Latest revision as of 22:03, 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This section is currently out-of-date and may contain errors but is retained for historical reference.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 4.10 Tutorials

This page contains "How to" tutorials with matched sample data sets. They demonstrate how to use the 3D Slicer environment (version 4.10 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 4.10 documentation page
For questions related to 3D Slicer training materials and to the organization of 3D Slicer training workshops, please send an e-mail to Sonia Pujol, Ph.D., Director of Training and Education of 3D Slicer.

Some of these tutorials are based on older releases of 3D Slicer and are being upgraded to Slicer5.0. The concepts are still useful but some interface elements and features may be different in updated versions.

1 Introduction: Slicer 4.10 Tutorials
2 Quick Start Guide
- 2.1 Downloading and Installing Slicer
3 General Introduction
- 3.1 Slicer Welcome Tutorial
- 3.2 Slicer4Minute Tutorial
4 3D Visualization
5 Tutorials for software developers
6 Segmentation
7 Image Phenotyping
8 Registration
- 8.1 Slicer4 Image Registration
- 8.2 Slicer Registration Case Library
9 Slicer Extensions
10 3D Slicer version 4.7 Tutorial Contest
11 YouTube videos
12 Teams Contributions

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 5.0 / 4.11

General Introduction

Slicer Welcome Tutorial

The Slicer Welcome tutorial 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 4.8
Compatible with Slicer 4.10.1

Slicer4Minute Tutorial

The Slicer4 Minute Tutorial is a brief introduction to the advanced 3D visualization capabilities of Slicer.
Author: Sonia Pujol, Ph.D.
Audience: First-time users who want to discover Slicer in 4 minutes
Modules: Welcome to Slicer, Models
Based on Slicer version 4.8
Compatible with Slicer 4.10.1
The Slicer4Minute dataset contains an MR scan of the brain and 3D reconstructions of the anatomy

3D Visualization

Data Loading and 3D Visualization

Slicer 5.0
- The Slicer 5.0 Basics of data loading and visualization tutorial shows how to load and visualize DICOM images and 3D models in 3D Slicer. French version
- Author: Sonia Pujol, Ph.D.
- Modules: DICOM, Volume Rendering, Models
- Audience: End-users
- Based on: 3D Slicer version 5.0/4.11
- The Data Loading and Visualization dataset contains a thoraco-abdominal CT scan, an MRI brain dataset and 3D models of brain structures.

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 Slicer 4.9
- Compatible with Slicer 4.10.1
- The 3DVisualization dataset contains an MR scan and a series of 3D models of the brain.

DICOM

The DICOM and Slicer tutorial provides an introduction to the DICOM standard and shows how to load and visualize DICOM datasets in 3D Slicer version 5.0.
Author: Sonia Pujol, Ph.D.
Modules: DICOM, Volumes
Based on: 3D Slicer version 5.0/4.11
The 3D Slicer DICOM Tutorial Data contains a torso-CT and a breast MRI.

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
Compatible with 3D Slicer version 4.10
The 3DVisualizationDICOM_part1 and 3DVisualizationDICOM_part2 datasets contain a series of MR and CT scans, and 3D models of the brain, lung and liver.

Open Anatomy Browser

The Open Anatomy Browser tutorial is an introduction to the OABrowser technology for viewing and interacting with atlases.
Author: Sonia Pujol, Ph.D., Mike Halle, Ph.D.
Audience: End-users

Tutorials for software developers

PerkLab's Slicer bootcamp training materials

The Laboratory for Percutaneous Surgery at Queen's University has made available training material of its internal yearly bootcamp, covering topics, such as 3D Slicer overview, basic visualization, segmentation, registration, scripting and module development, surgical navigation, DICOM, reproducible medical image computing research methodology, version control, and research project management.
- Scripting and module development tutorial
- All other tutorials
Author: Andras Lasso, Csaba Pinter, Tamas Ungi, Csaba Pinter, Matthew Holden, Kyle Sunderland
Audience: Developers, Users
Based on: 3D Slicer version 4.10

Slicer Programming Tutorial

The Slicer Programming tutorial guides through the integration of a python module in Slicer. It provides an introduction to the Python Console and the Qt Widget toolkit in 3D Slicer.
Author: Sonia Pujol, Ph.D., Steve Pieper, Ph.D.
Audience: Developers
Based on: 3D Slicer version 5.0/4.11

Slicer script repository

For additional Python scripts examples, please visit the Script repository.

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, Jean-Christophe Fillion-Robin, Steve Pieper
Audience: Developers
Based on: 3D Slicer version 4.4

Segmentation

Segmentation for 3D printing: shows how to use the Segment Editor module for combining CAD designed parts with patient-specific models. Video tutorial. Author: Hillary Lia. Segmentation for 3D printing Step-by-step tutorial. Author: Csaba Pinter, MSc Audience: Users and developers interested in segmentation and 3D printing Dataset: Phantom base STL model Source: PerkLab. Based on: 3D Slicer version 4.7
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
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
Slicer Segmentation Recipes provide step-by-step description of useful segmentation techniques. Segmentation tutorials for common tasks, such as skin surface extraction, craniotomy (splitting segments), sorta segmentation, cerebral vessel segmentation by subtraction, segmentation on arbitrarily oriented slices, skull stripping.
The Skull Stripping tutorial shows how to perform skull-stripping in CT and MR data. Author: Sonia Pujol, PhD, Andras Lasso, PhD, Ron Kikinis, MD Audience: Users interested in brain segmentation Based on: 3D Slicer version 4.11

Image Phenotyping

Based on: 3D Slicer version 4.10
The Image Phenotyping tutorial is an introduction to brain tumor segmentation and image phenotyping using the Slicer Radiomics extension.
Authors: Sonia Pujol, Ph.D.
Audience: Clinical researchers
Dataset: Meningioma dataset

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

Based on: 3D Slicer version 4.8; Compatible with Slicer 4.10

The Brain Tumor Registration is a video-based tutorial that shows how to register two MRI datasets in a brain tumor case for surgical resection follow-up.
Authors: Sonia Pujol, Ph.D., Dominik Meier, Ph.D.
Audience: Users and developers interested in image registration
Dataset: Registration Library Case #37

Based on: 3D Slicer version 4.10

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

Slicer Extensions

Slicer4 Diffusion Tensor Imaging Tutorial

The Diffusion MRI Tutorial 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; Compatible with Slicer version 4.10.2
The Slicer Diffusion MRI Tutorial dataset contains an MR Diffusion Weighted Imaging scan of the brain.
Please visit dmri.slicer.org/docs for the latest documentation of SlicerDMRI.

