Difference between revisions of "Documentation/4.8/Training"

From Slicer Wiki
Jump to: navigation, search
 
(30 intermediate revisions by the same user not shown)
Line 8: Line 8:
  
  
* 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 Slicer4.8. The concepts are still useful but bear in mind that some interface elements and features will be different in updated versions.
  
 
__TOC__
 
__TOC__
Line 17: Line 17:
 
{|width="100%"
 
{|width="100%"
 
|
 
|
*The [https://www.dropbox.com/s/n45e6xsikh6oaep/QuickStartGuide_SoniaPujol.pdf?dl=0| Quick Start Guide] shows how to install and start 3D Slicer
+
*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.
 
*Author: Sonia Pujol, Ph.D.
 
*Based on: 3D Slicer version 4.8
 
*Based on: 3D Slicer version 4.8
Line 41: Line 41:
 
{|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"|
Line 68: Line 68:
 
{|width="100%"
 
{|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.  
+
*The [https://www.dropbox.com/s/9jcjpl33qfh5pi6/3DVisualizationDICOM_Slicer4.8_SoniaPujol.pdf?dl=0 3D Visualization of DICOM images]  course guides through 3D data loading and visualization of DICOM images for Radiology Applications in Slicer4.  
 
*Author: Sonia Pujol, Ph.D., Kitt Shaffer, M.D., Ph.D., Ron Kikinis, M.D.
 
*Author: Sonia Pujol, Ph.D., Kitt Shaffer, M.D., Ph.D., Ron Kikinis, M.D.
 
*Audience: Radiologists and users of Slicer who need a more comprehensive overview over Slicer4 visualization capabilities.
 
*Audience: Radiologists and users of Slicer who need a more comprehensive overview over Slicer4 visualization capabilities.
 
*Modules: DICOM, Volumes, Volume Rendering, Models.
 
*Modules: DICOM, Volumes, Volume Rendering, Models.
*Based on: 3D Slicer version 4.5
+
*Based on: 3D Slicer version 4.8
 
*The [[Media:3DVisualization_DICOM_images_part1.zip‎  | 3DVisualizationDICOM_part1]] and [[Media:3DVisualization_DICOM_images_part2.zip | 3DVisualizationDICOM_part2]] datasets contain a series of MR and CT scans, and 3D models of the brain, lung and liver.
 
*The [[Media:3DVisualization_DICOM_images_part1.zip‎  | 3DVisualizationDICOM_part1]] and [[Media:3DVisualization_DICOM_images_part2.zip | 3DVisualizationDICOM_part2]] datasets contain a series of MR and CT scans, and 3D models of the brain, lung and liver.
 
|align="right"|
 
|align="right"|
 
[[Image:Slicer4RSNA_2.png|right|250px|]]
 
[[Image:Slicer4RSNA_2.png|right|250px|]]
 
|}
 
|}
 +
 
=Programming=
 
=Programming=
  
Line 110: Line 111:
 
|
 
|
 
* Segmentation for 3D printing: shows how to use the Segment Editor module for combining CAD designed parts with patient-specific models.
 
* Segmentation for 3D printing: shows how to use the Segment Editor module for combining CAD designed parts with patient-specific models.
** '''[https://discourse.slicer.org/t/new-video-tutorial-for-segment-editor-lumbar-spine-segmentation-for-3d-printing/700 Video tutorial]'''. Author: Hillary Lia.
 
 
** '''[[Documentation/{{documentation/version}}/Training#Segmentation_for_3D_printing|Segmentation for 3D printing Step-by-step tutorial]]'''. Author: Csaba Pinter, MSc
 
** '''[[Documentation/{{documentation/version}}/Training#Segmentation_for_3D_printing|Segmentation for 3D printing Step-by-step tutorial]]'''. Author: Csaba Pinter, MSc
 
** Audience: Users and developers interested in segmentation and 3D printing
 
** Audience: Users and developers interested in segmentation and 3D printing
Line 137: Line 137:
 
|align="right"|[[File:registration_Slicer4.png|250px]]
 
|align="right"|[[File:registration_Slicer4.png|250px]]
 
|}
 
|}
*Based on: 3D Slicer version 4.8
+
*Based on: 3D Slicer version 4.8; Compatible with Slicer4.10
See [[Documentation/{{documentation/version}}/Registration/RegistrationLibrary|the Registration Library for worked out registration examples with data]].
 
  
 
== Slicer Registration Case Library==
 
== Slicer Registration Case Library==
 
{|width="100%"
 
{|width="100%"
 
|
 
|
*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.  
+
*The ''[[Documentation/{{documentation/version}}/Registration/RegistrationLibrary|Slicer Registration Case Library]]'' provides real-life example cases of using the Slicer registration tools. They include pre-computed dataset and step-by-step instructions for users to follow.  
 
:Author: Dominik Meier, Ph.D.
 
:Author: Dominik Meier, Ph.D.
 
