Slicer 3.6:Training

From SlicerWiki
(Redirected from Slicer3.6:Training)
Jump to: navigation, search
Home < Slicer3.6: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
Slicer3Minute 3.6RC2.png
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.
VisualizationTutorial 3.6RC3.png
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.
Programming
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.
Programming
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.
InteractiveEditor.png
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.
Slicer3 ManualRegistrationTutorial.gif
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 Cc.PNG
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) Slicer3.4.1-ChangeTracker.jpg
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 FreeSurferTutorial.PNG
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 NeurosurgicalPlanningOverview.png
Specialized PET/CT SUV Tutorial

This tutorial takes the trainee through the computation of SUV body weight on a baseline and followup study.
PETCTFusion PETCTFusionBig.png
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 EMSegmenter-Simple-Mode.png
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 EMSegmenter-Advanced-Mode.png
OpenIGTLink

This tutorial shows to connect an IGT device using the OpenIGTLink.
OpenIGTLink Data Simulator OpenIGT.PNG
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 WhiteMatterExploration.PNG

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 TBI image.png
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 Vmtkcloseupvoronoicenterlinewithreference.png

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.)
Meshing Workflow Data

FEMesh.png
Specialized Fiducials

Audience: All users and developers.
Fiducials Data

Fiducials.png
Specialized Robust Statistic Segmenter

Audience: All users and developers.
Robust Statistic Segmenter Data

RSS.png
Specialized Longitudinal Lesion Comparison

Audience: All users and developers. (Note: Mac and Linux only.)
Longitudinal Lesion Comparison Data Longitudinal Lesion.png
Specialized Robot-Assisted MRI-Guided Prostate Biopsy

Audience: All users and developers.
Robot-Assisted MRI-Guided Prostate Biopsy ProstateNav.png
Specialized Atlas Label Fusion & Surface Registration

Audience: All users and developers.
Atlas Label Fusion & Surface Registration AtlasLabelFusion.png
Specialized Stochastic Tractography

Audience: All users and developers. (Note: Mac and Linux only.)
Stochastic Tractography Stochastic tutorial uncinate.JPG
Specialized PERK Station Module

Audience: All users and developers. (Note: Windows only.)
PERK Station Module PERKStation.png

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:

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