Difference between revisions of "Documentation/4.10/Training"

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(Nightly -> 4.10)
 
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* 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.
+
* 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.
  
 
__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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{|width="100%"
 
|
 
|
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*The [[media:SlicerWelcome-tutorial_Slicer4.5.pdf|SlicerWelcome tutorial]] is an introduction to Slicer based on the Welcome module.
+
*The [https://www.dropbox.com/s/vn8sqlof2kag2kk/SlicerWelcome-tutorial_Slicer4.8_SoniaPujol.pdf?dl=0] is an introduction to Slicer.
 
*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 4.6
+
*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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{|width="100%"
 
{|width="100%"
 
|
 
|
−
*The [[media:Slicer4.5minute_SoniaPujol.pdf|Slicer4Minute tutorial]]  is a brief introduction to the advanced 3D visualization capabilities of Slicer 4.5.
+
*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: 3D Slicer version 4.5
+
*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
 
|align="right"|
 
|align="right"|
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|}
 
|}
  
 +
=3D Visualization=
 
==Slicer4 Data Loading and 3D Visualization ==
 
==Slicer4 Data Loading and 3D Visualization ==
 
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{|width="100%"
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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==
 +
{|width="100%"
 +
|
 +
*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.
 +
*Audience: Radiologists and users of Slicer who need a more comprehensive overview over Slicer4 visualization capabilities.
 +
*Modules: DICOM, Volumes, Volume Rendering, Models.
 +
*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.
 +
|align="right"|
 +
[[Image:Slicer4RSNA_2.png|right|250px|]]
 +
|}
 +
 +
== DICOM ==
 +
 +
{|width="100%"
 +
|
 +
* DICOM export: '''[https://youtu.be/nzWf4xHy1BM Export CT and segmentation to DICOM - video tutorial]'''
 +
* Author: Andras Lasso, Csaba Pinter.
 +
* Dataset: CTChest sample data in Slicer.
 +
* Based on Slicer 4.9
 +
|align="right"|
 +
<!-- [[Image:TUTORIAL-IMAGE-HERE.png|right|150px|]] -->
 +
|}
 +
  
 
=Tutorials for software developers=
 
=Tutorials for software developers=
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|}
 
|}
  
−
=Specific functions=
+
=Segmentation=
 +
== Slicer4 Image Segmentation ==
 +
 
 +
{|width="100%"
 +
|
 +
* 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
 +
** Audience: Users and developers interested in segmentation and 3D printing
 +
** Based on: 3D Slicer version 4.7
 +
|align="right"|[[Image:20170717_3DPrintingTutorialYoutube.PNG|280px]]
 +
|---
 +
|
 +
* '''[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.
 +
** [http://slicer.kitware.com/midas3/download/bitstream/738905/CTA-cardio2.nrrd Sample data set]
 +
** Based on: 3D Slicer version 4.8
 +
|align="right"|[[Image:WholeHeartSegYoutube.png|280px]]
 +
|}
 +
 
 +
=Registration=
 +
 
 +
== Slicer4 Image Registration ==
 +
 
 +
{|width="100%"
 +
|
 +
*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.
 +
* Audience: Users and developers interested in image registration
 +
* Dataset: [[Media:RegistrationData.zip| 3D Slicer Registration Data]]
 +
|align="right"|[[File:registration_Slicer4.png|250px]]
 +
|}
 +
*Based on: 3D Slicer version 4.8
 +
 
  
 +
== Slicer Registration Case Library==
 +
{|width="100%"
 +
|
 +
*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.
 +
:Audience:  users interested learning/applying Slicer image registration technology
 +
|align="right"|[[Image:RegLib_table.png|250px|link=http://wiki.slicer.org/slicerWiki/index.php/Documentation/{{documentation/version}}/Registration/RegistrationLibrary]]
 +
|}
 +
=Slicer Extensions=
 
==Slicer4 Diffusion Tensor Imaging Tutorial ==
 
==Slicer4 Diffusion Tensor Imaging Tutorial ==
 
{|width="100%"
 
{|width="100%"
 
|
 
|
 
*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 [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.  
+
*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 4.6
+
*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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|
 
|
 
*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 [http://dmri.slicer.org/tutorials/neurosurgical_planning_dti Neurosurgical Planning tutorial] course guides through the generation of fiber tracts in the vicinity of a tumor.
+
*The [http://dmri.slicer.org/tutorials/Slicer-4.8/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 4.6
 
