Difference between revisions of "Documentation/Nightly/Training"
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− | *The [https:// | + | *The [https://spujol.github.io/3DSlicerQuickStartGuide/ Quick Start Guide] shows how to install and start 3D Slicer |
*Author: Sonia Pujol, Ph.D. | *Author: Sonia Pujol, Ph.D. | ||
*Based on: 3D Slicer version 4.8 | *Based on: 3D Slicer version 4.8 | ||
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{| width="100%" | {| width="100%" | ||
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+ | *Slicer 5.0 | ||
+ | **The [https://spujol.github.io/SlicerVisualizationTutorial/ Slicer 5.0 Basics of data loading and visualization tutorial] shows how to load and visualize DICOM images and 3D models in 3D Slicer. | ||
+ | **Author: Sonia Pujol, Ph.D. | ||
+ | **Modules: DICOM, Volume Rendering, Models | ||
+ | **Audience: End-users | ||
+ | **Based on: 3D Slicer version 5.0/4.11 | ||
+ | **The [https://www.dropbox.com/s/03emcqnlec4t2s5/3DVisualizationDataset.zip?dl=1 Data Loading and Visualization dataset] contains a thoraco-abdominal CT scan, an MRI brain dataset and 3D models of brain structures. | ||
+ | |||
*Slicer 4.10 | *Slicer 4.10 | ||
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**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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| align="right" | | | align="right" | | ||
− | [[Image:20180426_DataLoadingAndVisualizationTutorial.png|right| | + | [[Image:20180426_DataLoadingAndVisualizationTutorial.png|right|200px|]] |
− | [[Image:Slicer4DataLoading_tutorial.png|right|250px|]] | + | [[Image:Slicer4DataLoading_tutorial.png|right|200px|]] |
+ | |} | ||
+ | |||
+ | ==DICOM== | ||
+ | {| width="100%" | ||
+ | | | ||
+ | *The [https://spujol.github.io/SlicerDICOMTutorial/ DICOM and Slicer] tutorial provides an introduction to the DICOM standard and shows how to load and visualize DICOM datasets in 3D Slicer version 5.0. | ||
+ | *Author: Sonia Pujol, Ph.D. | ||
+ | *Modules: DICOM, Volumes | ||
+ | *Based on: 3D Slicer version 5.0/4.11 | ||
+ | *The [https://spujol.github.io/SlicerDICOMTutorial/ 3D Slicer DICOM Tutorial Data] contains a torso-CT and a breast MRI. | ||
+ | | align="right" | | ||
+ | [[Image:SlicerAndDICOM.png|right|250px|]] | ||
|} | |} | ||
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{| width="100%" | {| width="100%" | ||
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|} | |} | ||
+ | =Tutorials for software developers= | ||
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==PerkLab's Slicer bootcamp training materials== | ==PerkLab's Slicer bootcamp training materials== | ||
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| align="right" | | | align="right" | | ||
[[Image:PerkLabSlicerProgrammingTutorial.png|right|250px|]] | [[Image:PerkLabSlicerProgrammingTutorial.png|right|250px|]] | ||
+ | |} | ||
+ | |||
+ | ==Slicer4 Programming Tutorial== | ||
+ | {| width="100%" | ||
+ | | | ||
+ | *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. | ||
+ | *Audience: Developers | ||
+ | *Based on: 3D Slicer version 5.0/4.11 | ||
+ | | align="right" | | ||
+ | [[Image:SlicerProgrammingTutorial.png|right|250px|]] | ||
|} | |} | ||
==Slicer script repository== | ==Slicer script repository== | ||
− | For additional Python scripts examples, please visit the [ | + | For additional Python scripts examples, please visit the [https://slicer.readthedocs.io/en/latest/developer_guide/script_repository.html Script repository]. |
==Developing and contributing extensions for 3D Slicer== | ==Developing and contributing extensions for 3D Slicer== | ||
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|--- | |--- | ||
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− | *[https://lassoan.github.io/SlicerSegmentationRecipes/ Slicer Segmentation Recipes] | + | *'''[https://lassoan.github.io/SlicerSegmentationRecipes/ Slicer Segmentation Recipes]''' provide step-by-step description of useful segmentation techniques. |
+ | ** Segmentation tutorials for common tasks, such as skin surface extraction, craniotomy (splitting segments), sorta segmentation, cerebral vessel segmentation by subtraction, segmentation on arbitrarily oriented slices, skull stripping. | ||
+ | | align="right" |[[Image:SegmentationRecipes.png|280px]] | ||
+ | |--- | ||
+ | | | ||
+ | *'''[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]] | ||
|} | |} | ||
+ | |||
+ | |||
+ | =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]] | ||
+ | |||
+ | |} | ||
+ | |||
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=Registration= | =Registration= | ||
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| align="right" |[[Image:RegLib_table.png|250px|link=https://www.slicer.org/wiki/Documentation/{{documentation/version}}/Registration/RegistrationLibrary]]<nowiki>|}</nowiki> | | align="right" |[[Image:RegLib_table.png|250px|link=https://www.slicer.org/wiki/Documentation/{{documentation/version}}/Registration/RegistrationLibrary]]<nowiki>|}</nowiki> | ||
|} | |} | ||
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+ | =Slicer Extensions= | ||
==Slicer4 Diffusion Tensor Imaging Tutorial== | ==Slicer4 Diffusion Tensor Imaging Tutorial== | ||
{| width="100%" | {| width="100%" | ||
