Difference between revisions of "Documentation/Nightly/Training"
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*Audience: End-users | *Audience: End-users | ||
*Based on: 3D Slicer version 4.5 | *Based on: 3D Slicer version 4.5 | ||
− | *The [ | + | *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. |
|align="right"| | |align="right"| | ||
[[Image:Slicer4DataLoading_tutorial.png|right|250px|]] | [[Image:Slicer4DataLoading_tutorial.png|right|250px|]] | ||
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− | *The [ | + | *The [https://www.dropbox.com/s/wrhrvvmplosiis1/Slicer4_ProgrammingTutorial_SPujol-SPieper_Nightly.pdf?dl=0# 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 4.7 |
− | *The [ | + | *The [https://www.dropbox.com/s/6yxu8qepmvywk0n/HelloPython_Nightly.zip?dl=0 HelloPython dataset] contains sample data set (MR scan of the brain) and complete Python module examples. |
|align="right"| | |align="right"| | ||
[[Image:HelloPythonTutorial.png|right|250px|]] | [[Image:HelloPythonTutorial.png|right|250px|]] | ||
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− | *The [ | + | *Please visit [http://dmri.slicer.org/docs/ dmri.slicer.org/docs] for the latest documentation of SlicerDMRI. |
+ | *The [https://github.com/SlicerDMRI/slicerdmri.github.io/raw/master/docs/tutorials/DiffusionMRIanalysis.pdf Diffusion Tensor Imaging Tutorial] course guides through 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 4.6 |
*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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{|width="100%" | {|width="100%" | ||
| | | | ||
− | *The [ | + | *Please visit [http://dmri.slicer.org/docs/ dmri.slicer.org/docs] for the latest documentation of SlicerDMRI. |
+ | *The [https://github.com/SlicerDMRI/slicerdmri.github.io/raw/master/docs/tutorials/WhiteMatterExplorationTutorial.pdf Neurosurgical Planning tutorial] course guides 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: End-users and developers | *Audience: End-users and developers | ||
*Modules: Volumes, Editor, Tractography Label Map Seeding, Tractography Interactive Seeding | *Modules: Volumes, Editor, Tractography Label Map Seeding, Tractography Interactive Seeding | ||
− | *Based on: 3D Slicer version 4. | + | *Based on: 3D Slicer version 4.6 |
*The [[Media:WhiteMatterExplorationData.zip| White Matter Exploration datasets]] contains a Diffusion Weighted Imaging scan of brain tumor patient. | *The [[Media:WhiteMatterExplorationData.zip| White Matter Exploration datasets]] contains a Diffusion Weighted Imaging scan of brain tumor patient. | ||
|align="right"| | |align="right"| | ||
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|} | |} | ||
− | == Slicer4 | + | == Slicer4 Image Segmentation == |
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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. |
− | + | ** '''[https://discourse.slicer.org/t/new-video-tutorial-for-segment-editor-lumbar-spine-segmentation-for-3d-printing/700 Video tutorial]'''. Author: Hillary Lia. | |
− | * Audience: Users and developers interested in 3D printing | + | ** '''[https://www.slicer.org/wiki/Documentation/4.6/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 |
− | * Author: | + | ** Based on: 3D Slicer version 4.7 |
− | * Audience: Users | + | |align="right"|[[Image:20170717_3DPrintingTutorialYoutube.PNG|280px]] |
− | |align="right"|[[Image: | + | |--- |
+ | | | ||
+ | * '''[https://youtu.be/BJoIexIvtGo Video tutorial: Whole heart segmentation from cardiac CT]''' shows how to use the Segment Editor module for segmenting heart ventricles, atria, and great vessels from cardiac CT volumes. | ||
+ | ** Author: Andras Lasso, PhD | ||
+ | ** Audience: Users who need to segment heart structures, for example for visualization, quantification, or simulation. | ||
+ | ** Sample data set: http://slicer.kitware.com/midas3/download/bitstream/738905/CTA-cardio2.nrrd | ||
