Difference between revisions of "Training:Slicer4 Tutorials"

From NAMIC Wiki
Jump to: navigation, search
Line 197: Line 197:
 
|}
 
|}
  
 +
===Slicer Pathology===
 +
{|width="100%"
 +
|
 +
*The [[Documentation/{{documentation/version}}/Extensions/SlicerPathology|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.
 +
|align="right"|
 +
[[File:SlicerPathologyScreenShot8.png | 200px]].
 +
|}
 +
 +
===SPHARM-PDM===
 +
{|width="100%"
 +
|
 +
*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: Jonathan Perdomo (UNC), Beatriz Paniagua (Kitware Inc.)
 +
*Dataset:  [https://www.nitrc.org/docman/view.php/308/1981/SPHARM_Tutorial_Data_July2015.zip Tutorial Data]
 +
|align="right"|
 +
[[File:SlicerWinterProjectWeek2017-SPHARM-PDM.png | 200px]].
 +
|}
 +
 +
===Fiber Bundle Volume Measurement===
 +
{|width="100%"
 +
|
 +
*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: Shun Gong (Shanghai Changzheng Hospital, China)
 +
*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]]).
 +
|align="right"|
 +
[[File:SlicerWinterProjectWeek2017-FiberBundleVolumeMeasurements.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]]
 +
|}
 +
 +
===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]]
 +
|}
  
  
Line 207: Line 256:
 
==Winter 2017 Tutorial contest==
 
==Winter 2017 Tutorial contest==
  
−
===Segmentation for 3D printing===
+
===Segmentation for 3D printing (Winter 2017 Tutorial contest)===
 
{|width="100%"
 
{|width="100%"
 
|
 
|
Line 216: Line 265:
 
|align="right"|
 
|align="right"|
 
[[File:SlicerWinterProjectWeek2017-Segmentation-for-3d-printing.png | 200px]].  
 
[[File:SlicerWinterProjectWeek2017-Segmentation-for-3d-printing.png | 200px]].  
−
|}
 
−
 
−
===Slicer Pathology===
 
−
{|width="100%"
 
−
|
 
−
*The [[Documentation/{{documentation/version}}/Extensions/SlicerPathology|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.
 
−
|align="right"|
 
−
[[File:SlicerPathologyScreenShot8.png | 200px]].
 
 
|}
 
|}
  
Line 238: Line 277:
 
|}
 
|}
  
−
===SPHARM-PDM===
 
−
{|width="100%"
 
−
|
 
−
*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: Jonathan Perdomo (UNC), Beatriz Paniagua (Kitware Inc.)
 
−
*Dataset:  [https://www.nitrc.org/docman/view.php/308/1981/SPHARM_Tutorial_Data_July2015.zip Tutorial Data]
 
−
|align="right"|
 
−
[[File:SlicerWinterProjectWeek2017-SPHARM-PDM.png | 200px]].
 
−
|}
 
  
 
===Integration of Robot Operating System (ROS) and 3D Slicer using OpenIGTLink===
 
===Integration of Robot Operating System (ROS) and 3D Slicer using OpenIGTLink===
Line 258: Line 288:
 
|}
 
|}
  
−
===Fiber Bundle Volume Measurement===
 
−
{|width="100%"
 
−
|
 
−
*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: Shun Gong (Shanghai Changzheng Hospital, China)
 
−
*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]]).
 
−
|align="right"|
 
−
[[File:SlicerWinterProjectWeek2017-FiberBundleVolumeMeasurements.png | 200px]].
 
−
|}
 
  
 
==Winter 2016 Tutorial contest==
 
==Winter 2016 Tutorial contest==
Line 280: Line 301:
 
|}
 
|}
  
−
===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 ===
 
===Plastimatch ===
Line 298: Line 310:
 
|align="right"|
 
|align="right"|
 
[[File:PlastimatchTutorial_Winter2016Contest.png|200px]]
 
[[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==  
 
==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===
 
===CMR Toolkit LA workflow===

Revision as of 13:22, 27 March 2018

Home < Training:Slicer4 Tutorials

( Page under construction)

