This page will contain information about the upcoming BioImage Suite training course to be taught at Yale University beginning on Thursday, Jan 24th. This will consist of a number of weekly sessions and all notes/examples/test-data from this course will be made available through this webpage.

Provisional Course Outline

The Course will take place on Thursdays at 11:30 am in TAC N137 (the Yale MRRC Conference Room). Handouts and data will be made available via this webpage to both local and interested outside users. The schedule below is provisional and is subject to change.

Core Course

This will be a 14 week course on BioImage Suite with an emphasis on neuroimaging.

1. Overview, Installing BioImage Suite on Mac/Win/Linux -- Jan 24
• Installation
• Design
• Starting BioImage Suite
• A quick primer on 3D Graphics
2. Looking at Images -- Jan 31
• A quick primer on images
• Orthogonal/Mosaic Viewers
• Neuroimaging Coordinates MNI/Talairach
• Using the Atlas Tool
3. More Advanced Visualization -- Feb 7
• Volume Rendering
• Animations and Movies - Supplemental Material
4. Basic Image Manipulation -- Feb 14
• Image Type as an Issue
• Smoothing incl Anisotropic Diffusion
• Cropping/Padding/Blanking
• Piecewise Linear Mapping
• Thresholding
5. Interactive Segmentation Tool -- Feb 21
• Editing Surfaces using the Surface Editor.
• Painting Voxels using the Objectmap Editor
• Cardiac 4D Editing
• Abdominal Fat Stuff
• Tracing Subcortical Structures
• Using Objectmap Editor to correct skull stripping
Example data for this session can be found here.


6. Bias Field Correction and Tissue Classification -- Feb 28
• Histogram Segmentation
• MRF Segmentation
• Bias Field Correction
• Calling FSL for Brain Stripping and Gray/White Segmentation
Example data for this session can be found here.


7. Linear Registration -- March 6
This presentation from 2003 provides some useful background. [ pdf file] ,[powerpoint slides)]
• Intro to Registration
• Manual Initialization
• Overlay of Function on Structure via Image Reslicing
Example data for this session can be found here.


8. Non Linear Intensity Based Registration -- March 27
• More Theory
• Distortion Correction for fMRI/DTI
• Batch Jobs
Example data for this session can be found here.


9. Landmarks, Surfaces and Point-Based Registration -- April 3
• Landmark and Surface Control
• Linear and Non Linear Point-Based Registration
10. Multi-Subject Analysis -- The Multisubject Control -- April 10
• The .msb file format
• Computing Composite Averages
• Overlays
• Group Comparisons etc
11. Diffusion Weighted Image Analysis -- May 1
• Intro to DTI
• Computing Tensorts
• Visualizing Tensors
• Reslicing Tensors
• Tracking Issues
• Analyzing Fiber Tracks etc.
12. fMRI Analysis -- May 15
• XML Editor
• Single Subject Analysis
• Overlay of Function on Structure using Brain Register
• VOI Analysis and defining VOIs
• Multisubject Analysis

Special Sessions

A number of Special Sessions will be held in parallel with the main course for smaller groups.

1. Neurosurgery Tools -- Date to be determined
• Electrode Editor
• Data Tree
2. Cardiac Deformation Estimation -- Date to be determined
• Surface-based tracking
• FEM Analysis
• Post-processing
3. Vascular Image Analysis -- Date to be determined
• Hessian Computation
• Tracking Vessels
4. Mouse micro-CT Image Analysis -- Date to be determined
• The Mouse Chopper
• Parcellating VOIs

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See the main BioImage Suite (www.bioimagesuite.org) webpage for more details on BioImage Suite.

We acknowledge support from the National Institutes of Health (NIH)/National Institute of Biomedical Imaging and Bioengineering (NIBIB) under grant R01 EB006494.