*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 dataset]] contains a Diffusion Weighted Imaging scan of  brain tumor patient.
 
|align="right"|
 
|align="right"|
 
[[Image:NeurosurgicalPlanningTutorial.png|right|250px|link=http://vimeo.com/67336069]]
 
[[Image:NeurosurgicalPlanningTutorial.png|right|250px|link=http://vimeo.com/67336069]]
 
|}
 
|}
  
−
==Slicer4 3D Visualization of DICOM images for Radiology Applications==
+
 
−
{|width="100%"
 
−
|
 
−
*The [[Media:3DSlicer_Dicom_RSNA2015_SoniaPujol.pdf |3D Visualization of DICOM images for Radiology Applications]]  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.
 
−
*Audience: Radiologists and users of Slicer who need a more comprehensive overview over Slicer4 visualization capabilities.
 
−
*Modules: DICOM, Volumes, Volume Rendering, Models.
 
−
*Based on: 3D Slicer version 4.5
 
−
*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"|
 
−
[[Image:Slicer4RSNA_2.png|right|250px|]]
 
−
|}
 
  
 
==Slicer4 Quantitative Imaging tutorial==
 
==Slicer4 Quantitative Imaging tutorial==
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|}
 
|}
  
−
== Slicer4 Image Segmentation ==
+
 
 +
==Slicer4 Radiation Therapy Tutorial ==
  
 
{|width="100%"
 
{|width="100%"
 
|
 
|
−
* Segmentation for 3D printing: shows how to use the Segment Editor module for combining CAD designed parts with patient-specific models.
+
* The [https://github.com/SlicerRt/SlicerRtDoc/raw/master/tutorials/SlicerRT_WorldCongress_TutorialIGRT.pdf SlicerRT tutorial] is an introduction to the Radiation Therapy functionalities of Slicer.
−
** '''[https://discourse.slicer.org/t/new-video-tutorial-for-segment-editor-lumbar-spine-segmentation-for-3d-printing/700 Video tutorial]'''. Author: Hillary Lia.
+
* Author: Csaba Pinter, Andras Lasso, An Wang, Gregory C. Sharp, David Jaffray, Gabor Fichtinger.  
−
** '''[[Documentation/{{documentation/version}}/Training#Segmentation_for_3D_printing|Segmentation for 3D printing Step-by-step tutorial]]'''. Author: Csaba Pinter, MSc
+
* Dataset: [http://slicer.kitware.com/midas3/download/item/205404/SlicerRT_WorldCongress_TutorialIGRT_Dataset.zip download] from MIDAS server
−
** Audience: Users and developers interested in segmentation and 3D printing
+
* Based on Slicer 4.7
−
** Dataset: [[:File:BasePiece.zip|Phantom base STL model]] Source: [http://perk-software.cs.queensu.ca/plus/doc/nightly/modelcatalog/ PerkLab].
+
|align="right"|
−
** Based on: 3D Slicer version 4.7
+
<!-- [[Image:TUTORIAL-IMAGE-HERE.png|right|150px|]] -->
−
|align="right"|[[Image:20170717_3DPrintingTutorialYoutube.PNG|280px]]
 
−
|---
 
−
|
 
−
* '''[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]]
 
−
|---
 
−
|
 
−
* [https://lassoan.github.io/SlicerSegmentationRecipes/ Slicer Segmentation Recipes]
 
 
|}
 
|}
  
−
== Slicer4 Image Registration ==
 
  
 +
==Slicer Pathology==
 
{|width="100%"
 
{|width="100%"
 
|
 
|
−
*The [https://www.slicer.org/slicerWiki/index.php/File:RegistrationTutorial_3DSlicer4.5_spujol.pdf Registration tutorial] shows how to perform intra- and inter-subject registration within Slicer.
+
*The [[Documentation/{{documentation/version}}/Extensions/SlicerPathology|Slicer Pathology Tutorial]] describes how to use the corresponding tools for automatic and semi-automatic pathology image segmentation.
−
* Authors: Sonia Pujol, Ph.D., Dominik Meier, Ph.D., Ron Kikinis, M.D.
+
*Author: Erich Bremer (Stonybrook), Andriy Fedorov (Brigham and Women’s Hospital)
−
* Audience: Users and developers interested in image registration
+
*Dataset: Available directly with the Slicer Pathology Slicer extension.
−
* Dataset: [[Media:RegistrationData.zip| 3D Slicer Registration Data]]
+
|align="right"|
−
|align="right"|[[File:registration_Slicer4.png|250px]]
+
[[File:SlicerPathologyScreenShot8.png | 200px]].
 
|}
 
|}
−
*Based on: 3D Slicer version 4.5
 
−
See [[Documentation/{{documentation/version}}/Registration/RegistrationLibrary|the Registration Library for worked out registration examples with data]].
 