Slicer4 Neurosurgical Planning Tutorial

The Neurosurgical Planning tutorial course guides end-users through the generation of fiber tracts in the vicinity of a tumor.
Author: Sonia Pujol, Ph.D., Ron Kikinis, M.D.
Audience: Clinicians and Clinical Researchers
Modules: Segment Editor, Tractography
Based on 3D Slicer version 4.10
The White Matter Exploration dataset contains a Diffusion Weighted Imaging scan of a brain tumor patient.

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 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

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.

.

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

.

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).

.

Slicer4 Lung CT Analyzer

The LungCTAnalyzer tutorial and the LungCTAnalyzer video-based demo show how to visualize and quantify infiltration, emphysema and collapsed lung areas in CT datasets acquired on COVID-19 patients.
Authors: Rudolph Bumm, MD, Andras Lasso, PhD.
Audience: End-users
Modules: LungCTSegmenter, LungCTAnalyzer
Based on: 3D Slicer version 5.0 (4.11)

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

The Segmentation for 3D printing Tutorial (pptx) is an introduction to the new Segment Editor module, demonstrated through the popular topic of 3D printing.
Author: Csaba Pinter (Queen's University, Canada)
Narrated video version on YouTube.
Dataset: Phantom base STL model Source: PerkLab.

.

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.

.

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 nifti file format (separated bvecs, bvals files).
Author: Laurent Chauvin (ETS Montreal)
Dataset: Not available.

.

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

.

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

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

.

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).

.

YouTube videos

How to segment multiple vertebrae in spine CT for 3D printing - Author: Hillary Lia

Creating a femur model from CT volume using 3D Slicer - Author: PerkLab

Preparing data for 3D printing - Author: Nabgha Farhat

How to export CT and segmentation data to DICOM- Author: Andras Lasso, Csaba Pinter

Local Threshold Effect - Author: Kyle Sunderland

SlicerVMTK centerline extraction (Slicer 4.11)- Author: Andras Lasso

MONAI Label(Slicer 4.11)- Author: Andres Diaz-Pinto

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

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

International resources

International resources in Chinese and in German are made available by the Slicer community.

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. The tutorials below are examples of Slicer tutorials in Chinese.

Getting started 大脑前动脉远端动脉瘤手术夹闭治疗

distal anterior cerebral artery aneurysm 3D Slicer：漂亮得不像实力派

meningioma skull resection 脑膜瘤患者颅骨切除一期修补的3DSlicer方案

Cerebral hemorrhage by forehead positioning method 脑出血经额手术定位法（五

Hematoma modeling 血肿建模的第11种方法

The WeChat 3D Slicer Group in China offers a comprehensive list of tutorials in Chinese.

Resources in German

A series of four YouTube videos on python programming in Slicer (German narration with English subtitles)

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

Video-based segmentation tutorials from CHU de Rouen (France)
- Segmentation tutorials, including liver, wrist bones, lungs, kidneys, hips.

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:

@@ Line 1: / Line 1: @@
-<noinclude>{{documentation/versioncheck}}</noinclude>
+<noinclude>{{Historical|Up-to-date training materials can be found at [[Documentation/Nightly/Training]]}}
+</noinclude>
 =Introduction: Slicer {{documentation/version}} Tutorials=
 *This page contains "How to" tutorials with matched sample data sets. They demonstrate how to use the 3D Slicer environment (version {{documentation/version}} release) to accomplish certain tasks.
 *For tutorials for other versions of Slicer, please visit the [[Training| Slicer training portal]].
 *For "reference manual" style documentation, please visit the [[Documentation/{{documentation/version}}|Slicer {{documentation/version}} documentation page]]
-*For questions related to the Slicer4 Training Compendium, please send an e-mail to '''[http://www.na-mic.org/Wiki/index.php/User:SPujol Sonia Pujol, Ph.D., Director of Training of 3D Slicer.]'''
+*For questions related to 3D Slicer training materials and to the organization of 3D Slicer training workshops, please send an e-mail to '''[https://scholar.harvard.edu/soniapujol/home Sonia Pujol, Ph.D., Director of Training and Education of 3D Slicer.]'''
-* 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.
+*Some of these tutorials are based on older releases of 3D Slicer and are being upgraded to Slicer5.0. The concepts are still useful but some interface elements and features may be different in updated versions.
 __TOC__
-=Quick Start Guide =
+=Quick Start Guide=
 ==Downloading and Installing Slicer==
-{|width="100%"
+{| 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
+*The [https://spujol.github.io/3DSlicerQuickStartGuide/ Quick Start Guide] shows how to install and start 3D Slicer
 *Author: Sonia Pujol, Ph.D.
-*Based on: 3D Slicer version 4.8
+*Based on 3D Slicer 5.0 / 4.11
-|align="right"|
+| align="right" |
 [[image:QuickStart_image.png|250px|SlicerWelcome tutorial]]
 |}
@@ Line 27: / Line 28: @@
 ==Slicer Welcome Tutorial==
-{|width="100%"
+{| width="100%"
 |
 *The [https://www.dropbox.com/s/vn8sqlof2kag2kk/SlicerWelcome-tutorial_Slicer4.8_SoniaPujol.pdf?dl=0 Slicer Welcome tutorial] is an introduction to Slicer.
@@ Line 33: / Line 34: @@
 *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
+*Based on 3D Slicer 4.8
-|align="right"|
+*Compatible with Slicer 4.10.1
+| align="right" |
 [[image:SlicerWelcome-image.png|250px|SlicerWelcome tutorial]]
 |}
 ==Slicer4Minute Tutorial==
-{|width="100%"
+{| width="100%"
 |
-*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.
+*The [https://www.dropbox.com/s/v3lyivwgdoro7yn/Slicer4.10minute_SoniaPujol.pdf?dl=0| Slicer4 Minute Tutorial]  is a brief introduction to the advanced 3D visualization capabilities of Slicer.
 *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
+*Based on Slicer version 4.8
-*The [[media:Slicer4minute.zip|Slicer4Minute dataset]] contains an MR scan of the brain and 3D reconstructions of the anatomy
+*Compatible with Slicer 4.10.1
-|align="right"|
+*The [[Media:Slicer4minute.zip|Slicer4Minute dataset]] contains an MR scan of the brain and 3D reconstructions of the anatomy
+| align="right" |
 [[image:Slicer4minute-image.png|250px|right|Slicer4Minute tutorial]]
 |}
 =3D Visualization=
-==Slicer4 Data Loading and 3D Visualization ==
+==Data Loading and 3D Visualization==
-{|width="100%"
+{| width="100%"
 |
+*Slicer 5.0
+**The [https://spujol.github.io/SlicerVisualizationTutorial/ Slicer 5.0 Basics of data loading and visualization tutorial] shows how to load and visualize DICOM images and 3D models in 3D Slicer. [https://docs.google.com/presentation/d/12Lbq-QBCxP2p9FkF3_YM5Ng7pItfspMG0FP_20wQglA/edit?usp=sharing French version]
+**Author: Sonia Pujol, Ph.D.
+**Modules: DICOM, Volume Rendering, Models
+**Audience: End-users
+**Based on: 3D Slicer version 5.0/4.11
+**The [https://www.dropbox.com/s/03emcqnlec4t2s5/3DVisualizationDataset.zip?dl=1 Data Loading and Visualization dataset] contains a thoraco-abdominal CT scan, an MRI brain dataset and 3D models of brain structures.
+*Slicer 4.10
+**The [http://slicer.kitware.com/midas3/download/item/356408/20180430_DataLoadingAndVisualizationTutorial.pdf Data loading and visualization] ([http://slicer.kitware.com/midas3/download/item/356409/20180430_DataLoadingAndVisualizationTutorial.pptx 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 Slicer 4.9
+**Compatible with Slicer 4.10.1
+**The [http://slicer.kitware.com/midas3/download/?items=330421,1 3DVisualization dataset] contains an MR scan and a series of 3D models of the brain.
-* Slicer 4.10
+| align="right" |
-** The [http://slicer.kitware.com/midas3/download/item/356408/20180430_DataLoadingAndVisualizationTutorial.pdf Data loading and visualization] ([http://slicer.kitware.com/midas3/download/item/356409/20180430_DataLoadingAndVisualizationTutorial.pptx pptx]) course guides through the basics of loading and viewing volumes and 3D models in Slicer 4.10.
+[[Image:20180426_DataLoadingAndVisualizationTutorial.png|right|200px|]]
-** Author: Csaba Pinter
+[[Image:Slicer4DataLoading_tutorial.png|right|200px|]]
-** Modules: Welcome to Slicer, Data, Volume Rendering, Models.
+|}
-** Audience: End-users
-** Based on: 3D Slicer version 4.10
-** The [http://slicer.kitware.com/midas3/download/?items=330421,1 3DVisualization dataset] contain an MR scan and a series of 3D models of the brain.
-* Slicer 4.5
+==DICOM==
-** The [[Media:3DDataLoadingandVisualization_Slicer4.5_SoniaPujol.pdf | Data loading and 3D visualization]] course guides through the basics of loading and viewing volumes and 3D models in Slicer 4.5.
+{| width="100%"
-** Author: Sonia Pujol, Ph.D.
+|
-** Modules: Welcome to Slicer, Sample Data, Models.
+*The [https://spujol.github.io/SlicerDICOMTutorial/ DICOM and Slicer] tutorial provides an introduction to the DICOM standard and shows how to load and visualize DICOM datasets in 3D Slicer version 5.0.
-** Audience: End-users
+*Author: Sonia Pujol, Ph.D.
-** Based on: 3D Slicer version 4.5
+*Modules: DICOM, Volumes
-** The [http://slicer.kitware.com/midas3/download/?items=330421,1 3DVisualization dataset] contain an MR scan and a series of 3D models of the brain.
+*Based on: 3D Slicer version 5.0/4.11
-|align="right"|
+*The [https://spujol.github.io/SlicerDICOMTutorial/ 3D Slicer DICOM Tutorial Data] contains a torso-CT and a breast MRI.
-[[Image:20180426_DataLoadingAndVisualizationTutorial.png|right|250px|]]
