Difference between revisions of "Documentation/Nightly/Training"
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{| width="100%" | {| width="100%" | ||
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− | *The [https:// | + | *The [https://spujol.github.io/SlicerProgrammingTutorial/ Slicer Programming tutorial] guides through the integration of a python module in Slicer4. |
*Author: Sonia Pujol, Ph.D., Steve Pieper, Ph.D. | *Author: Sonia Pujol, Ph.D., Steve Pieper, Ph.D. | ||
*Audience: Developers | *Audience: Developers | ||
− | *Based on: 3D Slicer version 4. | + | *Based on: 3D Slicer version 4.11 |
− | |||
| align="right" | | | align="right" | | ||
− | [[Image: | + | [[Image:SlicerProgrammingTutorial.png|right|250px|]] |
|} | |} | ||
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*[https://lassoan.github.io/SlicerSegmentationRecipes/ Slicer Segmentation Recipes] | *[https://lassoan.github.io/SlicerSegmentationRecipes/ Slicer Segmentation Recipes] | ||
+ | |--- | ||
+ | | | ||
+ | *'''[https://spujol.github.io/SkullStrippingTutorial/ The Skull Stripping tutorial]''' shows how to perform skull-stripping in CT and MR data. | ||
+ | **Author: Sonia Pujol, PhD, Andras Lasso, PhD, Ron Kikinis, MD | ||
+ | **Audience: Users interested in brain segmentation | ||
+ | **Based on: 3D Slicer version 4.11 | ||
+ | | align="right" |[[Image:SkullStripping.png|280px]] | ||
|} | |} | ||
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*Based on Slicer 4.7 | *Based on Slicer 4.7 | ||
| align="right" | | | align="right" | | ||
− | + | [[Image:SlicerRTUseCaseImage.png|right|150px|]] | |
|} | |} | ||
− | |||
==Slicer Pathology== | ==Slicer Pathology== | ||
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=YouTube videos= | =YouTube videos= | ||
{| border="1" cellpadding="5" width="1200px" | {| border="1" cellpadding="5" width="1200px" | ||
− | | style="width: | + | | 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: | + | | 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: PerkLab] |
− | | style="width: | + | | style="width:33%" |[[Image:3DPrinting.png|right|250px|]] [https://www.youtube.com/watch?v=MKLWzD0PiIc Preparing data for 3D printing - Author: Nabgha Farhat] |
− | | style="width: | + | |} |
− | | style="width: | + | {| border="1" cellpadding="5" width="1200px" |
+ | | style="width:33%" |[[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:33%" |[[Image:LocalThresholdEffect.png|right|250px|]] [https://www.youtube.com/watch?time_continue=26&v=cevlMLyhfK8&feature=emb_logo Local Threshold Effect - Author: Kyle Sunderland] | ||
+ | | style="width:33%" |[[Image:VMTKCenterlines.png|right|250px|]] [https://www.youtube.com/watch?v=yi07mjr3JeU&feature=youtu.be SlicerVMTK centerline extraction (Slicer 4.11)- Author: Andras Lasso] | ||
|- | |- | ||
|} | |} | ||
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<br> | <br> | ||
==International resources== | ==International resources== | ||
+ | International resources in Chinese and in German are made available by the Slicer community. | ||
==Resources in Chinese== | ==Resources in Chinese== | ||
{| width="100%" | {| width="100%" | ||
| | | | ||
− | 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. | + | 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. The tutorials below are examples of Slicer tutorials in Chinese. |
*[https://mp.weixin.qq.com/s?__biz=MzI3MDY4ODA5Mw==&mid=2247486116&idx=1&sn=772e9d431ac32cbb73d08cf0e6bc219a&chksm=eacc0096ddbb89805d93ac4be181d1a35058031bac673d7a91b3b44dccee2bfd1d8461397635#rd Getting started 大脑前动脉远端动脉瘤手术夹闭治疗] | *[https://mp.weixin.qq.com/s?__biz=MzI3MDY4ODA5Mw==&mid=2247486116&idx=1&sn=772e9d431ac32cbb73d08cf0e6bc219a&chksm=eacc0096ddbb89805d93ac4be181d1a35058031bac673d7a91b3b44dccee2bfd1d8461397635#rd Getting started 大脑前动脉远端动脉瘤手术夹闭治疗] | ||