−
 
−
==Slicer4 Radiation Therapy Tutorial ==
 
  
 +
==SPHARM-PDM==
 
{|width="100%"
 
{|width="100%"
 
|
 
|
−
* The [https://github.com/SlicerRt/SlicerRtDoc/raw/master/tutorials/SlicerRT_WorldCongress_TutorialIGRT.pdf SlicerRT tutorial] is an introduction to the Radiation Therapy functionalities of Slicer.
+
*The [https://www.nitrc.org/docman/view.php/308/1982/SPHARM-PDM_Tutorial_July2015.pdf SPHARM-PDM Tutorial] describes how to use SPHARM-PDM and ShapePopulationViewer Slicer extensions to respectively compute point-based models using a parametric boundary description for the computing of Shape Analysis and perform the quality control between the different models.
−
* Author: Csaba Pinter, Andras Lasso, An Wang, Gregory C. Sharp, David Jaffray, Gabor Fichtinger.  
+
*Author: Jonathan Perdomo (UNC), Beatriz Paniagua (Kitware Inc.)
−
* Dataset: [http://slicer.kitware.com/midas3/download/item/205404/SlicerRT_WorldCongress_TutorialIGRT_Dataset.zip download] from MIDAS server
+
*Dataset: [https://www.nitrc.org/docman/view.php/308/1981/SPHARM_Tutorial_Data_July2015.zip Tutorial Data]
−
* Based on Slicer 4.7
 
 
|align="right"|
 
|align="right"|
−
<!-- [[Image:TUTORIAL-IMAGE-HERE.png|right|150px|]] -->
+
[[File:SlicerWinterProjectWeek2017-SPHARM-PDM.png | 200px]].
 
|}
 
|}
  
−
== DICOM ==
+
==Fiber Bundle Volume Measurement==
−
 
 
 
{|width="100%"
 
{|width="100%"
 
|
 
|
−
* DICOM export: '''[https://youtu.be/nzWf4xHy1BM Export CT and segmentation to DICOM - video tutorial]'''
+
*The [http://www.na-mic.org/Wiki/images/5/57/Fiber_Bundle_Volume_Measurement.pptx Fiber Bundle Volume Measurement Tutorial] aim is to calculate the volume of the fiber bundle that passes through the Corpus Callosum(CC). Following this tutorial, you’ll be able to (1) convert fiber bundles to label map and (2) calculate volume measurements from the fiber bundles.
−
* Author: Andras Lasso, Csaba Pinter.
+
*Author: Shun Gong (Shanghai Changzheng Hospital, China)
−
* Dataset: CTChest sample data in Slicer.
+
*Dataset: [http://www.na-mic.org/Wiki/images/4/4c/FiberVolume_data.zip Tutorial data]: The following data are provided: Baseline image, Down sampled whole brain tractography (conducted as in the [[Documentation/{{documentation/version}}/Training#Slicer4_Diffusion_Tensor_Imaging_Tutorial|DWI tutorial]] and down-sampled to about 10000 fibers using Tractography Display module), Corpus callosum label map (drawn as in the [[Documentation/{{documentation/version}}/Training#Slicer4_Diffusion_Tensor_Imaging_Tutorial|DWI tutorial]]).
−
* Based on Slicer 4.9
 
 
|align="right"|
 
|align="right"|
−
<!-- [[Image:TUTORIAL-IMAGE-HERE.png|right|150px|]] -->
+
[[File:SlicerWinterProjectWeek2017-FiberBundleVolumeMeasurements.png | 200px]].
 
|}
 
|}
  
−
== Other ==
+
= 3D Slicer version 4.7 Tutorial Contest=
  
−
Additional (non-curated) videos-based demonstrations using 3D Slicer are accessible on  [http://www.youtube.com/results?search_query=3d+slicer&sm=3 You Tube].
+
For previous editions of the contest, please visit the [https://na-mic.org/wiki/Tutorial_Contests 3D Slicer Tutorial Contests page]
−
 
 
−
= 3D Slicer Tutorial contests=
 
−
 
 
−
==Winter 2017 Tutorial contest==
 
  
 
===Segmentation for 3D printing===
 
===Segmentation for 3D printing===
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|}
 
|}
  
−
==Winter 2016 Tutorial contest==
+
=YouTube videos=
  
−
===Subject Hierarchy===
 
−
{|width="100%"
 
−
|
 
−
*The [http://wiki.na-mic.org/Wiki/images/2/27/SubjectHierarchy.TutorialContestWinter2016.pdf Subject Hierarchy] tutorial demonstrates the basic usage and potential of Slicer’s data manager module Subject Hierarchy using a two-timepoint radiotherapy phantom dataset.
 
