Visualization-based Brain Mapping

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Visualization-based Brain Mapping

• Jim Brinkley (PI)
• Structural Informatics Group
• Dept Biological Structure
• University of Washington, Seattle
• Funded by the Human Brain Project
• NIDCD
• NIMH

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Goals

• An information framework for brain mapping
• Organized around structure
• Spatial
• Symbolic
• Implemented in a distributed, web-accessible
  system
• Optimized for language mapping

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Photo
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Visual Brain Mapper (VBM)
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Requirements for visualization-based brain mapping

• Accurate reconstruction of brain surface as seen
  at neurosurgery
• Different problem than surface reconstruction
  for unfolding, flattening, analysis

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Reconstructing the surface

• Isosurface following
• Needs cleanly segmented cortex the
  skull-stripping problem

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Approaches to skull-stripping

• Manual
• Deformable models
• 3-D region growing/mathematical morphology

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A shape-based approach

• Represent knowledge of expected shape and range
  of variation of cortical envelope
• Use to guide the search for gray-CSF boundary
• Infer the boundary where none is present
• Allow user corrections

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Representing shape

• Geometric constraint networks
• Set of local constraints
• Interact together to generate a global shape
  description

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Constraint Network
Vi (Vi1, Vi2,)
Cij
Vj (Vj1, Vj2,)
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Geometric Constraint Network
Vi (Vi1, Vi2,)
Cij
Vj (Vj1, Vj2,)
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Radial contour modelStructural component
Ri Ri,inner Ri,outer
Cij
Rj Rj,inner, Rj,outer
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Radial contour modelShape component
Ri
Cij Ri/Rjmin Ri/Rjmax
Rj
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Constraint Propagation
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Radial surface model
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Radial surface model neighbors
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Shape-based skull stripping

• A module of VBM
• Load previously trained shape model
• Load MRI, MRV, MRA volumes
• Find cortical envelope
• Mask skull
• Find cortical surface
• Find veins and arteries

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Mid-sagittal plane
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Anterior Commissure
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Posterior commissure
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Cortical bounding box
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Initial model
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Initial model - end-on
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Initial model - lateral view
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Propagation from poles
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Define one radial
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Propagation from one radial
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Error
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Correct error
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Generate mask
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Generate mask
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Error in mask
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Generate mask
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Generate isosurface
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Extract veins
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Mask veins
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Vein isosurface
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Extract arteries
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Mask arteries
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Artery isosurface
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Vessels
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All
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Map
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Workflow
Select Model
Select Patient
Find Envelope
Define Landmarks
Align
Propagate Search
Mask Volume
Segment Cortex
Segment Veins
Iso- Surface
Segment Arteries
Map
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Workflow Architecture
Select Patient
Align
Segment Cortex
Segment Veins
Segment Arteries
Map
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End User Web Interfaces
Authoring Programs
Experiment Manager
Brain Map Visualizer
Analyzer
Visual Brain Mapper
Symbolic Model Builder
Internet
Graphics Server
Repository Manager
Knowledge Server
Structural Information Servers
Spatial Knowledge
3-D Maps
Symbolic Knowledge
3-D Models
Images
Metadata
Spatial Information
Symbolic Information
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Contributors

• Kevin Hinshaw
• Jeff Prothero
• Andrew Poliakov
• Richard Martin
• David Corina
• Ken Maravilla
• George Ojemann

• Rex Jakobovits
• Kate Mulligan
• Hector Lettich
• Linda Shapiro
• Cornelius Rosse