+ | ** Based on: 3D Slicer version 4.8 | ||
+ | |align="right"|[[Image:WholeHeartSegYoutube.png|280px]] | ||
+ | |--- | ||
+ | | | ||
+ | * '''[https://youtu.be/0at15gjk-Ns Video tutorial: Femur and pelvis segmentation from CT]''' shows how to use the Segment Editor module for segmenting pelvis and femur from CT volumes. | ||
+ | ** Author: Andras Lasso, PhD | ||
+ | ** Audience: Users who need to segment bones in CT images for visualization, quantification, or simulation. | ||
+ | ** Sample data set: https://wiki.cancerimagingarchive.net/display/Public/TCGA-PRAD (Subject TCGA-VP-A878) | ||
+ | ** Based on: 3D Slicer version 4.8 | ||
+ | |align="right"|[[Image:FemurSegmentationYoutube.png|280px]] | ||
|} | |} | ||
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See [[Documentation/{{documentation/version}}/Registration/RegistrationLibrary|the Registration Library for worked out registration examples with data]]. | See [[Documentation/{{documentation/version}}/Registration/RegistrationLibrary|the Registration Library for worked out registration examples with data]]. | ||
− | == | + | ==Slicer4 Radiation Therapy Tutorial == |
{|width="100%" | {|width="100%" | ||
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− | * The [ | + | * The [https://app.assembla.com/spaces/slicerrt/subversion/source/HEAD/trunk/SlicerRt/doc/tutorials/SlicerRT_TutorialIGRT_4.7.pdf?_format=raw SlicerRT tutorial] is an introduction to the Radiation Therapy functionalities of Slicer. |
− | * | + | * Author: Csaba Pinter, Andras Lasso, An Wang, Gregory C. Sharp, David Jaffray, Gabor Fichtinger. |
− | * | + | * Dataset: [http://slicer.kitware.com/midas3/download/item/205404/SlicerRT_WorldCongress_TutorialIGRT_Dataset.zip download] from MIDAS server |
− | |align="right"|[[ | + | * Based on Slicer 4.7 |
+ | |align="right"| | ||
+ | <!-- [[Image:TUTORIAL-IMAGE-HERE.png|right|150px|]] --> | ||
|} | |} | ||
− | |||
− | |||
− | |||
− | |||
− | |||
− | |||
== Other == | == Other == | ||
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− | *The [ | + | *The [https://www.assembla.com/spaces/slicerrt/documents/bmRQGEzzur54v-dmr6CpXy/download/bmRQGEzzur54v-dmr6CpXy Segmentation for 3D printing Tutorial] is an introduction to the new [[Documentation/{{documentation/version}}/Modules/SegmentEditor|Segment Editor]] module, demonstrated through the popular topic of 3D printing. |
*Author: Csaba Pinter (Queen's University, Canada) | *Author: Csaba Pinter (Queen's University, Canada) | ||
− | * | + | * [https://www.youtube.com/watch?v=Uht6Fwtr9hE Narrated video version on YouTube]. |
+ | *Dataset: [[:File:BasePiece.zip|Phantom base STL model]] Source: [http://perk-software.cs.queensu.ca/plus/doc/nightly/modelcatalog/ PerkLab]. | ||
|align="right"| | |align="right"| | ||
[[File:SlicerWinterProjectWeek2017-Segmentation-for-3d-printing.png | 200px]]. | [[File:SlicerWinterProjectWeek2017-Segmentation-for-3d-printing.png | 200px]]. | ||
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{|width="100%" | {|width="100%" | ||
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− | *The [ | + | *The [https://github.com/SlicerDMRI/slicerdmri.github.io/raw/master/docs/tutorials/FiberBundleSelectionAndScalarMeasurement.pdf Fiber Bundle Selection and Scalar Measurements] tutorial guides through the use of the Diffusion Bundle Selection module and the Fiber Tract Scalar Measurement module for diffusion MRI tractography data analysis. |
− | *Author: Fan Zhang, University of Sydney Australia | + | *Author: Fan Zhang, University of Sydney Australia and Brigham and Women's Hospital |
*Dataset: [[media:FiberBundleSelectionAndScalarMeasurement_TutorialContestWinter2016.zip| Fiber Bundle Selection And Scalar Measurement Tutorial Dataset]] | *Dataset: [[media:FiberBundleSelectionAndScalarMeasurement_TutorialContestWinter2016.zip| Fiber Bundle Selection And Scalar Measurement Tutorial Dataset]] | ||
|align="right"| | |align="right"| | ||
