- 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
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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.
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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.
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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.
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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
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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
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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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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
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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
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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
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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
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
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- 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
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International resources
Resources in Chinese
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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.
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Resources in German
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
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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:
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