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*[https://mp.weixin.qq.com/s?__biz=MzI3MDY4ODA5Mw==&mid=2247486025&idx=1&sn=b281324893be4ab116d20826f1b426c3&chksm=eacc007bddbb896d9deb096f209278f40c0b52c6410a8a9ff3ce8c3697c99304f18eb678f11e&mpshare=1&scene=24&srcid=02125v1kxvIGmfkxx7mUZcCM#rd Mobile phone positioning and AR application 手机定位及AR应用的初步探索] | *[https://mp.weixin.qq.com/s?__biz=MzI3MDY4ODA5Mw==&mid=2247486025&idx=1&sn=b281324893be4ab116d20826f1b426c3&chksm=eacc007bddbb896d9deb096f209278f40c0b52c6410a8a9ff3ce8c3697c99304f18eb678f11e&mpshare=1&scene=24&srcid=02125v1kxvIGmfkxx7mUZcCM#rd Mobile phone positioning and AR application 手机定位及AR应用的初步探索] | ||
− | The WeChat 3D Slicer Group in China offers a [https://spujol.github.io/SlicerTutorialsInChinese/ comprehensive list of tutorials in Chinese.] | + | |
+ | The WeChat 3D Slicer Group in China offers a [https://spujol.github.io/SlicerTutorialsInChinese/ comprehensive list of tutorials in Chinese.] | ||
| align="right" | | | align="right" | | ||
[[image:Wechat-hemorage-2018-02-12.png|250px|Example WeChat tutorial slides]] | [[image:Wechat-hemorage-2018-02-12.png|250px|Example WeChat tutorial slides]] | ||
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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] | *[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] | *[http://openpaleo.blogspot.com/2009/03/3d-slicer-tutorial-part-vi.html Open Source Paleontologist: 3D Slicer: The Tutorial Part VI] | ||
+ | |||
|} | |} |
Revision as of 12:16, 22 June 2020
Home < Documentation < Nightly < Training
For the latest Slicer documentation, visit the read-the-docs. |
Introduction: Slicer Nightly Tutorials
- This page contains "How to" tutorials with matched sample data sets. They demonstrate how to use the 3D Slicer environment (version Nightly 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 Nightly 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 Slicer4.10. The concepts are still useful but some interface elements and features may be different in updated versions.
Contents
- 1 Introduction: Slicer Nightly Tutorials
- 2 Quick Start Guide
- 3 General Introduction
- 4 3D Visualization
- 5 Tutorials for software developers
- 6 Segmentation
- 7 Registration
- 7.1 Slicer4 Image Registration
- 7.2 Slicer Registration Case Library
- 7.3 Slicer Extensions
- 7.4 Slicer4 Diffusion Tensor Imaging Tutorial
- 7.5 Slicer4 Neurosurgical Planning Tutorial
- 7.6 Slicer4 Quantitative Imaging tutorial
- 7.7 Slicer4 IGT
- 7.8 Slicer4 Radiation Therapy Tutorial
- 7.9 Slicer Pathology
- 7.10 SPHARM-PDM
- 7.11 Fiber Bundle Volume Measurement
- 8 3D Slicer version 4.7 Tutorial Contest
- 9 YouTube videos
- 10 Teams Contributions
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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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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Registration
Slicer4 Image Registration
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- Based on: 3D Slicer version 4.8
Slicer Registration Case Library
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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
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|
International resources
International resources in Chinese and in German are made available by the Slicer community.
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. The tutorials below are examples of Slicer tutorials in Chinese.
|
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
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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
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