Latest revision as of 22:12, 22 November 2022

This section is currently out-of-date and may contain errors but is retained for historical reference.

Up-to-date training materials can be found at Documentation/Nightly/Training

Introduction: Slicer 4.6 Tutorials

The 3D Slicer compendium is a collection of hands-on tutorials with anonymized sample data sets. The tutorials demonstrate how to use the 3D Slicer software platform (version 4.6 release) to accomplish certain tasks.
For tutorials for other versions of Slicer, please visit the Slicer training portal.
For "reference manual" style documentation, please visit the Slicer 4.6 documentation page
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.
For general questions related to the Slicer4 Training Compendium and to 3D Slicer training events, please send an e-mail to Sonia Pujol, Ph.D, Director of Training of 3D Slicer

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 4.5

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

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 3D Visualization dataset contain an MR scan and a series of 3D models of the brain.

Tutorials for Software Developers

Slicer4 Programming Tutorial

The Hello Python Programming Tutorial course 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 4.5
The HelloPython dataset contains three Python files and an MR scan of the brain.

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

Developing and Contributing Extensions for 3D Slicer

The Developing and Contributing Extensions for 3D Slicer Tutorial is an introduction to the internals of 3D Slicer and the process of contributing a 3D Slicer extension.
Authors: Andrey Fedorov, Ph.D., Jean-Christophe Fillion-Robin, Ph.D., Steve Pieper, Ph.D.
Audience: Developers
Based on: 3D Slicer version 4.4

Specific functions

Slicer4 Diffusion Tensor Imaging Tutorial

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.

Slicer4 Neurosurgical Planning Tutorial

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 4.5
The White Matter Exploration datasets contains a Diffusion Weighted Imaging scan of brain tumor patient.

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.

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 IGT

Slicer IGT Tutorial
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

Slicer4 3D Printing

This 3D Printing Tutorial is a video-based tutorial that shows how to prepare 3D Slicer data for 3D printing using Slicer4.3.
- Author: Nabgha Farhat, MSc
The Segmentation for 3D printing Step-by-step tutorial shows how to use the Segment Editor of 3D Slicer for 3D printing using Slicer4.6.
- Author: Csaba Pinter, MSc
- Audience: Users and developers interested in 3D printing

Slicer4 Image Registration

The Image 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

Based on: 3D Slicer version 4.5

See the Registration Library for worked out registration examples with data.

Fast GrowCut

The Fast GrowCut Tutorial shows how to perform segmentation using the Fast GrowCut effect in Slicer.
Author: Hillary Lia
Audience: Users interested in segmentation

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
- Based on Slicer 4.6

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

The Segmentation for 3D printing Tutorial (pptx) is an introduction to the new Segment Editor module of Slicer.
Author: Csaba Pinter (Queen's University, Canada)
Dataset: Phantom base STL model Source: PerkLab.

.

Slicer Pathology

The Slicer Pathology Tutorial describes how to use the automated and semi-automated segmentation tools of the Slicer Pathology Extension.
Author: Erich Bremer (Stonybrook), Andriy Fedorov (Brigham and Women’s Hospital)

.

Simple Python Tool for Quality Control of DWI data

The Simple Multi-shell Diffusion Gradients Information Extractor Tutorial describes how to use a simple Python script for parsing multi-shell sensitizing gradients information from diffusion MRI datasets in Nifti file.
Author: Laurent Chauvin (ETS Montreal)

.

SPHARM-PDM

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

.

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

The Integration of Robot Operating System (ROS) and 3D Slicer using OpenIGTLink Tutorial is an introduction to the software architecture of surgical robot systems. The tutorial provides hands-on experience on the integration of software and hardware for medical robotics applications.
Author: Junichi Tokuda (Brigham and Women’s Hospital)
Dataset: Not available.

.

Fiber Bundle Volume Measurement

The Fiber Bundle Volume Measurement Tutorial shows how to calculate the volume of tractography reconstructions of white matter tracts.
Author: Shun Gong (Shanghai Changzheng Hospital, China)
Dataset: Tutorial data

.

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 time point radiotherapy phantom dataset.
Author: Csaba Pinter, Queen's University, Canada
Dataset: SlicerRT_WorldCongress_TutorialIGRT_Dataset The tutorial dataset is a two time point 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 time point consists of a CT NRRD volume and a dose NRRD volume.

.