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− | *The [https:// | + | *The [https://spujol.github.io/SlicerDiffusionMRITutorial Diffusion MRI Tutorial] 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 4.8 | + | *Based on: 3D Slicer version 4.8; Compatible with Slicer version 4.10.2 |
− | *The [ | + | *The [https://www.dropbox.com/s/gba2zsn276x43up/SlicerDiffusionMRITutorialData.zip?dl=1 Slicer Diffusion MRI Tutorial dataset] contains an MR Diffusion Weighted Imaging scan of the brain. |
+ | *Please visit [http://dmri.slicer.org/docs/ dmri.slicer.org/docs] for the latest documentation of SlicerDMRI. | ||
| align="right" | | | align="right" | | ||
[[Image:Slicer4DTI Tutorial.png|right|250px|]] | [[Image:Slicer4DTI Tutorial.png|right|250px|]] | ||
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*Based on Slicer 4.7 | *Based on Slicer 4.7 | ||
| align="right" | | | align="right" | | ||
− | + | [[Image:SlicerRTUseCaseImage.png|right|150px|]] | |
|} | |} | ||
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==Slicer Pathology== | ==Slicer Pathology== | ||
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[[File:SlicerWinterProjectWeek2017-FiberBundleVolumeMeasurements.png | 200px]]. | [[File:SlicerWinterProjectWeek2017-FiberBundleVolumeMeasurements.png | 200px]]. | ||
|} | |} | ||
+ | |||
+ | ==Slicer4 Lung CT Analyzer== | ||
+ | {| width="100%" | ||
+ | | | ||
+ | *The [https://github.com/rbumm/SlicerLungCTAnalyzer LungCTAnalyzer tutorial] and the [https://www.youtube.com/watch?v=fpLxm7uAvZQ LungCTAnalyzer video-based demo] show how to visualize and quantify infiltration, emphysema and collapsed lung areas in CT datasets acquired on COVID-19 patients. | ||
+ | *Authors: Rudolph Bumm, MD, Andras Lasso, PhD. | ||
+ | *Audience: End-users | ||
+ | *Modules: LungCTSegmenter, LungCTAnalyzer | ||
+ | *Based on: 3D Slicer version 5.0 (4.11) | ||
+ | | align="right" | | ||
+ | [[Image:LungCTAnalyzer.png|right|250px|]] | ||
+ | |||
+ | |} | ||
+ | |||
=3D Slicer version 4.7 Tutorial Contest= | =3D Slicer version 4.7 Tutorial Contest= | ||
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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== | ||
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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.] | ||
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*[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) | ||
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==Murat Maga's blog posts about using 3D Slicer for biology== | ==Murat Maga's blog posts about using 3D Slicer for biology== | ||
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*[https://blogs.uw.edu/maga/2017/04/11/morphosource-data-and-dealing-with-dicom-series-in-slicer/ Fixing problem DICOM] | *[https://blogs.uw.edu/maga/2017/04/11/morphosource-data-and-dealing-with-dicom-series-in-slicer/ Fixing problem DICOM] | ||
*[https://blogs.uw.edu/maga/2017/04/12/scissors-tool-is-awesome/ Scissors tool is awesom] | *[https://blogs.uw.edu/maga/2017/04/12/scissors-tool-is-awesome/ Scissors tool is awesom] | ||
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===Fast GrowCut=== | ===Fast GrowCut=== | ||
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*Audience: Users interested in segmentation | *Audience: Users interested in segmentation | ||
| align="right" |[[File:FastGrowCutLogo.png|200px]] | | align="right" |[[File:FastGrowCutLogo.png|200px]] | ||
+ | |} | ||
+ | |||
+ | {| width="100%" | ||
+ | *'''[https://www.youtube.com/channel/UC8vxI0-dEWrw0_tBF-v8xGA/videos Video-based segmentation tutorials from CHU de Rouen (France)] | ||
+ | ** Segmentation tutorials, including liver, wrist bones, lungs, kidneys, hips. | ||
+ | | align="right" |[[Image:ChuRouen.png|180px]] | ||
|} | |} | ||
Revision as of 04:11, 24 April 2021
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
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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DICOM
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Tutorials for software developers
PerkLab's Slicer bootcamp training materials
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Slicer4 Programming Tutorial
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Slicer script repository
For additional Python scripts examples, please visit the Script repository.
Developing and contributing extensions for 3D Slicer
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Segmentation
Slicer4 Image Segmentation
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Image Phenotyping
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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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Slicer4 Lung CT Analyzer
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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.
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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
Fast GrowCut
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- Video-based segmentation tutorials from CHU de Rouen (France)
- Segmentation tutorials, including liver, wrist bones, lungs, kidneys, hips.
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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