−
*Author: Csaba Pinter, Queen's University, Canada
 
−
*Dataset:  [http://slicer.kitware.com/midas3/download/item/205404/SlicerRT_WorldCongress_TutorialIGRT_Dataset.zip SlicerRT_WorldCongress_TutorialIGRT_Dataset] The tutorial dataset is a two-timepoint phantom dataset taken from a RANDO head&neck phantom. It contains two studies, the planning one is a DICOM study consisting of a CT grayscale image and radiotherapy data: contours, dose distribution, treatment beams, plan information. The second timepoint consists of a CT NRRD volume and a dose NRRD volume.
 
−
|align="right"|
 
−
[[File:SubjectHierarchyTutorial.png | 200px]].
 
−
|}
 
−
 
−
===Fiber Bundle Selection and Scalar Measurements===
 
−
{|width="100%"
 
−
|
 
−
*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 and Brigham and Women's Hospital
 
−
*Dataset:  [[media:FiberBundleSelectionAndScalarMeasurement_TutorialContestWinter2016.zip| Fiber Bundle Selection And Scalar Measurement Tutorial Dataset]]
 
−
|align="right"|
 
−
[[File:FiberBundleSelectionAndScalarMeasurement_TutorialContestWinter2016_Snapshot.png|200px]]
 
−
|}
 
−
 
−
===Plastimatch ===
 
−
{|width="100%"
 
−
|
 
−
*The [http://www.na-mic.org/Wiki/images/5/5c/Plastimatch_TutorialContestWinter2016.pdf Plastimatch tutorial] guides through registration and wrapping of DICOM and DICOM-RT data using the Plastimatch extension of 3D Slicer.
 
−
*Author: Gregory Sharp, Massachusetts General Hospital
 
−
*Dataset:  [http://www.na-mic.org/Wiki/index.php/File:Plastimatch_TutorialContestWinter2016.zip Plastimatch Tutorial Dataset]
 
−
|align="right"|
 
−
[[File:PlastimatchTutorial_Winter2016Contest.png|200px]]
 
−
|}
 
−
 
−
===UKF ===
 
−
{|width="100%"
 
−
|
 
−
*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
 
−
*Dataset:  [http://www.na-mic.org/Wiki/index.php/File:UKF-Tractography_TutorialContestWinter2016.zip UKF tutorial Dataset]
 
−
|align="right"|
 
−
[[File:UKF_Winter2016.png|200px]]
 
−
|}
 
−
 
−
==Summer 2014 Tutorial contest==
 
−
 
−
===Cardiac Agatston Tutorial===
 
−
{|width="100%"
 
−
|
 
−
*[http://wiki.na-mic.org/Wiki/index.php/File:TutorialContest_CardiacAgatstonScoring_2014.pdf  Cardiac Agatston Scoring Tutorial]
 
−
*Authors:  Jessica Forbes, Hans Johnson, University of Iowa
 
−
*Dataset:  [http://wiki.na-mic.org/Wiki/index.php/File:CardiacAgatstonMeasures_TutorialContestSummer2014.zip Cardiac Agatston Scoring Tutorial Dataset]
 
−
|align="right"|
 
−
[[File:CardiacAgatstonMeasuresModuleScreenshot.jpg| 250px]]
 
−
|}
 
  
−
===CMR Toolkit LA workflow===
+
{| border="1" cellpadding="5" width="1200px"
−
{|width="100%"
+
| 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 ]
−
*[http://wiki.na-mic.org/Wiki/index.php/File:CMRToolkitLAWorkflow_TutorialContestSummer2014.pdf  CMR Toolkit LA Workflow Tutorial]
+
| style="width:33%" | [[Image:3DPrinting.png|right|250px|]] [https://www.youtube.com/watch?v=MKLWzD0PiIc Preparing data for 3D printing - Author: PerkLab ]
−
*Authors: Salma Bengali, Josh Cates, University of Utah
+
|-
−
*Dataset: [http://wiki.na-mic.org/Wiki/index.php/File:CMRToolkitLAWorkflowData_TutorialContestSummer2014.zip CMRToolkitLAWorkflow Dataset]
 
−
|align="right"|
 
−
[[Image:Utah_SummerContest2014_tutorial.png|300px]]
 
 
|}
 
|}
  
−
==Summer 2013 Tutorial contest==
+
Additional [http://www.youtube.com/results?search_query=3d+slicer&sm=3 non-curated videos-based demonstrations using 3D Slicer are accessible on YouTube].
  
