Revision as of 18:30, 22 November 2022

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

Introduction: Slicer Nightly Tutorials

This page contains "How to" tutorials with matched sample data sets. They demonstrate how to use the 3D Slicer environment (version Nightly 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 Nightly 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 Nightly 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.

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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

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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).

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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.

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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.

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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

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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.

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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).

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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 6: / Line 6: @@
 *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 '''[https://scholar.harvard.edu/soniapujol/home 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__
@@ Line 20: / Line 20: @@
 *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" |
 [[image:QuickStart_image.png|250px|SlicerWelcome tutorial]]
@@ Line 34: / 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
+*Compatible with Slicer 4.10.1
 | align="right" |
 [[image:SlicerWelcome-image.png|250px|SlicerWelcome tutorial]]
@@ Line 42: / Line 43: @@
 {| 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
+*Compatible with Slicer 4.10.1
 *The [[Media:Slicer4minute.zip|Slicer4Minute dataset]] contains an MR scan of the brain and 3D reconstructions of the anatomy
 | align="right" |
@@ Line 72: / Line 74: @@
 **Based on Slicer 4.9
 **Compatible with Slicer 4.10.1
-**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.
+**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.
 | align="right" |
@@ Line 93: / Line 95: @@
 {| 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
+*Compatible with 3D Slicer version 4.10
 *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" |
@@ Line 103: / Line 106: @@
 |}
-=Tutorials for software developers=
+==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=
 ==PerkLab's Slicer bootcamp training materials==
@@ Line 147: / Line 159: @@
 =Segmentation=
-==Slicer4 Image Segmentation==
 {| width="100%"
 |
 *Segmentation for 3D printing: shows how to use the Segment Editor module for combining CAD designed parts with patient-specific models.
 **'''[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
+**'''[[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].
@@ Line 163: / Line 173: @@
 **Author: Andras Lasso, PhD
 **Audience: Users who need to segment heart structures, for example for visualization, quantification, or simulation.
-**Sample data set: http://slicer.kitware.com/midas3/download/bitstream/738905/CTA-cardio2.nrrd
+**[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]]
@@ Line 193: / Line 203: @@
 |
 *Based on: 3D Slicer version 4.10
-*The [https://www.dropbox.com/s/lg417kr754fo6ji/ImagePhenotypingTutorial_SoniaPujol.pdf?dl=0 Image Phenotyping tutorial] is an introduction to image phenotyping using the Slicer Radiomics extension..
+*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
@@ Line 200: / Line 210: @@
 |}
 =Registration=
@@ Line 216: / Line 224: @@
 |}
-*Based on: 3D Slicer version 4.8
+*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 4.10
 ==Slicer Registration Case Library==
 {| width="100%"
 |
@@ Line 227: / Line 244: @@
 :Author: Dominik Meier, Ph.D.
 :Audience:  users interested learning/applying Slicer image registration technology
-| align="right" |[[Image:RegLib_table.png|250px|link=https://www.slicer.org/wiki/Documentation/{{documentation/version}}/Registration/RegistrationLibrary]]<nowiki>|}</nowiki>
+| align="right" |[[Image:RegLib_table.png|250px|link=https://www.slicer.org/wiki/Documentation/{{documentation/version}}/Registration/RegistrationLibrary]]
 |}
@@ Line 234: / Line 251: @@
 {| width="100%"
 |
+*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://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.
 *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; Compatible with Slicer version 4.10.2
 *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.
@@ Line 333: / Line 349: @@
 *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" |
@@ Line 340: / Line 356: @@
 |}
 =3D Slicer version 4.7 Tutorial Contest=
@@ Line 413: / Line 428: @@
 | style="width:33%" |[[Image:3DPrinting.png|right|250px|]] [https://www.youtube.com/watch?v=MKLWzD0PiIc Preparing data for 3D printing - Author: Nabgha Farhat]
 |}
-{| border="1" cellpadding="5" width="1200px"
+{| border="1" cellpadding="5" width="1200px" |
-| style="width:33%" |[[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: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:33%" |[[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: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:33%" |[[Image:VMTKCenterlines.png|right|250px|]] [https://www.youtube.com/watch?v=yi07mjr3JeU&feature=youtu.be SlicerVMTK centerline extraction (Slicer 4.11)- Author: Andras Lasso]
+| style="width:25%" |[[Image:VMTKCenterlines.png|right|250px|]] [https://www.youtube.com/watch?v=yi07mjr3JeU&feature=youtu.be 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]
 |}
@@ Line 464: / Line 479: @@
 *[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]
+The WeChat 3D Slicer Group in China offers a [https://spujol.github.io/SlicerTutorialsInChinese/ comprehensive list of tutorials in Chinese.]
+<br />
-The WeChat 3D Slicer Group in China offers a [https://spujol.github.io/SlicerTutorialsInChinese/ comprehensive list of tutorials in Chinese.]
 | align="right" |
 [[image:Wechat-hemorage-2018-02-12.png|250px|Example WeChat tutorial slides]]
@@ Line 474: / Line 492: @@
 *[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==
@@ Line 483: / Line 499: @@
 *[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]
+==Using the (legacy) Editor==
 ===Fast GrowCut===
@@ Line 510: / Line 528: @@
 *[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]
-|}

Difference between revisions of "Documentation/Nightly/Training"

Revision as of 18:30, 22 November 2022

Introduction: Slicer Nightly 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