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Visualization-based Brain Mapping Jim Brinkley (PI) Structural Informatics Group Dept Biological...

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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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Page 1: Visualization-based Brain Mapping Jim Brinkley (PI) Structural Informatics Group Dept Biological Structure University of Washington, Seattle Funded by.

Visualization-based Brain Mapping

Jim Brinkley (PI)

Structural Informatics Group

Dept Biological Structure

University of Washington, Seattle

Funded by the Human Brain ProjectNIDCD

NIMH

Page 2: Visualization-based Brain Mapping Jim Brinkley (PI) Structural Informatics Group Dept Biological Structure University of Washington, Seattle Funded by.

Goals

• An information framework for brain mapping

• Organized around structure– Spatial– Symbolic

• Implemented in a distributed, web-accessible system

• Optimized for language mapping

Page 3: Visualization-based Brain Mapping Jim Brinkley (PI) Structural Informatics Group Dept Biological Structure University of Washington, Seattle Funded by.

Photo

Page 4: Visualization-based Brain Mapping Jim Brinkley (PI) Structural Informatics Group Dept Biological Structure University of Washington, Seattle Funded by.

Visual Brain Mapper (VBM)

Page 5: Visualization-based Brain Mapping Jim Brinkley (PI) Structural Informatics Group Dept Biological Structure University of Washington, Seattle Funded by.

Requirements for visualization-based brain mapping

• Accurate reconstruction of brain surface as seen at neurosurgery

• Different problem than surface reconstruction for unfolding, flattening, analysis

Page 6: Visualization-based Brain Mapping Jim Brinkley (PI) Structural Informatics Group Dept Biological Structure University of Washington, Seattle Funded by.

Reconstructing the surface

• Isosurface following

• Needs cleanly segmented cortex: the skull-stripping problem

Page 7: Visualization-based Brain Mapping Jim Brinkley (PI) Structural Informatics Group Dept Biological Structure University of Washington, Seattle Funded by.

Approaches to skull-stripping

• Manual

• Deformable models

• 3-D region growing/mathematical morphology

Page 8: Visualization-based Brain Mapping Jim Brinkley (PI) Structural Informatics Group Dept Biological Structure University of Washington, Seattle Funded by.

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

Page 9: Visualization-based Brain Mapping Jim Brinkley (PI) Structural Informatics Group Dept Biological Structure University of Washington, Seattle Funded by.

Representing shape

• Geometric constraint networks

• Set of local constraints

• Interact together to generate a global shape description

Page 10: Visualization-based Brain Mapping Jim Brinkley (PI) Structural Informatics Group Dept Biological Structure University of Washington, Seattle Funded by.

Constraint Network

Vi (Vi1, Vi2,…)

Vj (Vj1, Vj2,…)

Cij

Page 11: Visualization-based Brain Mapping Jim Brinkley (PI) Structural Informatics Group Dept Biological Structure University of Washington, Seattle Funded by.

Geometric Constraint Network

Vi (Vi1, Vi2,…)

Vj (Vj1, Vj2,…)

Cij

Page 12: Visualization-based Brain Mapping Jim Brinkley (PI) Structural Informatics Group Dept Biological Structure University of Washington, Seattle Funded by.

Radial contour modelStructural component

Ri [Ri,inner … Ri,outer ]

Rj [Rj,inner, Rj,outer ]

Cij

Page 13: Visualization-based Brain Mapping Jim Brinkley (PI) Structural Informatics Group Dept Biological Structure University of Washington, Seattle Funded by.

Radial contour modelShape component

Ri

Rj

Cij = [Ri/Rjmin … Ri/Rjmax]

Page 14: Visualization-based Brain Mapping Jim Brinkley (PI) Structural Informatics Group Dept Biological Structure University of Washington, Seattle Funded by.

Constraint Propagation

Page 15: Visualization-based Brain Mapping Jim Brinkley (PI) Structural Informatics Group Dept Biological Structure University of Washington, Seattle Funded by.

Radial surface model

Page 16: Visualization-based Brain Mapping Jim Brinkley (PI) Structural Informatics Group Dept Biological Structure University of Washington, Seattle Funded by.

Radial surface model neighbors

Page 17: Visualization-based Brain Mapping Jim Brinkley (PI) Structural Informatics Group Dept Biological Structure University of Washington, Seattle Funded by.

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

Page 18: Visualization-based Brain Mapping Jim Brinkley (PI) Structural Informatics Group Dept Biological Structure University of Washington, Seattle Funded by.

Mid-sagittal plane

Page 19: Visualization-based Brain Mapping Jim Brinkley (PI) Structural Informatics Group Dept Biological Structure University of Washington, Seattle Funded by.

Anterior Commissure

Page 20: Visualization-based Brain Mapping Jim Brinkley (PI) Structural Informatics Group Dept Biological Structure University of Washington, Seattle Funded by.

Posterior commissure

Page 21: Visualization-based Brain Mapping Jim Brinkley (PI) Structural Informatics Group Dept Biological Structure University of Washington, Seattle Funded by.

Cortical bounding box

Page 22: Visualization-based Brain Mapping Jim Brinkley (PI) Structural Informatics Group Dept Biological Structure University of Washington, Seattle Funded by.