−
===Cardiac MRI Toolkit===
+
=Teams Contributions =
−
{|width="100%"
 
−
|
 
−
*[[Media:Cardiac MRI Toolkit Tutorial Summer2013.pdf|Cardiac MRI Toolkit]]
 
−
*Authors:  Salma Bengali, Josh Cates, SCI, Utah
 
−
*Dataset: [[Media:Cardiac_MRI_Toolkit_Tutorial_Data.zip|Cardiac MRI Toolkit Tutorial Dataset]]
 
−
|align="right"|
 
−
[[Image:CMRToolkit_Tutorial_Image.png|250px]]
 
−
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−
 
 
−
===HelloCLI===
 
−
{|width="100%"
 
−
|
 
−
*[[Media:Hello_CLI_TutorialContestSummer2013.pdf|HelloCLI]]
 
−
*Authors:  Nadya Shusharina, Greg Sharp, MGH, Boston
 
−
*Dataset:  [[Media:Hello_CLI_TutorialContestSummer2013.zip‎|HelloCLI Dataset]]
 
−
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−
[[Image:Cli_icon.png|300px]]
 
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===SlicerRT===
 
−
{|width="100%"
 
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−
*[[Media:SlicerRT_TutorialContestSummer2013.pdf|SlicerRT Tutorial]]
 
−
*Authors:    Csaba Pinter, Andras Lasso (Queen's), Kevin Wang (PMH, Toronto)
 
−
*Dataset:  [[Media:CsabaPinter-SlicerRtTutorial_Namic2013June.zip|SlicerRT Dataset]]
 
−
|align="right"|
 
−
[[Image:667px-SlicerRT_0.10_IsocenterShiftingEvaluation.png|250px]]
 
−
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−
 
 
−
===DTIPrep===
 
−
{|width="100%"
 
−
|
 
−
*[[Media:DTIPrep_TutorialContestSummer2013.pdf|DTIPrep]]
 
−
*Authors:    Dave Welch, SINAPSE, IOWA
 
−
*Dataset:  [[Media:DTIPrepData_TutorialContestSummer2013.zip|DTIPrep Dataset]]
 
−
|align="right"|
 
−
[[Image:DTIPrep-tutorial.png|250px]]
 
−
|}
 
−
 
 
−
== Summer 2012 Tutorial contest ==
 
−
 
 
−
===Automatic Left Atrial Scar Segmenter ===
 
−
{|width="100%"
 
−
|
 
−
*[http://wiki.na-mic.org/Wiki/index.php/CARMA-LA-Scar_TutorialContestSummer2012 Automatic Left Atrial Scar Segmenter]
 
−
*Authors:  Greg Gardner, Josh Cates, SCI, Utah
 
−
*Dataset: [http://wiki.na-mic.org/Wiki/index.php/File:CARMA-LA-Scar_TutorialContestSummer2012.zip CARMA-LA-Scar data]
 
−
|align="right"|
 
−
[[Image:Carma afib auto scar.png|250px]]
 
−
|}
 
−
 
 
−
===Qualitative and quantitative comparison of  two RT dose distributions===
 
−
{|width="100%"
 
−
|
 
−
*[http://www.na-mic.org/Wiki/index.php/File:PlastimatchDose_TutorialContestSummer2012.pdf Qualitative and quantitative comparison of  two RT dose distributions]
 
−
*Authors:  James Shackleford, Nadya Shusharina, Greg Sharp, MGH
 
−
|align="right"|
 
−
[[Image:PlastimatchDose.png|250px]]
 
−
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−
 
 
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===Dose accumulation for adaptive radiation therapy===
 
−
{|width="100%"
 
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|
 
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*[http://www.na-mic.org/Wiki/index.php/File:DoseAccumulationforAdaptiveRadiationTherapy_TutorialContestSummer2012.pdf Dose accumulation for adaptive radiation therapy]
 