Introduction: Slicer 4Tutorials

Contents

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 4.6

SlicerWelcome tutorial

Slicer4Minute Tutorial

  • The Slicer4Minute tutorial is a brief introduction to the advanced 3D visualization capabilities of Slicer 4.5.
  • 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 4.5
  • 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.
File:Slicer4DataLoading tutorial.png

Slicer4 3D Visualization of DICOM images for Radiology Applications

  • The 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 3DVisualizationDICOM_part1 and 3DVisualizationDICOM_part2 datasets contain a series of MR and CT scans, and 3D models of the brain, lung and liver.
File: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.
File:HelloPythonTutorial.png

For additional Python scripts examples, please visit the [[Documentation/Template:Documentation/version/ScriptRepository|Script Repository page]]

Developing and contributing extensions for 3D Slicer

File:Contributing3DSlicerExtension.png

Segmentation

Segmentation for 3D printing

  • The Segmentation for 3D printing tutorial shows how to use the Segment Editor module for combining CAD designed parts with patient-specific models.
    • Video tutorial. Author: Hillary Lia.
    • [[Documentation/Template: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
 280px

Whole heart segmentation from cardiac CT

* 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. 280px

Registration

Registration tutorial

  • 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
 250px
  • Based on: 3D Slicer version 4.5

Registration Case Library

See [[Documentation/Template:Documentation/version/Registration/RegistrationLibrary|the Registration Library for worked out registration examples with data]].


Extensions

Slicer4 Diffusion Tensor Imaging Tutorial

  • Please visit dmri.slicer.org/docs for the latest documentation of SlicerDMRI.
  • The 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.
  • 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 4.5
  • The DTI dataset contains an MR Diffusion Weighted Imaging scan of the brain.
File: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
  • Extension: SlicerDMRI
  • Based on: 3D Slicer version 4.6
  • The White Matter Exploration dataset contains a Diffusion Weighted Imaging scan of brain tumor patient.
250px

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
  • Extension: SlicerRT
  • Based on Slicer 4.7

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.
  • Extension: Change Tracker
  • Based on: 3D Slicer version 4.5
  • The Quantitative Imaging dataset contains a series of MR and PET/CT data.
File: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.
  • Extension: SlicerIGT
  • Based on: Slicer4.3.1-2014.09.14
  • Data: Slicer-IGT datasets
File:SlicetIGT.png

Slicer Pathology

  • The [[Documentation/Template:Documentation/version/Extensions/SlicerPathology|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.

200px.

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

200px.

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 [[Documentation/Template: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/Template:Documentation/version/Training#Slicer4_Diffusion_Tensor_Imaging_Tutorial|DWI tutorial]]).

200px.

UKF

  • The UKF tutorial guides through the use of the Unscented Kalman Filter (UKF) tractography module.
  • Author: Pegah Kahali, Brigham and Women's Hopital
  • Dataset: UKF tutorial Dataset

200px

Cardiac Agatston Tutorial

CardiacAgatstonMeasuresModuleScreenshot.jpg


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 (Winter 2017 Tutorial contest)

200px.

Simple Python Tool for Quality Control of DWI data

200px.


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

200px.


Winter 2016 Tutorial contest

Subject Hierarchy

  • The 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: 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.

200px.


Plastimatch

200px

Summer 2014 Tutorial contest

CMR Toolkit LA workflow

300px

Summer 2013 Tutorial contest

Cardiac MRI Toolkit

250px

HelloCLI

300px

SlicerRT

250px

DTIPrep

250px

Summer 2012 Tutorial contest

Automatic Left Atrial Scar Segmenter

Carma afib auto scar.png

Qualitative and quantitative comparison of two RT dose distributions

250px

Dose accumulation for adaptive radiation therapy

250px

WebGL Export

  • WebdGLExport
  • Authors: Nicolas Rannou, Daniel Haehn, Children's Hospital

250px

OpenIGTLink

250px

Additional resources

  • 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
 250px



  • 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
 250px



  • The [[Documentation/Template: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.
Audience: users interested learning/applying Slicer image registration technology
 250px

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.

Example WeChat tutorial slides


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
 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:

Team Contributions

See the collection of videos on the Kitware vimeo album.

User Contributions

YouTube videos about 3D Slicer

Retrieved from "https://www.na-mic.org/w/index.php?title=Training:Slicer4_Tutorials&oldid=98204"