Documentation/{{documentation/version}}/Training#Segmentation_for_3D_printing|Segmentation for 3D printing Step-by-step tutorial]]'''. Author: Csaba Pinter, MSc | ** '''[[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 | ** Audience: Users and developers interested in segmentation and 3D printing | ||
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** Author: Andras Lasso, PhD | ** Author: Andras Lasso, PhD | ||
** Audience: Users who need to segment heart structures, for example for visualization, quantification, or simulation. | ** Audience: Users who need to segment heart structures, for example for visualization, quantification, or simulation. | ||
− | ** | + | ** [http://slicer.kitware.com/midas3/download/bitstream/738905/CTA-cardio2.nrrd Sample data set] |
** Based on: 3D Slicer version 4.8 | ** Based on: 3D Slicer version 4.8 | ||
|align="right"|[[Image:WholeHeartSegYoutube.png|280px]] | |align="right"|[[Image:WholeHeartSegYoutube.png|280px]] | ||
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− | *The [https://www. | + | *The [https://www.dropbox.com/s/chrugp2j2as5gop/ImageRegistration_Slicer4.8_SoniaPujol.pdf?dl=0 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. | * 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 | ||
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|align="right"|[[File:registration_Slicer4.png|250px]] | |align="right"|[[File:registration_Slicer4.png|250px]] | ||
|} | |} | ||
− | *Based on: 3D Slicer version 4. | + | *Based on: 3D Slicer version 4.8; Compatible with Slicer4.10 |
− | |||
== Slicer Registration Case Library== | == Slicer Registration Case Library== | ||
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− | *The ''[[Documentation/{{documentation/version}}/Registration/RegistrationLibrary|Slicer Registration Case Library]]'' provides | + | *The ''[[Documentation/{{documentation/version}}/Registration/RegistrationLibrary|Slicer Registration Case Library]]'' provides real-life example cases of using the Slicer registration tools. They include pre-computed dataset and step-by-step instructions for users to follow. |
:Author: Dominik Meier, Ph.D. | :Author: Dominik Meier, Ph.D. | ||
:Audience: users interested learning/applying Slicer image registration technology | :Audience: users interested learning/applying Slicer image registration technology | ||
− | |align="right"|[[Image:RegLib_table.png|250px|link= | + | |align="right"|[[Image:RegLib_table.png|250px|link=https://www.slicer.org/wiki/Documentation/{{documentation/version}}/Registration/RegistrationLibrary]] |
− | |} | + | |} =Slicer Extensions= |
− | |||
− | =Slicer Extensions= | ||
==Slicer4 Diffusion Tensor Imaging Tutorial == | ==Slicer4 Diffusion Tensor Imaging Tutorial == | ||
{|width="100%" | {|width="100%" | ||
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*Please visit [http://dmri.slicer.org/docs/ dmri.slicer.org/docs] for the latest documentation of SlicerDMRI. | *Please visit [http://dmri.slicer.org/docs/ dmri.slicer.org/docs] for the latest documentation of SlicerDMRI. | ||
− | *The [ | + | *The [https://www.dropbox.com/s/m7rzeblbdzr49bc/DiffusionMRIAnalysis_Slicer4.8_SoniaPujol.pdf?dl=0| Diffusion Tensor Imaging] course is an introduction to the basics of loading Diffusion Weighted images in Slicer, estimating tensors and generating fiber tracts. |
*Author: Sonia Pujol, Ph.D. | *Author: Sonia Pujol, Ph.D. | ||
*Audience: End-users and developers | *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 | *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. | + | *Based on: 3D Slicer version 4.8 |
*The [[media:Dti tutorial data.zip|DTI dataset]] contains an MR Diffusion Weighted Imaging scan of the brain. | *The [[media:Dti tutorial data.zip|DTI dataset]] contains an MR Diffusion Weighted Imaging scan of the brain. | ||
|align="right"| | |align="right"| | ||
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− | + | ==Fiber Bundle Volume Measurement== | |
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− | = 3D Slicer Tutorial | + | = 3D Slicer version 4.7 Tutorial Contest= |
