Slicer 3.6:Training
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Slicer 3.6 Tutorials
- The following table contains "How to" tutorials with matched sample data sets. They demonstrate how to use the 3D Slicer environment (version 3.6 release) to accomplish certain tasks.
- For tutorials for other versions of Slicer, please visit the Slicer training portal.
- For questions related to the Slicer3 Compendium, please send an e-mail to Sonia Pujol, Ph.D
Category | Tutorial | Sample Data | Image |
Core | Slicer3Minute Tutorial-PDF The Slicer3Minute tutorial is an introduction to the advanced 3D visualization capabilities of Slicer3.6. Audience: First time users. |
Slicer3Minute Data The Slicer3Minute dataset contains an MR scan of the brain and 3D reconstructions of the anatomy |
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Core | Slicer3Visualization Tutorial-PDF The Slicer3Visualization tutorial guides through 3D data loading and visualization in Slicer3.6. Audience: All beginners including clinicians, scientists, engineers and programmers. |
Slicer3Visualization Data The Slicer3VisualizationDataset contains two MR scans of the brain, a pre-computed labelmap and 3D reconstructions of the anatomy. |
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Core | Programming in Slicer3 Tutorial-PDF The Programming in Slicer3 tutorial is an introduction to the integration of C++ stand-alone programs outside of the Slicer3 source tree. Audience: Programmers and Engineers. |
HelloWorld Plugin The HelloWorld tutorial dataset contains an MR scan of the brain and pre-computed xml and C++ files for integrating the Hello Python plug-in to Slicer3. |
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Core | Hello Python Tutorial The Hello Python tutorial is an introduction to the integration of Python stand-alone programs outside of the Slicer3 source tree. Audience: Programmers and Engineers. |
HelloPython Plugin The HelloPython tutorial dataset contains an MR scan of the brain and pre-computed xml and Python code for integrating the Hello Python plug-in to Slicer3. |
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Core | Interactive Editor-PDF Shows how to use the interactive editing tools in Slicer. Audience: All users and developers. |
Editor Data This dataset contains a MR dataset of the brain. |
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Core | Manual Registration-PDF Shows how to manually/interactively align two images in Slicer3.6 Audience: First time & early users. |
Manual Registration Data This dataset contains two brain MRI of a single subject, obtained in different orientations. |
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Specialized | Diffusion MRI tutorial-PDF This tutorial guides you through the process of loading diffusion MR data, estimating diffusion tensors, and performing tractography of white matter bundles. Audience: All users and developers. |
Diffusion Data | |
Specialized | Change Tracker Tutorial-PDF This tutorial describes the use of ChangeTracker module to detect changes in tumor volume from two MRI scans. Audience: All users interested in longitudinal analysis of pathology. |
Training Data download is integrated with the ChangeTracker module (see Tutorial) | |
Specialized | FreeSurfer Course The FreeSurfer dataset contains an MR scan of the brain and pre-computed FreeSurfer segmentation and cortical surface reconstructions.
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FreeSurfer tutorial data | |
Specialized | Neurosurgical Planning Tutorial This tutorial takes the trainee through a complete workup for neurosurgical patient-specific mapping. Also see this tutorial for information on how to use Slicer's affine registration, simple region growing, model maker and tractography modules. Audience: All users interested in image-guided therapy. |
Neurosurgical Planning Data | |
Specialized | PET/CT SUV Tutorial This tutorial takes the trainee through the computation of SUV body weight on a baseline and followup study. |
PET/CT Data (zip archive) | |
Specialized | EMSegmenter Simple Mode This tutorial takes the trainee through the segmentation of a MRI Human Brain without to adjust any parameters. |
Human Brain T1 Data | |
Specialized | EMSegmenter Advanced Mode (TESTING IN PROGRESS) This tutorial takes the trainee through the segmentation of a MRI Human Brain. The trainee will learn how to setup the EMSegmenter, this includes the creation of a task, the creation of an anatomical tree and adjusting the weights for the EM algorithm. |
Human Brain T1 Data | |
Specialized | OpenIGTLink This tutorial shows to connect an IGT device using the OpenIGTLink. |
OpenIGTLink Data Simulator |
Summer 2010 Tutorial Contest Entries (under construction)
The following tutorials were part of the Summer 2010 Slicer Tutorial Contest.
Category | Tutorial | Sample Data | Image |
Specialized | Meshing Workflow tutorial Audience: All users and developers. (Note: Mac and Linux only.) |
Meshing Workflow Data |
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Specialized | Fiducials tutorial Audience: All users and developers. |
Fiducials Data |
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Specialized | Robust Statistic Segmenter Audience: All users and developers. |
Robust Statistic Segmenter Data |
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Specialized | Longitudinal lesion comparison Audience: All users and developers. (Note: Mac and Linux only.) |
Longitudinal Lesion Comparison Data | |
Specialized | Robot-Assisted MRI-Guided Prostate Biopsy Audience: All users and developers. |
Robot-Assisted MRI-Guided Prostate Biopsy | |
Specialized | Atlas Label Fusion & Surface Registration Audience: All users and developers. |
Atlas Label Fusion & Surface Registration | |
Specialized | Stochastic Tractography Audience: All users and developers. (Note: Mac and Linux only.) |
Stochastic Tractography | |
Specialized | PERK Station Module Audience: All users and developers. (Note: Windows only.) |
PERK Station Module |
Software Installation
- The Slicer download page contains information on how to obtain a compiled version of Slicer for a variety of platforms and where to find the source code for Slicer 3.
Software Documentation
- For the Slicer 3.6 manual pages please click here. These pages are the reference manual for Slicer 3.6 and briefly explain the functionality found in panels and modules.