Slicer3.4:Training

Slicer 3.4 Tutorials

• The following table contains "How to" tutorials with matched sample data sets. They demonstrate how to use the 3D Slicer environment (version 3.4) to accomplish certain tasks.
• For questions related to the Slicer3.4 Compendium, please send an e-mail to Sonia Pujol, Ph.D. (spujol at bwh.harvard.edu).

Category	Tutorial	Sample Data	Image
Basic	Slicer3Minute Tutorial The Slicer3Minute tutorial is an introduction to the advanced 3D visualization capabilities of Slicer3.4. Audience: First time users.	Slicer3Minute dataset The Slicer3Minute dataset contains an MR scan of the brain and 3D reconstructions of the anatomy
Basic	Slicer3 Manual Registration Tutorial shows how to manually/interactively align two images in Slicer3.4 or 3.5 Audience: First time & early users.	Manual Registration example dataset This dataset contains two brain MRI of a single subject, obtained in different orientations.
Core	Slicer3Visualization Tutorial The Slicer3Visualization tutorial guides through 3D data loading and visualization in Slicer3.4. Audience: All beginning users including clinicians, scientists, engineers and programmers.	Slicer3Visualization dataset The Slicer3VisualizationDataset contains two MR scans of the brain, a pre-computed labelmap and 3D reconstructions of the anatomy.
Core	Programming in Slicer3 Tutorial The Programming in Slicer3 tutorial is an introduction to the the integration of 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 World plug-in to Slicer3.
Specialized	3D Visualization of FreeSurfer Data The course guides through 3D visualization of FreeSurfer brain segmentations, surface reconstruction and parcellation results in Slicer3.4. Audience: All users.	FreeSurfer Tutorial dataset The FreeSurfer dataset contains an MR scan of the brain and pre-computed FreeSurfer segmentation and cortical surface reconstructions.
Specialized	Automatic Segmentation Tutorial The course guides through the process of using the Expectation-Maximization Segmentation algorithm to automatically segment brain structures from MRI data. Audience: Programmers and Engineers.	Automatic Segmentation dataset
Specialized	Atlas Label Merging & Surface Based Registration Tutorial This tutorial guides through the creation and co-registration of surface models of atlas structures (thalamus & thalamic nuclei) and subsequent merging of two labelmaps.	Atlas Merging tutorial dataset (contains 2 full brain atlases + intermediate result files, 72MB)
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 dataset
Specialized	Diffusion MRI Tutorial 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 dataset
Specialized	ChangeTracker Tutorial 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	LiverSegmentation Tutorial This tutorial introduces translational clinical scientists to the capabilities of the 3D Slicer software through the segmentation of the liver. Audience: All users and developers.	Liver Segmentation dataset

Slicer Tutorial Contest

The following tutorials were part of the June 2009 Slicer tutorial contest and January 2009 Slicer tutorial contest.

Driving Biological Project/Collaboration	Tutorial	Sample Data	Image
Confocal Microscopy	Confocal Microscopy	Microscopy Confocal Dataset
Autism	ARCTIC: Automatic Regional Cortical ThICkness V2.1	ARCTIC Data
Prostate	‎Trans-rectal MR guided prostate biopsy	MR guided prostate biopsy Dataset
Schizophrenia	Python Stochastic Tractography Module	Stochastic Tractography Data
Lupus	White Matter Lesions Segmentation V2.2	Lesion Segmentation Tutorial Data
Automated FE Mesh	IA FEMesh Tutorial	Mesh Tutorial Example Data
Alcohol and Stress Interaction	Non-Human Primate Segmentation Tutorial	Non-Human Primate Segmentation Data	‎
Prostate	MR Guided Prostate Interventions	MR Guided Prostate Interventions Data
IGT	Basic Navigation Tutorial	Basic Navigation Data
Schizophrenia	Python Stochastic Tractography Tutorial V1.0	Stochastic Tractography Data
Autism	ARCTIC: Automatic Regional Cortical ThICkness V1.0	ARCTIC Data
Lupus	White Matter Lesions Segmentation V2.0	Lesion Segmentation Tutorial Data
Orbit Segmentation	Segmentation of the Orbit	Orbit Segmentation Data
VMTK	VMTK Coronary Arteries Centrelines Extraction	VMTK Centrelines Data
Fiber Clustering	EM Fiber Clustering	‎ EM Fiber Clustering Data

Slicer 3.5 Tutorials

• The following table contains "How to" tutorials with matched sample data sets. They demonstrate how to use the 3D Slicer environment (version 3.5) to accomplish certain tasks.

Contest	Tutorial	Sample Data	Image
Specialized	Robust Statistics Segmentation Tutorial	Robust Statistics Segmentation dataset

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 3.4 manual pages please click here. These pages are the reference manual for Slicer 3.4 and briefly explain the functionality found in panels and modules.

Older Tutorials

• Visit the Slicer 3.2 training page.
• Visit the Slicer 2 training page.