Slicer 3.6:Training

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 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
Core	Slicer3Visualization Tutorial 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.
Core	Programming in Slicer3 Tutorial 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.
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.
Core	Interactive Editor 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.
Core	Manual Registration 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.
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 Data
Specialized	Change Tracker 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.	Change Tracker Training Data Note: the dataset is also 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. Audience: All users	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.	PETCTFusion
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 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.	Data Simulator
Workflow	White Matter Exploration for Neurosurgical Planning This tutorial walks the user through a workflow for exploring white matter fibers surrounding a tumor using Diffusion Tensor Imaging (DTI) Tractography.	White Matter Exploration dataset

Summer 2011 Tutorial Contest Entries (under construction)

The following tutorials were part of the Summer2011 Tutorial Contest.

Category	Tutorial	Sample Data	Image
Specialized	Automatic Segmentation of Traumatic Brain Injury MRI Volumes This tutorial guides the user through the automatic segmentation of TBI volumes using Atlas Based classification.	TBI segmentation dataset
Specialized	Centerline Extraction of Coronary Arteries using VMTK in 3D Slicer This tutorial guides the user step by step through the process of centerline extraction of Coronary Arteries in a cardiac blood-pool MRI using VMTK based Tools.	Cardiac blood-pool MRI dataset

Summer 2010 Tutorial Contest Entries

The following tutorials were part of the Summer 2010 Slicer Tutorial Contest.

Category	Tutorial	Sample Data	Image
Specialized	Meshing Workflow Audience: All users and developers. (Note: Mac and Linux only.)	File:IAFEMeshData-TutorialContestSummer2010.zip
Specialized	Fiducials Audience: All users and developers.	Fiducials Data
Specialized	Robust Statistic Segmenter Audience: All users and developers.	Robust Statistic Segmenter Data
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	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.

External Resources

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

Narrated screencast video showing how to load data and make models: http://www.youtube.com/watch?v=GNsWRnm7gQw&context=C42d9859ADvjVQa1PpcFPhXz87xj_xyVq19zSUexfAbEm8Iz3DYEk=

• Brain Tumor Segmentation Manual (Slicer 3.6)