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*Authors:  Kevin Wang, Csaba Pinter, Andras Lasso, PMH, Queen's
 
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|align="right"|
 
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[[Image:AdaptiveradiationTherapy.png|250px]]
 
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===WebGL Export===
 
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*[http://www.na-mic.org/Wiki/index.php/File:WebGLExport_TutorialContestSummer2012.pdf  WebdGLExport]
 
−
*Authors:  Nicolas Rannou, Daniel Haehn, Children's Hospital
 
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[[Image:WebGLExport.png|250px]]
 
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*[http://wiki.slicer.org/slicerWiki/images/f/f1/OpenIGTLinkTutorial_Slicer4.1.0_JunichiTokuda_Apr2012.pdf OpenIGTLink]
 
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*Authors:  Junichi Tokuda, BWH
 
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== International resources==
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*The ''[[Documentation/{{documentation/version}}/Registration/RegistrationLibrary|Slicer Registration Case Library]]'' provides many real-life example cases of using the Slicer registration tools. They include the dataset and step-by-step instructions to follow and try yourself.
 
−
:Author: Dominik Meier, Ph.D.
 
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:Audience:  users interested learning/applying Slicer image registration technology
 
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|align="right"|[[Image:RegLib_table.png|250px|link=http://wiki.slicer.org/slicerWiki/index.php/Documentation/{{documentation/version}}/Registration/RegistrationLibrary]]
 
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= External Resources =
 
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== Resources in German ==
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==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)
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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]
−
 
−
== Team Contributions ==
 
−
See the collection of videos on the [http://vimeo.com/album/2363361 Kitware vimeo album].
 
−
 
−
== User Contributions ==
 
−
See the [[Documentation/{{documentation/version}}/Training/UserContributions|User Contributions Page]] for more content.
 
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[http://www.youtube.com/results?search_query=3d+slicer&sm=3 YouTube videos about 3D Slicer]
 

Revision as of 13:56, 24 October 2018

Home < Documentation < 4.10 < Training


For the latest Slicer documentation, visit the read-the-docs.


Introduction: Slicer 4.10 Tutorials


  • 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.

Quick Start Guide

Downloading and Installing Slicer

  • The Quick Start Guide shows how to install and start 3D Slicer
  • Author: Sonia Pujol, Ph.D.
  • Based on: 3D Slicer version 4.8

SlicerWelcome tutorial

General Introduction

Slicer Welcome Tutorial

  • The [1] is an introduction to Slicer.
  • Author: Sonia Pujol, Ph.D.
  • Audience: First-time users who want a general introduction to the software
  • Modules: Welcome to Slicer, Sample Data
  • Based on: 3D Slicer version 4.8

SlicerWelcome tutorial

Slicer4Minute Tutorial

  • The Slicer4 Minute Tutorial is a brief introduction to the advanced 3D visualization capabilities of Slicer 4.8.
  • Author: Sonia Pujol, Ph.D.
  • Audience: First-time users who want to discover Slicer in 4 minutes
  • Modules: Welcome to Slicer, Models
  • Based on: 3D Slicer version 4.8
  • The Slicer4Minute dataset contains an MR scan of the brain and 3D reconstructions of the anatomy
Slicer4Minute tutorial

3D Visualization

Slicer4 Data Loading and 3D Visualization

  • Slicer 4.10
    • The Data loading and visualization (pptx) course guides through the basics of loading and viewing volumes and 3D models in Slicer 4.10.
    • Author: Csaba Pinter
    • Modules: Welcome to Slicer, Data, Volume Rendering, Models.
    • Audience: End-users
    • Based on: 3D Slicer version 4.10
    • The 3DVisualization dataset contain an MR scan and a series of 3D models of the brain.
  • Slicer 4.5
    • The Data loading and 3D visualization course guides through the basics of loading and viewing volumes and 3D models in Slicer 4.5.
    • Author: Sonia Pujol, Ph.D.
    • Modules: Welcome to Slicer, Sample Data, Models.
    • Audience: End-users
    • Based on: 3D Slicer version 4.5
    • The 3DVisualization dataset contain an MR scan and a series of 3D models of the brain.
20180426 DataLoadingAndVisualizationTutorial.png
Slicer4DataLoading tutorial.png