Initial model

Page 23: Visualization-based Brain Mapping Jim Brinkley (PI) Structural Informatics Group Dept Biological Structure University of Washington, Seattle Funded by.

Initial model - end-on

Page 24: Visualization-based Brain Mapping Jim Brinkley (PI) Structural Informatics Group Dept Biological Structure University of Washington, Seattle Funded by.

Initial model - lateral view

Page 25: Visualization-based Brain Mapping Jim Brinkley (PI) Structural Informatics Group Dept Biological Structure University of Washington, Seattle Funded by.

Propagation from poles

Page 26: Visualization-based Brain Mapping Jim Brinkley (PI) Structural Informatics Group Dept Biological Structure University of Washington, Seattle Funded by.

Define one radial

Page 27: Visualization-based Brain Mapping Jim Brinkley (PI) Structural Informatics Group Dept Biological Structure University of Washington, Seattle Funded by.

Propagation from one radial

Page 28: Visualization-based Brain Mapping Jim Brinkley (PI) Structural Informatics Group Dept Biological Structure University of Washington, Seattle Funded by.

Error

Page 29: Visualization-based Brain Mapping Jim Brinkley (PI) Structural Informatics Group Dept Biological Structure University of Washington, Seattle Funded by.

Correct error

Page 30: Visualization-based Brain Mapping Jim Brinkley (PI) Structural Informatics Group Dept Biological Structure University of Washington, Seattle Funded by.

Generate mask

Page 31: Visualization-based Brain Mapping Jim Brinkley (PI) Structural Informatics Group Dept Biological Structure University of Washington, Seattle Funded by.

Generate mask

Page 32: Visualization-based Brain Mapping Jim Brinkley (PI) Structural Informatics Group Dept Biological Structure University of Washington, Seattle Funded by.

Error in mask

Page 33: Visualization-based Brain Mapping Jim Brinkley (PI) Structural Informatics Group Dept Biological Structure University of Washington, Seattle Funded by.

Generate mask

Page 34: Visualization-based Brain Mapping Jim Brinkley (PI) Structural Informatics Group Dept Biological Structure University of Washington, Seattle Funded by.

Generate isosurface

Page 35: Visualization-based Brain Mapping Jim Brinkley (PI) Structural Informatics Group Dept Biological Structure University of Washington, Seattle Funded by.

Extract veins

Page 36: Visualization-based Brain Mapping Jim Brinkley (PI) Structural Informatics Group Dept Biological Structure University of Washington, Seattle Funded by.

Mask veins

Page 37: Visualization-based Brain Mapping Jim Brinkley (PI) Structural Informatics Group Dept Biological Structure University of Washington, Seattle Funded by.

Vein isosurface

Page 38: Visualization-based Brain Mapping Jim Brinkley (PI) Structural Informatics Group Dept Biological Structure University of Washington, Seattle Funded by.

Extract arteries

Page 39: Visualization-based Brain Mapping Jim Brinkley (PI) Structural Informatics Group Dept Biological Structure University of Washington, Seattle Funded by.

Mask arteries

Page 40: Visualization-based Brain Mapping Jim Brinkley (PI) Structural Informatics Group Dept Biological Structure University of Washington, Seattle Funded by.

Artery isosurface

Page 41: Visualization-based Brain Mapping Jim Brinkley (PI) Structural Informatics Group Dept Biological Structure University of Washington, Seattle Funded by.

Vessels

Page 42: Visualization-based Brain Mapping Jim Brinkley (PI) Structural Informatics Group Dept Biological Structure University of Washington, Seattle Funded by.

All

Page 43: Visualization-based Brain Mapping Jim Brinkley (PI) Structural Informatics Group Dept Biological Structure University of Washington, Seattle Funded by.

Map

Page 44: Visualization-based Brain Mapping Jim Brinkley (PI) Structural Informatics Group Dept Biological Structure University of Washington, Seattle Funded by.

WorkflowSelectPatient

Align

SegmentCortex

SegmentVeins

SegmentArteries

Map

FindEnvelope

MaskVolume

Iso-Surface

SelectModel

DefineLandmarks

Propagate & Search

Page 45: Visualization-based Brain Mapping Jim Brinkley (PI) Structural Informatics Group Dept Biological Structure University of Washington, Seattle Funded by.

Workflow ArchitectureSelectPatient

Align

SegmentCortex

SegmentVeins

SegmentArteries

Map

(setq workflow (send class-workflow :new :name "BRAIN MAPPER" :steps (list select-step align-step segment-cortex-step segment-veins-step segment-arteries-step mapping-step ) ) )

Page 46: Visualization-based Brain Mapping Jim Brinkley (PI) Structural Informatics Group Dept Biological Structure University of Washington, Seattle Funded by.

SpatialKnowledge

3-D Models

Images3-D Maps

SymbolicModelBuilder

Visual Brain Mapper

Authoring Programs

Spatial Information

Internet

ExperimentManager

End User Web Interfaces

Brain MapVisualizer Analyzer

Graphics Server

KnowledgeServer

Structural Information Servers

RepositoryManager

SymbolicKnowledge

Metadata

Symbolic Information

Page 47: Visualization-based Brain Mapping Jim Brinkley (PI) Structural Informatics Group Dept Biological Structure University of Washington, Seattle Funded by.

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


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