+| align="right" |
-[[Image:Slicer4DataLoading_tutorial.png|right|250px|]]
+[[Image:SlicerAndDICOM.png|right|250px|]]
 |}
-==Slicer4 3D Visualization of DICOM images for Radiology Applications==
+{| width="100%"
-{|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.
+*The [https://www.dropbox.com/s/8pm5mty2c0zwmyk/3DVisualizationDICOM_Slicer4.10_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.
+*Compatible with 3D Slicer version 4.10
-|align="right"|
+*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|]]
 |}
+==Open Anatomy Browser==
+{| width="100%"
+|
+[[Image:OABrowser.png|right|250px|]]
+*The [https://www.dropbox.com/s/f2641iu27hif8p4/OpenAnatomyTutorial_SoniaPujol-MikeHalle.pdf?dl=0 Open Anatomy Browser]  tutorial is an introduction to the OABrowser technology for viewing and interacting with atlases.
+*Author: Sonia Pujol, Ph.D., Mike Halle, Ph.D.
+*Audience: End-users
+|}
 =Tutorials for software developers=
-== Slicer4 Programming Tutorial ==
+==PerkLab's Slicer bootcamp training materials==
-{|width="100%"
+{| width="100%"
-|
-*The [https://www.dropbox.com/s/wrhrvvmplosiis1/Slicer4_ProgrammingTutorial_SPujol-SPieper_Nightly.pdf?dl=0# Slicer Programming tutorial] guides through the integration of a python module in Slicer4.
-*Author: Sonia Pujol, Ph.D., Steve Pieper, Ph.D.
-*Audience: Developers
-*Based on: 3D Slicer version 4.7
-*The [https://www.dropbox.com/s/6yxu8qepmvywk0n/HelloPython_Nightly.zip?dl=0 HelloPython dataset] contains sample data set (MR scan of the brain) and complete Python module examples.
-|align="right"|
-[[Image:HelloPythonTutorial.png|right|250px|]]
-|}
-== PerkLab's Slicer bootcamp training materials ==
-{|width="100%"
 |
 *The [http://perk.cs.queensu.ca/ Laboratory for Percutaneous Surgery at Queen's University] has made available training material of its internal yearly bootcamp, covering topics, such as 3D Slicer overview, basic visualization, segmentation, registration, scripting and module development, surgical navigation, DICOM, reproducible medical image computing research methodology, version control, and research project management.
-** [https://github.com/PerkLab/PerkLabBootcamp/blob/master/Doc/day3_2_SlicerProgramming.pptx?raw=true Scripting and module development tutorial]
+**[https://github.com/PerkLab/PerkLabBootcamp/blob/master/Doc/day3_2_SlicerProgramming.pptx?raw=true Scripting and module development tutorial]
-** [https://github.com/PerkLab/PerkLabBootcamp/tree/master/Doc All other tutorials]
+**[https://github.com/PerkLab/PerkLabBootcamp/tree/master/Doc All other tutorials]
 *Author: Andras Lasso, Csaba Pinter, Tamas Ungi, Csaba Pinter, Matthew Holden, Kyle Sunderland
 *Audience: Developers, Users
-*Based on: 3D Slicer version 4.8
+*Based on: 3D Slicer version 4.10
-|align="right"|
+| align="right" |
 [[Image:PerkLabSlicerProgrammingTutorial.png|right|250px|]]
 |}
-== Slicer script repository ==
+==Slicer Programming Tutorial==
+{| width="100%"
+|
+*The [https://spujol.github.io/SlicerProgrammingTutorial/ Slicer Programming tutorial] guides through the integration of a python module in Slicer. It provides an introduction to the Python Console and the Qt Widget toolkit in 3D Slicer.
+*Author: Sonia Pujol, Ph.D., Steve Pieper, Ph.D.
+*Audience: Developers
+*Based on: 3D Slicer version 5.0/4.11
+| align="right" |
+[[Image:SlicerProgrammingTutorial.png|right|250px|]]
+|}
+==Slicer script repository==
-For additional Python scripts examples, please visit the [[Documentation/{{documentation/version}}/ScriptRepository|Script Repository page]]
+For additional Python scripts examples, please visit the [https://slicer.readthedocs.io/en/latest/developer_guide/script_repository.html Script repository].
 ==Developing and contributing extensions for 3D Slicer==
-{|width="100%"
+{| width="100%"
 |
-*The [http://goo.gl/IP4cdg 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.
+*The [http://goo.gl/IP4cdg 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, Jean-Christophe Fillion-Robin, Steve Pieper
 *Audience: Developers
 *Based on: 3D Slicer version 4.4
-|align="right"|
+| align="right" |
 [[Image:Contributing3DSlicerExtension.png|right|250px|]]
 |}
 =Segmentation=
-== Slicer4 Image Segmentation ==
+{| 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.
+**'''[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
+**Audience: Users and developers interested in segmentation and 3D printing
+**Dataset: [[:File:BasePiece.zip|Phantom base STL model]] Source: [http://perk-software.cs.queensu.ca/plus/doc/nightly/modelcatalog/ PerkLab].
+**Based on: 3D Slicer version 4.7
+| align="right" |[[Image:20170717_3DPrintingTutorialYoutube.PNG|280px]]
+|---
+|
+*'''[https://www.youtube.com/watch?v=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]]
+|---
+|
+*'''[https://www.youtube.com/watch?v=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]]
+|---
 |
-* Segmentation for 3D printing: shows how to use the Segment Editor module for combining CAD designed parts with patient-specific models.
+*'''[https://lassoan.github.io/SlicerSegmentationRecipes/ Slicer Segmentation Recipes]''' provide step-by-step description of useful segmentation techniques.
-** '''[[Documentation/{{documentation/version}}/Training#Segmentation_for_3D_printing|Segmentation for 3D printing Step-by-step tutorial]]'''. Author: Csaba Pinter, MSc
+** Segmentation tutorials for common tasks, such as skin surface extraction, craniotomy (splitting segments), sorta segmentation, cerebral vessel segmentation by subtraction, segmentation on arbitrarily oriented slices, skull stripping.
-** Audience: Users and developers interested in segmentation and 3D printing
+| align="right" |[[Image:SegmentationRecipes.png|280px]]
-** 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.
+*'''[https://spujol.github.io/SkullStrippingTutorial/ The Skull Stripping tutorial]''' shows how to perform skull-stripping in CT and MR data.
-** Author: Andras Lasso, PhD
+**Author: Sonia Pujol, PhD, Andras Lasso, PhD, Ron Kikinis, MD
-** Audience: Users who need to segment heart structures, for example for visualization, quantification, or simulation.
+**Audience: Users interested in brain segmentation
-** [http://slicer.kitware.com/midas3/download/bitstream/738905/CTA-cardio2.nrrd Sample data set]
+**Based on: 3D Slicer version 4.11
-** Based on: 3D Slicer version 4.8
+| align="right" |[[Image:SkullStripping.png|280px]]
-|align="right"|[[Image:WholeHeartSegYoutube.png|280px]]
+|}
+=Image Phenotyping=
+{| width="100%"
+|
+*Based on: 3D Slicer version 4.10
+*The [https://spujol.github.io/ImagePhenotypingTutorial/ Image Phenotyping tutorial] is an introduction to brain tumor segmentation and image phenotyping using the Slicer Radiomics extension.
+*Authors: Sonia Pujol, Ph.D.
+*Audience: Clinical researchers
+*Dataset: [https://www.dropbox.com/s/hdlduw6oqnf2n72/Meningioma.nrrd?dl=0 Meningioma dataset]
+| align="right" |[[File:ImagePhenotyping.png|250px]]
 |}
 =Registration=
-== Slicer4 Image Registration ==
+==Slicer4 Image Registration==
-{|width="100%"
+{| 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.
+*Authors: Sonia Pujol, Ph.D., Dominik Meier, Ph.D., Ron Kikinis, M.D.
-* Audience: Users and developers interested in image registration
+*Audience: Users and developers interested in image registration
-* Dataset: [[Media:RegistrationData.zip| 3D Slicer Registration Data]]
+*Dataset: [[Media:RegistrationData.zip| 3D Slicer Registration Data]]
-|align="right"|[[File:registration_Slicer4.png|250px]]
+| align="right" |[[File:registration_Slicer4.png|250px]]
+|}
+*Based on: 3D Slicer version 4.8; Compatible with Slicer 4.10
+{| width="100%"
+|
+*The [https://spujol.github.io/3DSlicerTutorial-Registration Brain Tumor Registration] is a video-based tutorial that shows how to register two MRI datasets in a brain tumor case for surgical resection follow-up.
+*Authors: Sonia Pujol, Ph.D., Dominik Meier, Ph.D.
+*Audience: Users and developers interested in image registration
+*Dataset: [[Special:FilePath/RegLib C37 Data.zip| Registration Library Case #37]]
+| align="right" |[[File:RigidRegistration.jpg|250px]]
 |}
-*Based on: 3D Slicer version 4.8
+*Based on: 3D Slicer version 4.10
-== Slicer Registration Case Library==
+==Slicer Registration Case Library==
-{|width="100%"
+{| 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]]
+| align="right" |[[Image:RegLib_table.png|250px|link=https://www.slicer.org/wiki/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.
+*The [https://spujol.github.io/SlicerDiffusionMRITutorial Diffusion MRI Tutorial] is an introduction to 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.
 *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 4.8
+*Based on: 3D Slicer version 4.8; Compatible with Slicer version 4.10.2
-*The [[media:Dti tutorial data.zip|DTI dataset]] contains an MR Diffusion Weighted Imaging scan of the brain.
+*The [https://www.dropbox.com/s/gba2zsn276x43up/SlicerDiffusionMRITutorialData.zip?dl=1 Slicer Diffusion MRI Tutorial dataset] contains an MR Diffusion Weighted Imaging scan of the brain.
-|align="right"|
+*Please visit [http://dmri.slicer.org/docs/ dmri.slicer.org/docs] for the latest documentation of SlicerDMRI.
+| align="right" |
 [[Image:Slicer4DTI Tutorial.png|right|250px|]]
 |}
 ==Slicer4 Neurosurgical Planning Tutorial==
-{|width="100%"
+{| width="100%"
 |
-*Please visit [http://dmri.slicer.org/docs/ dmri.slicer.org/docs] for the latest documentation of SlicerDMRI.
+*The [https://spujol.github.io/NeurosurgicalPlanningTutorial/ Neurosurgical Planning tutorial] course guides end-users 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.
-*Audience: End-users and developers
+*Audience: Clinicians and Clinical Researchers
-*Modules: Volumes, Editor, Tractography Label Map Seeding, Tractography Interactive Seeding
+*Modules: Segment Editor, Tractography
-*Based on: 3D Slicer version 4.6
+*Based on 3D Slicer version 4.10
-*The [[Media:WhiteMatterExplorationData.zip| White Matter Exploration dataset]] 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 a brain tumor patient.
-|align="right"|
+| align="right" |
 [[Image:NeurosurgicalPlanningTutorial.png|right|250px|link=http://vimeo.com/67336069]]
 |}
 ==Slicer4 Quantitative Imaging tutorial==
-{|width="100%"
+{| width="100%"
 |
-*The [[media:QuantitativeImaging_Slicer4.5.pdf‎ | 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.
+*The [[Media:QuantitativeImaging Slicer4.5.pdf| 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 [[media:QuantitativeImaging.zip‎| Quantitative Imaging dataset]]  contains a series of MR and PET/CT data.
+*The [[Media:QuantitativeImaging.zip| Quantitative Imaging dataset]]  contains a series of MR and PET/CT data.
-|align="right"|
+| align="right" |
 [[Image:Slicer4_QuantitativeImaging.png|right|250px|]]
 |}
-== Slicer4 IGT ==
+==Slicer4 IGT==
-{|width="100%"
+{| width="100%"
 |
 *[http://www.slicerigt.org/wp/user-tutorial/ Slicer IGT tutorials]
@@ Line 228: / Line 296: @@
 *Modules: SlicerIGT Extension
 *Based on: Slicer4.3.1-2014.09.14
-*Data: [https://onedrive.live.com/redir?resid=7230D4DEC6058018!2937&authkey=!AGQkSCZOwjVYXw8&ithint=folder%2cpptx  Slicer-IGT datasets]
+*Data: [https://onedrive.live.com/redir?resid=7230D4DEC6058018!2937&authkey=!AGQkSCZOwjVYXw8&ithint=folder%2cpptx Slicer-IGT datasets]
-|align="right"|
+| align="right" |
 [[Image:SlicetIGT.png|right|150px|]]
 |}
-==Slicer4 Radiation Therapy Tutorial ==
+==Slicer4 Radiation Therapy Tutorial==
-{|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://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.
+*Author: Csaba Pinter, Andras Lasso, An Wang, Gregory C. Sharp, David Jaffray, Gabor Fichtinger.
-* Dataset: [http://slicer.kitware.com/midas3/download/item/205404/SlicerRT_WorldCongress_TutorialIGRT_Dataset.zip download] from MIDAS server
+*Dataset: [http://slicer.kitware.com/midas3/download/item/205404/SlicerRT_WorldCongress_TutorialIGRT_Dataset.zip download] from MIDAS server
-* Based on Slicer 4.7
+*Based on Slicer 4.7
-|align="right"|
+| align="right" |
-<!-- [[Image:TUTORIAL-IMAGE-HERE.png|right|150px|]] -->
+[[Image:SlicerRTUseCaseImage.png|right|150px|]]
 |}
 ==Slicer Pathology==
-{|width="100%"
+{| 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"|
+| align="right" |
 [[File:SlicerPathologyScreenShot8.png | 200px]].
 |}
 ==SPHARM-PDM==
-{|width="100%"
+{| 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"|
+| align="right" |
 [[File:SlicerWinterProjectWeek2017-SPHARM-PDM.png | 200px]].
 |}
 ==Fiber Bundle Volume Measurement==
-{|width="100%"
+{| 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"|
+| align="right" |
 [[File:SlicerWinterProjectWeek2017-FiberBundleVolumeMeasurements.png | 200px]].
 |}
-= 3D Slicer version 4.7 Tutorial Contest=
+==Slicer4 Lung CT Analyzer==
+{| width="100%"
+|
+*The [https://github.com/rbumm/SlicerLungCTAnalyzer LungCTAnalyzer tutorial] and the [https://www.youtube.com/watch?v=fpLxm7uAvZQ LungCTAnalyzer video-based demo] show how to visualize and quantify infiltration, emphysema and collapsed lung areas in CT datasets acquired on COVID-19 patients.
+*Authors: Rudolph Bumm, MD, Andras Lasso, PhD.
+*Audience: End-users
+*Modules: LungCTSegmenter, LungCTAnalyzer
+*Based on: 3D Slicer version 5.0 (4.11)
+| align="right" |
+[[Image:LungCTAnalyzer.png|right|250px|]]
+|}
+=3D Slicer version 4.7 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===
-{|width="100%"
+{| width="100%"
 |
 *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, demonstrated through the popular topic of 3D printing.
 *Author: Csaba Pinter (Queen's University, Canada)
-* [https://www.youtube.com/watch?v=Uht6Fwtr9hE Narrated video version on YouTube].
+*[https://www.youtube.com/watch?v=Uht6Fwtr9hE Narrated video version on YouTube].
 *Dataset: [[:File:BasePiece.zip|Phantom base STL model]] Source: [http://perk-software.cs.queensu.ca/plus/doc/nightly/modelcatalog/ PerkLab].
-|align="right"|
+| align="right" |
 [[File:SlicerWinterProjectWeek2017-Segmentation-for-3d-printing.png | 200px]].
 |}
 ===Slicer Pathology===
-{|width="100%"
+{| 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"|
+| align="right" |
 [[File:SlicerPathologyScreenShot8.png | 200px]].
 |}
 ===Simple Python Tool for Quality Control of DWI data===
-{|width="100%"
+{| width="100%"
 |
 *The [http://www.na-mic.org/Wiki/images/3/3a/SimpleDiffusionGradientInformationExtractorTutorial_Chauvin_Jan2017.pptx 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).
 *Author: Laurent Chauvin (ETS Montreal)
 *Dataset:  Not available.
-|align="right"|
+| align="right" |
 [[File:SlicerWinterProjectWeek2017-SimpleDiffusionGradientInformationExtractorTutorial.png | 200px]].
 |}
 ===SPHARM-PDM===
-{|width="100%"
+{| 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"|
+| align="right" |
 [[File:SlicerWinterProjectWeek2017-SPHARM-PDM.png | 200px]].
 |}
 ===Integration of Robot Operating System (ROS) and 3D Slicer using OpenIGTLink===
-{|width="100%"
+{| width="100%"
 |
 *The [https://www.na-mic.org/Wiki/images/a/ab/ROSIGTLTutorial_Tokuda_Jan2017.pptx Integration of Robot Operating System (ROS) and 3D Slicer using OpenIGTLink Tutorial] describes the software architecture of surgical robot systems and allows to acquire hands-on experience of software-hardware integration for medical robotics.
 *Author: Junichi Tokuda (Brigham and Women’s Hospital)
 *Dataset:  Not available.
-|align="right"|
+| align="right" |
 [[File:SlicerWinterProjectWeek2017-Integration-ROS-3DSlicer-OpenIGTLink.png | 200px]].
 |}
 ===Fiber Bundle Volume Measurement===
-{|width="100%"
+{| 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"|
+| align="right" |
 [[File:SlicerWinterProjectWeek2017-FiberBundleVolumeMeasurements.png | 200px]].
 |}
@@ Line 344: / Line 424: @@
 =YouTube videos=
 {| border="1" cellpadding="5" width="1200px"
-| style="width:25%" | [[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: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:25%" | [[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 ]
+| 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: PerkLab]
-| style="width:25%" | [[Image:3DPrinting.png|right|250px|]] [https://www.youtube.com/watch?v=MKLWzD0PiIc Preparing data for 3D printing - Author: PerkLab ]
+| style="width:33%" |[[Image:3DPrinting.png|right|250px|]] [https://www.youtube.com/watch?v=MKLWzD0PiIc Preparing data for 3D printing - Author: Nabgha Farhat]
-| style="width:25%" | [[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:25%" | [[Image:DICOM2.png|right|250px|]] [https://www.youtube.com/watch?v=nzWf4xHy1BM& How to export CT and segmentation data to DICOM- Author: Andras Lasso, Csaba Pinter]
+{| border="1" cellpadding="5" width="1200px" |
-|-
+| style="width:25%" |[[Image:DICOM2.png|right|250px|]] [https://www.youtube.com/watch?v=nzWf4xHy1BM& How to export CT and segmentation data to DICOM- Author: Andras Lasso, Csaba Pinter]
+| style="width:25%" |[[Image:LocalThresholdEffect.png|right|250px|]] [https://www.youtube.com/watch?time_continue=26&v=cevlMLyhfK8&feature=emb_logo Local Threshold Effect - Author: Kyle Sunderland]
+| style="width:25%" |[[Image:VMTKCenterlines.png|right|250px|]] [https://www.youtube.com/watch?v=yi07mjr3JeU SlicerVMTK centerline extraction (Slicer 4.11)- Author: Andras Lasso]
+| style="width:25%" |[[Image:MONAILabel.png|right|250px|]] [https://www.youtube.com/watch?v=PmD8umlcpF4 MONAI Label(Slicer 4.11)- Author: Andres Diaz-Pinto]
 |}
 Additional [http://www.youtube.com/results?search_query=3d+slicer&sm=3 non-curated videos-based demonstrations using 3D Slicer are accessible on YouTube].
-=Teams Contributions  =
+=Teams Contributions=
-{|width="100%"
+{| width="100%"
 |
-* This ''Slicer 4.1 [http://vimeo.com/41096643 webinar]'' presents the new features and improvements of the release, and a brief overview of work for the next release.
+*This ''Slicer 4.1 [http://vimeo.com/41096643 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.
+*Authors: Steve Pieper Ph.D.
-* Audience: First time users and developers interested in Slicer 4.1 new features.
+*Audience: First time users and developers interested in Slicer 4.1 new features.
-* Length: 0h20m
+*Length: 0h20m
-|align="right"|[[Image:Webinar-Slicer-4.1.png|250px]]
+| align="right" |[[Image:Webinar-Slicer-4.1.png|250px]]
 |}
 <br>
 ----
 <br>
-{|width="100%"
+{| width="100%"
 |
 *This ''Intro to Slicer 4.0 [http://vimeo.com/37671358 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
-|align="right"|[[Image:Webinar.png|250px]]
+| align="right" |[[Image:Webinar.png|250px]]
 |}
 <br>
 ----
 <br>
-== International resources==
+==International resources==
+International resources in Chinese and in German are made available by the Slicer community.
-==Resources in Chinese ==
+==Resources in Chinese==
-{|width="100%"
+{| width="100%"
 |
-A 3D Slicer community on WeChat in China offers many tutorials and clinical examples in Chinese.  Note that the images are of interest to non-Chinese speakers and Google Translate does a reasonable job of translating some of the text.
+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. The tutorials below are examples of Slicer tutorials in Chinese.
-* [https://mp.weixin.qq.com/s?__biz=MzI3MDY4ODA5Mw==&mid=2247486116&idx=1&sn=772e9d431ac32cbb73d08cf0e6bc219a&chksm=eacc0096ddbb89805d93ac4be181d1a35058031bac673d7a91b3b44dccee2bfd1d8461397635#rd Getting started 大脑前动脉远端动脉瘤手术夹闭治疗]
+*[https://mp.weixin.qq.com/s?__biz=MzI3MDY4ODA5Mw==&mid=2247486116&idx=1&sn=772e9d431ac32cbb73d08cf0e6bc219a&chksm=eacc0096ddbb89805d93ac4be181d1a35058031bac673d7a91b3b44dccee2bfd1d8461397635#rd Getting started 大脑前动脉远端动脉瘤手术夹闭治疗]
-* [https://mp.weixin.qq.com/s?__biz=MzI3MDY4ODA5Mw==&mid=2247484787&idx=1&sn=1f6279bdccab168fc79b7275e9fe91ca&chksm=eacc0f41ddbb8657be92f617661133d87bb55a4ecf12f786e97a8b7d5249a05d11e0cd620c3f#rd distal anterior cerebral artery aneurysm 3D Slicer：漂亮得不像实力派]
+*[https://mp.weixin.qq.com/s?__biz=MzI3MDY4ODA5Mw==&mid=2247484787&idx=1&sn=1f6279bdccab168fc79b7275e9fe91ca&chksm=eacc0f41ddbb8657be92f617661133d87bb55a4ecf12f786e97a8b7d5249a05d11e0cd620c3f#rd distal anterior cerebral artery aneurysm 3D Slicer：漂亮得不像实力派]
-* [https://mp.weixin.qq.com/s?__biz=MzI3MDY4ODA5Mw==&mid=2247486360&idx=1&sn=f833b13a26f543aa9175419a03df7f52&chksm=eacc01aaddbb88bcb004773a4db8a9b3c7633d21cda3956f84b96515252eb861c5eb1e75a60b&mpshare=1&scene=24&srcid=0212LIfOkBRm9CvA7ImHCpRt#rd meningioma skull resection 脑膜瘤患者颅骨切除一期修补的3DSlicer方案]
+*[https://mp.weixin.qq.com/s?__biz=MzI3MDY4ODA5Mw==&mid=2247486360&idx=1&sn=f833b13a26f543aa9175419a03df7f52&chksm=eacc01aaddbb88bcb004773a4db8a9b3c7633d21cda3956f84b96515252eb861c5eb1e75a60b&mpshare=1&scene=24&srcid=0212LIfOkBRm9CvA7ImHCpRt#rd meningioma skull resection 脑膜瘤患者颅骨切除一期修补的3DSlicer方案]
-* [https://mp.weixin.qq.com/s?__biz=MzI3MDY4ODA5Mw==&mid=2247486079&idx=1&sn=9b926dc398a408e3441082b9e0ffde61&chksm=eacc004dddbb895bf9b60f5f1bc443513196e4cb90a6caf6f348a4da7b7fc22eb658661aeb49&mpshare=1&scene=24&srcid=0212AFtT2Wq7K7bvkMGTdyih#rd Cerebral hemorrhage by forehead positioning method 脑出血经额手术定位法（五 ]
+*[https://mp.weixin.qq.com/s?__biz=MzI3MDY4ODA5Mw==&mid=2247486079&idx=1&sn=9b926dc398a408e3441082b9e0ffde61&chksm=eacc004dddbb895bf9b60f5f1bc443513196e4cb90a6caf6f348a4da7b7fc22eb658661aeb49&mpshare=1&scene=24&srcid=0212AFtT2Wq7K7bvkMGTdyih#rd Cerebral hemorrhage by forehead positioning method 脑出血经额手术定位法（五]
-* [https://mp.weixin.qq.com/s?__biz=MzI3MDY4ODA5Mw==&mid=2247485356&idx=1&sn=044f5899b651b35994db00c32ab688ee&chksm=eacc0d9eddbb8488f16ff82bb1dda8456a4011790fed024781972d578783e67781443cf4a319&mpshare=1&scene=24&srcid=0212G45TadrPnX8tp9eaNXUs#rd Hematoma modeling 血肿建模的第11种方法]
+*[https://mp.weixin.qq.com/s?__biz=MzI3MDY4ODA5Mw==&mid=2247485356&idx=1&sn=044f5899b651b35994db00c32ab688ee&chksm=eacc0d9eddbb8488f16ff82bb1dda8456a4011790fed024781972d578783e67781443cf4a319&mpshare=1&scene=24&srcid=0212G45TadrPnX8tp9eaNXUs#rd Hematoma modeling 血肿建模的第11种方法]
-* [https://mp.weixin.qq.com/s?__biz=MzI3MDY4ODA5Mw==&mid=2247486025&idx=1&sn=b281324893be4ab116d20826f1b426c3&chksm=eacc007bddbb896d9deb096f209278f40c0b52c6410a8a9ff3ce8c3697c99304f18eb678f11e&mpshare=1&scene=24&srcid=02125v1kxvIGmfkxx7mUZcCM#rd Mobile phone positioning and AR application 手机定位及AR应用的初步探索]
+*[https://mp.weixin.qq.com/s?__biz=MzI3MDY4ODA5Mw==&mid=2247486025&idx=1&sn=b281324893be4ab116d20826f1b426c3&chksm=eacc007bddbb896d9deb096f209278f40c0b52c6410a8a9ff3ce8c3697c99304f18eb678f11e&mpshare=1&scene=24&srcid=02125v1kxvIGmfkxx7mUZcCM#rd Mobile phone positioning and AR application 手机定位及AR应用的初步探索]
+*[https://mp.weixin.qq.com/s?__biz=MzI3MDY4ODA5Mw==&mid=2247483658&idx=1&sn=ad08fe01c61d6999a36f2960b34287ec&chksm=eacc0b38ddbb822e60206afcf0bb67562432bb275463b20ad6ac7d243ccc1429afaa8f2177ea#rd 3D printing 如何用3D Slicer实现模型3D打印 束旭俊]
-|align="right"|
+The WeChat 3D Slicer Group in China offers a [https://spujol.github.io/SlicerTutorialsInChinese/ comprehensive list of tutorials in Chinese.]
+<br />
+| align="right" |
 [[image:Wechat-hemorage-2018-02-12.png|250px|Example WeChat tutorial slides]]
 |}
-==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)
-== Murat Maga's blog posts about using 3D Slicer for biology ==
+==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/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/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/2017/04/11/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 awesom]
+*[https://blogs.uw.edu/maga/2017/04/12/scissors-tool-is-awesome/ Scissors tool is awesom]
-== Using the (legacy) Editor ==
+==Using the (legacy) Editor==
-=== Fast GrowCut ===
+===Fast GrowCut===
-{|width="100%"
+{| width="100%"
 |
-* The [[media:FastGrowCutTutorial.pdf |Fast GrowCut tutorial]]  shows how to perform a segmentation using the Fast GrowCut effect in Slicer.
+*The [[Media:FastGrowCutTutorial.pdf|Fast GrowCut tutorial]]  shows how to perform a segmentation using the Fast GrowCut effect in Slicer.
-* Authors: Hillary Lia
+*Authors: Hillary Lia
-* Audience: Users interested in segmentation
+*Audience: Users interested in segmentation
-|align="right"|[[File:FastGrowCutLogo.png|200px]]
+| align="right" |[[File:FastGrowCutLogo.png|200px]]
+|}
+{| width="100%"
+*'''[https://www.youtube.com/channel/UC8vxI0-dEWrw0_tBF-v8xGA/videos Video-based segmentation tutorials from CHU de Rouen (France)]
+** Segmentation tutorials, including liver, wrist bones, lungs, kidneys, hips.
+| align="right" |[[Image:ChuRouen.png|180px]]
 |}
-=== Use case: Slicer in paleontology ===
+===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:
-* [http://openpaleo.blogspot.com/2008/12/3d-slicer-tutorial.html Open Source Paleontologist: 3D Slicer: The Tutorial]
+*[http://openpaleo.blogspot.com/2008/12/3d-slicer-tutorial.html Open Source Paleontologist: 3D Slicer: The Tutorial]
-* [http://openpaleo.blogspot.com/2008/12/3d-slicer-tutorial-part-ii.html Open Source Paleontologist: 3D Slicer: The Tutorial Part II]
+*[http://openpaleo.blogspot.com/2008/12/3d-slicer-tutorial-part-ii.html Open Source Paleontologist: 3D Slicer: The Tutorial Part II]
-* [http://openpaleo.blogspot.com/2008/12/3d-slicer-tutorial-part-iii.html Open Source Paleontologist: 3D Slicer: The Tutorial Part III]
+*[http://openpaleo.blogspot.com/2008/12/3d-slicer-tutorial-part-iii.html Open Source Paleontologist: 3D Slicer: The Tutorial Part III]
-* [http://openpaleo.blogspot.com/2008/12/3d-slicer-tutorial-part-iv.html Open Source Paleontologist: 3D Slicer: The Tutorial Part IV]
+*[http://openpaleo.blogspot.com/2008/12/3d-slicer-tutorial-part-iv.html Open Source Paleontologist: 3D Slicer: The Tutorial Part IV]
-* [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]

Difference between revisions of "Documentation/4.10/Training"

Latest revision as of 22:03, 22 November 2022

Introduction: Slicer 4.10 Tutorials

Contents

Quick Start Guide

Downloading and Installing Slicer

General Introduction

Slicer Welcome Tutorial

Slicer4Minute Tutorial

3D Visualization

Data Loading and 3D Visualization

DICOM

Open Anatomy Browser

Tutorials for software developers

PerkLab's Slicer bootcamp training materials

Slicer Programming Tutorial

Slicer script repository

Developing and contributing extensions for 3D Slicer

Segmentation

Image Phenotyping

Registration

Slicer4 Image Registration

Slicer Registration Case Library

Slicer Extensions

Slicer4 Diffusion Tensor Imaging Tutorial

Slicer4 Neurosurgical Planning Tutorial

Slicer4 Quantitative Imaging tutorial

Slicer4 IGT

Slicer4 Radiation Therapy Tutorial

Slicer Pathology

SPHARM-PDM

Fiber Bundle Volume Measurement

Slicer4 Lung CT Analyzer

3D Slicer version 4.7 Tutorial Contest

Segmentation for 3D printing

Slicer Pathology

Simple Python Tool for Quality Control of DWI data

SPHARM-PDM

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

Fiber Bundle Volume Measurement

YouTube videos

Teams Contributions

International resources

Resources in Chinese

Resources in German

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

Using the (legacy) Editor

Fast GrowCut

Use case: Slicer in paleontology

Navigation menu

Search