Slicer4 3D Visualization of DICOM images for Radiology Applications

  • The 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.
  • Audience: Radiologists and users of Slicer who need a more comprehensive overview over Slicer4 visualization capabilities.
  • Modules: DICOM, Volumes, Volume Rendering, Models.
  • Based on: 3D Slicer version 4.8
  • The 3DVisualizationDICOM_part1 and 3DVisualizationDICOM_part2 datasets contain a series of MR and CT scans, and 3D models of the brain, lung and liver.
Slicer4RSNA 2.png

DICOM


Tutorials for software developers

Slicer4 Programming Tutorial

  • The 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 4.7
  • The HelloPython dataset contains sample data set (MR scan of the brain) and complete Python module examples.
HelloPythonTutorial.png

For additional Python scripts examples, please visit the Script Repository page

Developing and contributing extensions for 3D Slicer

Contributing3DSlicerExtension.png

Segmentation

Slicer4 Image Segmentation

  • Segmentation for 3D printing: shows how to use the Segment Editor module for combining CAD designed parts with patient-specific models.
20170717 3DPrintingTutorialYoutube.PNG
  • 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
    • Based on: 3D Slicer version 4.8
 WholeHeartSegYoutube.png

Registration

Slicer4 Image Registration

  • The 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.
  • Audience: Users and developers interested in image registration
  • Dataset: 3D Slicer Registration Data
 Registration Slicer4.png
  • Based on: 3D Slicer version 4.8


Slicer Registration Case Library

  • The 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.
Audience: users interested learning/applying Slicer image registration technology
 RegLib table.png

Slicer Extensions

Slicer4 Diffusion Tensor Imaging Tutorial

  • Please visit dmri.slicer.org/docs for the latest documentation of SlicerDMRI.
  • The 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.
  • 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
  • Based on: 3D Slicer version 4.8
  • The DTI dataset contains an MR Diffusion Weighted Imaging scan of the brain.
Slicer4DTI Tutorial.png

Slicer4 Neurosurgical Planning Tutorial

  • Please visit dmri.slicer.org/docs for the latest documentation of SlicerDMRI.
  • The 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.
  • Audience: End-users and developers
  • Modules: Volumes, Editor, Tractography Label Map Seeding, Tractography Interactive Seeding
  • Based on: 3D Slicer version 4.6
  • The White Matter Exploration dataset contains a Diffusion Weighted Imaging scan of brain tumor patient.
NeurosurgicalPlanningTutorial.png


Slicer4 Quantitative Imaging tutorial

  • The Slicer4 Quantitative Imaging tutorial guides through the use for Slicer for quantifying small volumetric changes in slow-growing tumors, and for calculating Standardized Uptake Value (SUV) from PET/CT data.
  • Authors: Sonia Pujol, Ph.D., Katarzyna Macura, M.D., Ron Kikinis, M.D.
  • Audience: Radiologists and users of Slicer who need a more comprehensive overview over Slicer4 quantitative imaging capabilities.
  • Modules: Data, Volumes, Models, Change Tracker, PET Standard Uptake Value Computation
  • Based on: 3D Slicer version 4.5
  • The Quantitative Imaging dataset contains a series of MR and PET/CT data.
Slicer4 QuantitativeImaging.png

Slicer4 IGT

  • Slicer IGT tutorials
  • Authors: Tamas Ungi, M.D, Ph.D., Junichi Tokuda, Ph.D.
  • Audience: End-users interested in using Slicer for real-time navigated procedures. E.g. navigated needle insertions or other minimally invasive medical procedures.
  • Modules: SlicerIGT Extension
  • Based on: Slicer4.3.1-2014.09.14
  • Data: Slicer-IGT datasets
SlicetIGT.png


Slicer4 Radiation Therapy Tutorial

  • The 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: download from MIDAS server
  • Based on Slicer 4.7


Slicer Pathology

  • The Slicer Pathology Tutorial describes how to use the corresponding tools for automatic and semi-automatic pathology image segmentation.
  • Author: Erich Bremer (Stonybrook), Andriy Fedorov (Brigham and Women’s Hospital)
  • Dataset: Available directly with the Slicer Pathology Slicer extension.

SlicerPathologyScreenShot8.png.

SPHARM-PDM

  • The SPHARM-PDM Tutorial describes how to use SPHARM-PDM and ShapePopulationViewer Slicer extensions to respectively compute point-based models using a parametric boundary description for the computing of Shape Analysis and perform the quality control between the different models.
  • Author: Jonathan Perdomo (UNC), Beatriz Paniagua (Kitware Inc.)
  • Dataset: Tutorial Data

SlicerWinterProjectWeek2017-SPHARM-PDM.png.