− | + | For previous editions of the contest, please visit the [https://na-mic.org/wiki/Tutorial_Contests 3D Slicer Tutorial Contests page] | |
===Segmentation for 3D printing=== | ===Segmentation for 3D printing=== | ||
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− | + | | style="width:33%" | [[Image:Verterbra.png|right|250px|]] [https://www.youtube.com/watch?v=Uht6Fwtr9hE How to segment multiple vertebrae in spine CT for 3D printing - Author: Hillary Lia] | |
− | | | + | | style="width:33%" | [[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:33%" | [[Image:3DPrinting.png|right|250px|]] [https://www.youtube.com/watch?v=MKLWzD0PiIc Preparing data for 3D printing - Author: PerkLab ] | |
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− | + | Additional [http://www.youtube.com/results?search_query=3d+slicer&sm=3 non-curated videos-based demonstrations using 3D Slicer are accessible on YouTube]. | |
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=Teams Contributions = | =Teams Contributions = | ||
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= External Resources = | = External Resources = | ||
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− | == Resources in Chinese == | + | |
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− | == Resources in German == | + | ==Resources in German == |
* [https://www.youtube.com/watch?v=sl-00kGpuPk&list=PLJWCUXz3GeAfmYLiFcKus_c0jcsMnVsgb A series of four YouTube videos on python programming in Slicer] (German narration with English subtitles) | * [https://www.youtube.com/watch?v=sl-00kGpuPk&list=PLJWCUXz3GeAfmYLiFcKus_c0jcsMnVsgb A series of four YouTube videos on python programming in Slicer] (German narration with English subtitles) |
Revision as of 13:21, 27 November 2019
Home < Documentation < 4.8 < Training
For the latest Slicer documentation, visit the read-the-docs. |
Introduction: Slicer 4.8 Tutorials
- This page contains "How to" tutorials with matched sample data sets. They demonstrate how to use the 3D Slicer environment (version 4.8 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 4.8 documentation page
- For questions related to the Slicer4 Training Compendium, please send an e-mail to Sonia Pujol, Ph.D., Director of Training of 3D Slicer.
- Some of these tutorials are based on older releases of 3D Slicer, and are being upgraded to Slicer4.8. The concepts are still useful but bear in mind that some interface elements and features will be different in updated versions.
Contents
- 1 Introduction: Slicer 4.8 Tutorials
- 2 Quick Start Guide
- 3 General Introduction
- 4 3D Visualization
- 5 Programming
- 6 Segmentation
- 7 Registration
- 7.1 Slicer4 Image Registration
- 7.2 Slicer Registration Case Library
- 7.3 Slicer4 Diffusion Tensor Imaging Tutorial
- 7.4 Slicer4 Neurosurgical Planning Tutorial
- 7.5 Slicer4 Quantitative Imaging tutorial
- 7.6 Slicer4 IGT
- 7.7 Slicer4 Radiation Therapy Tutorial
- 7.8 Slicer Pathology
- 7.9 SPHARM-PDM
- 7.10 Fiber Bundle Volume Measurement
- 8 3D Slicer version 4.7 Tutorial Contest
- 9 YouTube videos
- 10 Teams Contributions
- 11 External Resources
Quick Start Guide
Downloading and Installing Slicer
|
General Introduction
Slicer Welcome Tutorial
|
Slicer4Minute Tutorial
|
3D Visualization
Slicer4 Data Loading and 3D Visualization
|
Slicer4 3D Visualization of DICOM images for Radiology Applications
|
Programming
Slicer4 Programming Tutorial
|
For additional Python scripts examples, please visit the Script Repository page
Developing and contributing extensions for 3D Slicer
|
Segmentation
Slicer4 Image Segmentation
|
|
|
Registration
Slicer4 Image Registration
|
- Based on: 3D Slicer version 4.8; Compatible with Slicer4.10
Slicer Registration Case Library
|
=Slicer Extensions=
Slicer4 Diffusion Tensor Imaging Tutorial
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Slicer4 Neurosurgical Planning Tutorial
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Slicer4 Quantitative Imaging tutorial
|
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
|
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
|
|
See the collection of videos on the Kitware vimeo album.
External Resources
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