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− | *The [ | + | *The [https://github.com/SlicerDMRI/slicerdmri.github.io/raw/master/docs/tutorials/UKFTractography.pdf UKF tutorial] guides through the use of the Unscented Kalman Filter (UKF) tractography module. |
*Author: Pegah Kahali, Brigham and Women's Hopital | *Author: Pegah Kahali, Brigham and Women's Hopital | ||
*Dataset: [http://www.na-mic.org/Wiki/index.php/File:UKF-Tractography_TutorialContestWinter2016.zip UKF tutorial Dataset] | *Dataset: [http://www.na-mic.org/Wiki/index.php/File:UKF-Tractography_TutorialContestWinter2016.zip UKF tutorial Dataset] | ||
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= External Resources = | = External Resources = | ||
+ | |||
+ | == Resources for Chinese users == | ||
+ | |||
+ | |||
+ | {|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. | ||
+ | |||
+ | * [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=2247484787&idx=1&sn=1f6279bdccab168fc79b7275e9fe91ca&chksm=eacc0f41ddbb8657be92f617661133d87bb55a4ecf12f786e97a8b7d5249a05d11e0cd620c3f#rd distal anterior cerebral artery aneurysm 3D Slicer:漂亮得不像实力派] | ||
+ | |||
+ | * [https://mp.weixin.qq.com/s?__biz=MzI3MDY4ODA5Mw==&mid=2247486360&idx=1&sn=f833b13a26f543aa9175419a03df7f52&chksm=eacc01aaddbb88bcb004773a4db8a9b3c7633d21cda3956f84b96515252eb861c5eb1e75a60b&mpshare=1&scene=24&srcid=0212LIfOkBRm9CvA7ImHCpRt#rd meningioma skull resection 脑膜瘤患者颅骨切除一期修补的3DSlicer方案] | ||
+ | |||
+ | * [https://mp.weixin.qq.com/s?__biz=MzI3MDY4ODA5Mw==&mid=2247486079&idx=1&sn=9b926dc398a408e3441082b9e0ffde61&chksm=eacc004dddbb895bf9b60f5f1bc443513196e4cb90a6caf6f348a4da7b7fc22eb658661aeb49&mpshare=1&scene=24&srcid=0212AFtT2Wq7K7bvkMGTdyih#rd Cerebral hemorrhage by forehead positioning method 脑出血经额手术定位法(五 ] | ||
+ | |||
+ | * [https://mp.weixin.qq.com/s?__biz=MzI3MDY4ODA5Mw==&mid=2247485356&idx=1&sn=044f5899b651b35994db00c32ab688ee&chksm=eacc0d9eddbb8488f16ff82bb1dda8456a4011790fed024781972d578783e67781443cf4a319&mpshare=1&scene=24&srcid=0212G45TadrPnX8tp9eaNXUs#rd Hematoma modeling 血肿建模的第11种方法] | ||
+ | |||
+ | * [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] | ||
+ | |||
+ | |align="right"| | ||
+ | [[image:Wechat-hemorage-2018-02-12.png|250px|Example WeChat tutorial slides]] | ||
+ | |} | ||
+ | |||
== 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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== Using the (legacy) Editor == | == Using the (legacy) Editor == | ||
+ | |||
+ | === Fast GrowCut === | ||
+ | |||
+ | {|width="100%" | ||
+ | | | ||
+ | * The [[media:FastGrowCutTutorial.pdf |Fast GrowCut tutorial]] shows how to perform a segmentation using the Fast GrowCut effect in Slicer. | ||
+ | * Authors: Hillary Lia | ||
+ | * Audience: Users interested in segmentation | ||
+ | |align="right"|[[File:FastGrowCutLogo.png|200px]] | ||
+ | |} | ||
+ | |||
+ | === 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: | 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: |
Revision as of 14:51, 12 February 2018
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. 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 Nightly 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 Image Segmentation
- 4.7 Slicer4 Image Registration
- 4.8 Slicer4 Radiation Therapy Tutorial
- 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 Image Segmentation
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|
|
|
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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.
Slicer4 Radiation Therapy Tutorial
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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
|
|
|
External Resources
Resources for Chinese users
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. |
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
Team Contributions
See the collection of videos on the Kitware vimeo album.
User Contributions
See the User Contributions Page for more content.