Fiber Bundle Volume Measurement

  • The Fiber Bundle Volume Measurement Tutorial aim is to calculate the volume of the fiber bundle that passes through the Corpus Callosum(CC). Following this tutorial, you’ll be able to (1) convert fiber bundles to label map and (2) calculate volume measurements from the fiber bundles.
  • Author: Shun Gong (Shanghai Changzheng Hospital, China)
  • Dataset: Tutorial data: The following data are provided: Baseline image, Down sampled whole brain tractography (conducted as in the DWI tutorial and down-sampled to about 10000 fibers using Tractography Display module), Corpus callosum label map (drawn as in the DWI tutorial).

SlicerWinterProjectWeek2017-FiberBundleVolumeMeasurements.png.

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

SlicerWinterProjectWeek2017-Segmentation-for-3d-printing.png.

Slicer Pathology

  • The Slicer Pathology Tutorial describes how to use the corresponding tools for automatic and semi-automatic pathology image segmentation.
  • Author: Erich Bremer (Stonybrook), Andriy Fedorov (Brigham and Women’s Hospital)
  • Dataset: Available directly with the Slicer Pathology Slicer extension.

SlicerPathologyScreenShot8.png.

Simple Python Tool for Quality Control of DWI data

SlicerWinterProjectWeek2017-SimpleDiffusionGradientInformationExtractorTutorial.png.

SPHARM-PDM

  • The SPHARM-PDM Tutorial describes how to use SPHARM-PDM and ShapePopulationViewer Slicer extensions to respectively compute point-based models using a parametric boundary description for the computing of Shape Analysis and perform the quality control between the different models.
  • Author: Jonathan Perdomo (UNC), Beatriz Paniagua (Kitware Inc.)
  • Dataset: Tutorial Data

SlicerWinterProjectWeek2017-SPHARM-PDM.png.

Integration of Robot Operating System (ROS) and 3D Slicer using OpenIGTLink

SlicerWinterProjectWeek2017-Integration-ROS-3DSlicer-OpenIGTLink.png.

Fiber Bundle Volume Measurement

  • The Fiber Bundle Volume Measurement Tutorial aim is to calculate the volume of the fiber bundle that passes through the Corpus Callosum(CC). Following this tutorial, you’ll be able to (1) convert fiber bundles to label map and (2) calculate volume measurements from the fiber bundles.
  • Author: Shun Gong (Shanghai Changzheng Hospital, China)
  • Dataset: Tutorial data: The following data are provided: Baseline image, Down sampled whole brain tractography (conducted as in the DWI tutorial and down-sampled to about 10000 fibers using Tractography Display module), Corpus callosum label map (drawn as in the DWI tutorial).

SlicerWinterProjectWeek2017-FiberBundleVolumeMeasurements.png.

YouTube videos

Verterbra.png
How to segment multiple vertebrae in spine CT for 3D printing - Author: Hillary Lia
Femurmodel.png
Creating a femur model from CT volume using 3D Slicer - Author: Nabgha Farhat
3DPrinting.png
Preparing data for 3D printing - Author: PerkLab

Additional non-curated videos-based demonstrations using 3D Slicer are accessible on YouTube.

Teams Contributions

  • This Slicer 4.1 webinar presents the new features and improvements of the release, and a brief overview of work for the next release.
  • Authors: Steve Pieper Ph.D.
  • Audience: First time users and developers interested in Slicer 4.1 new features.
  • Length: 0h20m
 Webinar-Slicer-4.1.png



  • This Intro to Slicer 4.0 webinar provides an introduction to 3DSlicer, and demonstrates core functionalities such as loading, visualizing and saving data. Basic processing tools, including manual registration, manual segmentation and tractography tools are also highlighted. This webinar is a general overview. For in depth information see the modules above and the documentation pages.
  • Authors: Julien Finet, M.S., Steve Pieper, Ph.D., Jean-Christophe Fillion-Robin, M.S.
  • Audience: First time users interested in a broad overview of Slicer’s features and tools.
  • Length: 1h20m
 Webinar.png



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.

Example WeChat tutorial slides

Resources in German

Murat Maga's blog posts about using 3D Slicer for biology

Using the (legacy) Editor

Fast GrowCut

  • The Fast GrowCut tutorial shows how to perform a segmentation using the Fast GrowCut effect in Slicer.
  • Authors: Hillary Lia
  • Audience: Users interested in segmentation
 FastGrowCutLogo.png

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:

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