Fiber Bundle Selection and Scalar Measurements

The 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, Brigham and Women's Hospital
Dataset: Fiber Bundle Selection And Scalar Measurement Tutorial Dataset

Plastimatch

The 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: Plastimatch Tutorial Dataset

UKF

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

Summer 2014 Tutorial contest

Cardiac Agatston Tutorial

Cardiac Agatston Scoring Tutorial
Authors: Jessica Forbes, Hans Johnson, University of Iowa
Dataset: Cardiac Agatston Scoring Tutorial Dataset

CMR Toolkit LA workflow

CMR Toolkit LA Workflow Tutorial
Authors: Salma Bengali, Josh Cates, University of Utah
Dataset: CMRToolkitLAWorkflow Dataset

Summer 2013 Tutorial contest

Cardiac MRI Toolkit

Cardiac MRI Toolkit Tutorial
Authors: Salma Bengali, Josh Cates, SCI, Utah
Dataset: Cardiac MRI Toolkit Tutorial Dataset

HelloCLI

HelloCLI
Authors: Nadya Shusharina, Greg Sharp, MGH, Boston
Dataset: HelloCLI Dataset

SlicerRT

SlicerRT Tutorial
Authors: Csaba Pinter, Andras Lasso (Queen's), Kevin Wang (PMH, Toronto)
Dataset: SlicerRT Dataset

DTIPrep

DTIPrep
Authors: Dave Welch, SINAPSE, IOWA
Dataset: DTIPrep Dataset

Summer 2012 Tutorial contest

Automatic Left Atrial Scar Segmenter

Automatic Left Atrial Scar Segmenter Tutorial
Authors: Greg Gardner, Josh Cates, SCI, Utah
Dataset: CARMA-LA-Scar data

Qualitative and Quantitative Comparison of Two RT Dose Distributions

Qualitative and Quantitative Comparison of Two RT Dose Distributions Tutorial
Authors: James Shackleford, Nadya Shusharina, Greg Sharp, MGH

Dose Accumulation for Adaptive Radiation Therapy

Dose Accumulation for Adaptive Radiation Therapy Tutorial
Authors: Kevin Wang, Csaba Pinter, Andras Lasso, PMH, Queen's

WebGL Export

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

OpenIGTLink

OpenIGTLink
Authors: Junichi Tokuda, BWH

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

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

The 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

|}

Some hands on example videos of basic slicer tasks shows looping gif screen captures of several tasks that you can practice yourself. (Made with version 4.6.2)

Author: Steve Pieper, Ph.D.

Audience: new users needing to get a visual feel for the software

External Resources

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

Using the (legacy) Editor

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

See the User Contributions Page for more content.