:Audience:  users interested learning/applying Slicer image registration technology
 
:Audience:  users interested learning/applying Slicer image registration technology
Line 154: Line 153:
 
|
 
|
 
*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 [[Media:DiffusionMRIanalysisTutorial_Slicer4.5_SoniaPujol.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 4.5
+
*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"|
Line 250: Line 249:
 
|}
 
|}
  
= 3D Slicer Tutorial contests=
+
= 3D Slicer version 4.7 Tutorial Contest=
  
==Winter 2017 Tutorial contest==
+
For previous editions of the contest, please visit the [https://na-mic.org/wiki/Tutorial_Contests 3D Slicer Tutorial Contests page]
  
 
===Segmentation for 3D printing===
 
===Segmentation for 3D printing===
Line 315: Line 314:
 
|}
 
|}
  
==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===
+
{| 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:TutorialContest_CardiacAgatstonScoring_2014.pdf  Cardiac Agatston Scoring Tutorial]
+
| style="width:33%" | [[Image:3DPrinting.png|right|250px|]] [https://www.youtube.com/watch?v=MKLWzD0PiIc Preparing data for 3D printing - Author: PerkLab ]
*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===
+
Additional [http://www.youtube.com/results?search_query=3d+slicer&sm=3 non-curated videos-based demonstrations using 3D Slicer are accessible on YouTube].
{|width="100%"
 
|
 
*[http://wiki.na-mic.org/Wiki/index.php/File:CMRToolkitLAWorkflow_TutorialContestSummer2014.pdf  CMR Toolkit LA Workflow Tutorial]
 
*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==
 
 
 
===Cardiac MRI Toolkit===
 
{|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]]
 
|}
 
 
 
===HelloCLI===
 
{|width="100%"
 
|
 
*[[Media:Hello_CLI_TutorialContestSummer2013.pdf|HelloCLI]]
 
*Authors:  Nadya Shusharina, Greg Sharp, MGH, Boston
 
*Dataset:  [[Media:Hello_CLI_TutorialContestSummer2013.zip‎|HelloCLI Dataset]]
 
|align="right"|
 
[[Image:Cli_icon.png|300px]]
 
|}
 
 
 
===SlicerRT===
 
{|width="100%"
 
|
 
*[[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]]
 
|}
 
 
 
===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]]
 
|}
 
 
 
===Dose accumulation for adaptive radiation therapy===
 
{|width="100%"
 
|
 
*[http://www.na-mic.org/Wiki/index.php/File:DoseAccumulationforAdaptiveRadiationTherapy_TutorialContestSummer2012.pdf Dose accumulation for adaptive radiation therapy]
 
*Authors:  Kevin Wang, Csaba Pinter, Andras Lasso, PMH, Queen's
 
|align="right"|
 
[[Image:AdaptiveradiationTherapy.png|250px]]
 
|}
 
 
 
===WebGL Export===
 
{|width="100%"
 
|
 
*[http://www.na-mic.org/Wiki/index.php/File:WebGLExport_TutorialContestSummer2012.pdf  WebdGLExport]
 
*Authors:  Nicolas Rannou, Daniel Haehn, Children's Hospital
 
|align="right"|
 
[[Image:WebGLExport.png|250px]]
 
|}
 
 
 
===OpenIGTLink===
 
{|width="100%"
 
|
 
*[http://wiki.slicer.org/slicerWiki/images/f/f1/OpenIGTLinkTutorial_Slicer4.1.0_JunichiTokuda_Apr2012.pdf OpenIGTLink]
 
*Authors:  Junichi Tokuda, BWH
 
|align="right"|
 
[[Image:OpenIGTLink.png|250px]]
 
|}
 
  
 
=Teams Contributions =
 
=Teams Contributions =
Line 495: Line 352:
  
 
= External Resources =
 
= External Resources =
==Non-curated videos==
+
 
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].
+
== International resources==
== Resources in Chinese ==
+
 
 +
==Resources in Chinese ==
 
{|width="100%"
 
{|width="100%"
 
|
 
|
Line 518: Line 376:
 
|}
 
|}
  
== Resources in German ==
+
==Resources in German ==
  
 
* [https://www.youtube.com/watch?v=sl-00kGpuPk&list=PLJWCUXz3GeAfmYLiFcKus_c0jcsMnVsgb A series of four YouTube videos on python programming in Slicer] (German narration with English subtitles)
 
* [https://www.youtube.com/watch?v=sl-00kGpuPk&list=PLJWCUXz3GeAfmYLiFcKus_c0jcsMnVsgb A series of four YouTube videos on python programming in Slicer] (German narration with English subtitles)

Latest revision as of 18:26, 14 January 2019

Home < Documentation < 4.8 < Training

For the latest Slicer documentation, visit the 4.10 page.

Introduction: Slicer 4.8 Tutorials


  • Some of these tutorials are based on older releases of 3D Slicer, and are being upgraded to Slicer4.8. The concepts are still useful but bear in mind that some interface elements and features will be different in updated versions.

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 SlicerWelcome tutorial is an introduction to Slicer based on the Welcome module.
  • 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

  • The Data loading and 3D visualization course guides through the basics of loading and viewing volumes and 3D models in Slicer4 .
  • 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 contains an MR scan and a series of 3D models of the brain.
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

Programming

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; Compatible with Slicer4.10

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




See the collection of videos on the Kitware vimeo album.

External Resources

International resources

Resources in Chinese

A 3D Slicer community on WeChat in China offers many tutorials and clinical examples in Chinese. Note that the images are of interest to non-Chinese speakers and Google Translate does a reasonable job of translating some of the text.

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: