Documentation/Nightly/Training

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 the Slicer4 Training Compendium, please send an e-mail to Sonia Pujol, Ph.D., Director of Training 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.

Quick Start Guide

Downloading and Installing Slicer

The Quick Start Guide shows how to install and start 3D Slicer Author: Sonia Pujol, Ph.D. Based on: 3D Slicer version 4.8

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 version 4.8

Slicer4Minute Tutorial

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

3D Visualization

Slicer4 Data Loading and 3D Visualization

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: 3D Slicer version 4.10 The 3DVisualization dataset contain an MR scan and a series of 3D models of the brain. Slicer 4.5 The Data loading and 3D visualization course guides through the basics of loading and viewing volumes and 3D models in Slicer 4.5. Author: Sonia Pujol, Ph.D. Modules: Welcome to Slicer, Sample Data, Models. Audience: End-users Based on: 3D Slicer version 4.5 The 3DVisualization dataset contain an MR scan and a series of 3D models of the brain.

Slicer4 3D Visualization of DICOM images for Radiology Applications

The 3D Visualization of DICOM images course guides through 3D data loading and visualization of DICOM images for Radiology Applications in Slicer4. Author: Sonia Pujol, Ph.D., Kitt Shaffer, M.D., Ph.D., Ron Kikinis, M.D. Audience: Radiologists and users of Slicer who need a more comprehensive overview over Slicer4 visualization capabilities. Modules: DICOM, Volumes, Volume Rendering, Models. Based on: 3D Slicer version 4.8 The 3DVisualizationDICOM_part1 and 3DVisualizationDICOM_part2 datasets contain a series of MR and CT scans, and 3D models of the brain, lung and liver.

Tutorials for software developers

Slicer4 Programming Tutorial

The Slicer Programming tutorial guides through the integration of a python module in Slicer4. Author: Sonia Pujol, Ph.D., Steve Pieper, Ph.D. Audience: Developers Based on: 3D Slicer version 4.7 The HelloPython dataset contains sample data set (MR scan of the brain) and complete Python module examples.

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 script repository

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

Developing and contributing extensions for 3D Slicer

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

Segmentation

Slicer4 Image Segmentation

Segmentation for 3D printing: shows how to use the Segment Editor module for combining CAD designed parts with patient-specific models. 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: http://slicer.kitware.com/midas3/download/bitstream/738905/CTA-cardio2.nrrd 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

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

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 Please visit dmri.slicer.org/docs for the latest documentation of SlicerDMRI. The Diffusion Tensor Imaging course is an introduction to the basics of loading Diffusion Weighted images in Slicer, estimating tensors and generating fiber tracts. Author: Sonia Pujol, Ph.D. Audience: End-users and developers Modules: Data, Volumes, DWI to DTI Estimation, Diffusion Tensor Scalar Measurements, Editor, Markups,Tractography Label Map Seeding, Tractography Interactive Seeding Based on: 3D Slicer version 4.8 The DTI dataset contains an MR Diffusion Weighted Imaging scan of the brain. 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). . 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 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 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. 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 Mobile phone positioning and AR application 手机定位及AR应用的初步探索 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 Slicer for Biologists Loading data from DigiMorph Fixing problem DICOM Scissors tool is awesom 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 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: Open Source Paleontologist: 3D Slicer: The Tutorial Open Source Paleontologist: 3D Slicer: The Tutorial Part II Open Source Paleontologist: 3D Slicer: The Tutorial Part III Open Source Paleontologist: 3D Slicer: The Tutorial Part IV Open Source Paleontologist: 3D Slicer: The Tutorial Part V Open Source Paleontologist: 3D Slicer: The Tutorial Part VI