YouTube Videos About 3D Slicer

@@ Line 1: / Line 1: @@
-<noinclude>{{documentation/versioncheck}}</noinclude>
+<noinclude>{{documentation/historicaltraining}}
 =Introduction: Slicer {{documentation/version}} Tutorials=
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-* This ''Slicer 4.3 [https://www.youtube.com/watch?v=MKLWzD0PiIc 3D Printing Tutorial]''  shows how to prepare 3D Slicer data for 3D printing.
+* This [https://www.youtube.com/watch?v=MKLWzD0PiIc 3D Printing Tutorial] is a video-based tutorial that shows how to prepare 3D Slicer data for 3D printing using Slicer4.3.
-* Authors: Nabgha Farhat, MSc
+** Author: Nabgha Farhat, MSc
-* Audience: Users and developers interested in 3D printing
+* The [[Documentation/{{documentation/version}}/Training#Segmentation_for_3D_printing|Segmentation for 3D printing Step-by-step tutorial]] shows how to use the Segment Editor of 3D Slicer for 3D printing using Slicer4.6.
+** Author: Csaba Pinter, MSc
+** Audience: Users and developers interested in 3D printing
 |align="right"|[[Image:3DPrinting_tutorial.png|250px]]
 |}
@@ Line 174: / Line 176: @@
 |}
+==Slicer4 Radiation Therapy Tutorial ==
+** 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.
+** Author: Csaba Pinter, Andras Lasso, An Wang, Gregory C. Sharp, David Jaffray, Gabor Fichtinger.
+** Dataset: [http://slicer.kitware.com/midas3/download/item/205404/SlicerRT_WorldCongress_TutorialIGRT_Dataset.zip download] from MIDAS
+**Based on Slicer 4.6
 == Other ==
@@ Line 186: / Line 193: @@
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-*The [http://www.na-mic.org/Wiki/images/a/a6/SegmentationFor3DPrinting_TutorialContestWinter2017.pdf Segmentation for 3D printing Tutorial] is an introduction to the new [[Documentation/{{documentation/version}}/Modules/SegmentEditor|Segment Editor]] module of Slicer.
+*The [https://github.com/SlicerRt/SlicerRtDoc/raw/master/tutorials/SegmentationFor3DPrinting_TutorialContestWinter2017.pdf Segmentation for 3D printing Tutorial] ([https://github.com/SlicerRt/SlicerRtDoc/raw/master/tutorials/SegmentationFor3DPrinting_TutorialContestWinter2017.pptx pptx]) is an introduction to the new [[Documentation/{{documentation/version}}/Modules/SegmentEditor|Segment Editor]] module of Slicer.
 *Author: Csaba Pinter (Queen's University, Canada)
-*Dataset:  [http://www.na-mic.org/Wiki/images/1/1e/BasePiece.stl Phantom base STL model] Source: [http://perk-software.cs.queensu.ca/plus/doc/nightly/modelcatalog/ PerkLab].
+*Dataset: [[:File:BasePiece.zip|Phantom base STL model]] Source: [http://perk-software.cs.queensu.ca/plus/doc/nightly/modelcatalog/ PerkLab].
 |align="right"|
 [[File:SlicerWinterProjectWeek2017-Segmentation-for-3d-printing.png | 200px]].
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-*The [[Documentation/{{documentation/version}}/Extensions/SlicerPathology|Slicer Pathology Tutorial]] describes how to use the corresponding tools for automatic and semi-automatic pathology image segmentation.
+*The [[Documentation/{{documentation/version}}/Extensions/SlicerPathology|Slicer Pathology Tutorial]] describes how to use the automated and semi-automated segmentation tools of the Slicer Pathology Extension.
 *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 206: / Line 212: @@
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-*The [https://www.na-mic.org/Wiki/index.php/File:SimpleDiffusionGradientInformationExtractorTutorial_Chauvin_Jan2017.pdf Simple Multi-shell Diffusion Gradients Information Extractor Tutorial] describes how to use a simple Python script for parsing multi-shell sensitizing gradients information from nifti file format (separated bvecs, bvals files).
+*The [https://www.na-mic.org/Wiki/index.php/File:SimpleDiffusionGradientInformationExtractorTutorial_Chauvin_Jan2017.pdf Simple Multi-shell Diffusion Gradients Information Extractor Tutorial] describes how to use a simple Python script for parsing multi-shell sensitizing gradients information from diffusion MRI datasets in Nifti file.
 *Author: Laurent Chauvin (ETS Montreal)
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-*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.
+*The [https://www.nitrc.org/docman/view.php/308/1982/SPHARM-PDM_Tutorial_July2015.pdf SPHARM-PDM Tutorial] describes how to use the SPHARM-PDM and ShapePopulationViewer Slicer extensions to compute point-based models for Shape Analysis and perform quality control of 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]
@@ Line 225: / Line 231: @@
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-*The [https://www.na-mic.org/Wiki/index.php/File:ROSIGTLTutorial.pdfx Integration of Robot Operating System (ROS) and 3D Slicer using OpenIGTLink Tutorial] is an introduction to the software architecture of surgical robot systems. The tutorial provides hands-on experience on the integration of software and hardware for medical robotics applications.
+*The [https://www.na-mic.org/Wiki/index.php/File:ROSIGTLTutorial.pdf Integration of Robot Operating System (ROS) and 3D Slicer using OpenIGTLink Tutorial] is an introduction to the software architecture of surgical robot systems. The tutorial provides hands-on experience on the integration of software and hardware for medical robotics applications.
 *Author: Junichi Tokuda (Brigham and Women’s Hospital)
 *Dataset:  Not available.
@@ Line 235: / Line 241: @@
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-*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.
+*The [https://www.na-mic.org/Wiki/index.php/File:Fiber_Bundle_Volume_Measurement_TutorialContestWinter2017.pdf Fiber Bundle Volume Measurement Tutorial] shows how to calculate the volume of tractography reconstructions of white matter tracts.
 *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]]).
+*Dataset:  [http://www.na-mic.org/Wiki/images/4/4c/FiberVolume_data.zip Tutorial data]
 |align="right"|
 [[File:SlicerWinterProjectWeek2017-FiberBundleVolumeMeasurements.png | 200px]].
 |}
 ==Winter 2016 Tutorial contest==
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-*[http://wiki.slicer.org/slicerWiki/images/f/f1/OpenIGTLinkTutorial_Slicer4.1.0_JunichiTokuda_Apr2012.pdf OpenIGTLink]
+*[http://www.slicer.org/w/img_auth.php/f/f1/OpenIGTLinkTutorial_Slicer4.1.0_JunichiTokuda_Apr2012.pdf OpenIGTLink]
 *Authors:  Junichi Tokuda, BWH
 |align="right"|
@@ Line 425: / Line 430: @@
 :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]]
+|align="right"|[[Image:RegLib_table.png|250px|link=https://www.slicer.org/wiki/Documentation/{{documentation/version}}/Registration/RegistrationLibrary]]|}
-|}
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 <br>
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 = External Resources =
-== Using the Editor ==
+== Murat Maga's blog posts about using 3D Slicer for biology ==
+* [https://blogs.uw.edu/maga/2017/04/11/getting-started-with-3d-slicer-as-a-biologist/ Slicer for Biologists]
+* [https://blogs.uw.edu/maga/2017/04/11/a-worked-example-getting-and-visualizing-data-from-digimorph/ Loading data from DigiMorph]
+* [https://blogs.uw.edu/maga/2017/04/11/morphosource-data-and-dealing-with-dicom-series-in-slicer/ Fixing problem DICOM]
+* [https://blogs.uw.edu/maga/2017/04/12/scissors-tool-is-awesome/ Scissors tool is awesome]
+== Using the (legacy) Editor ==
 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:

Difference between revisions of "Documentation/4.6/Training"