Visualization-based Brain Mapping

Jim Brinkley (PI)

Structural Informatics Group

Dept Biological Structure

University of Washington, Seattle

Funded by the Human Brain ProjectNIDCD

NIMH

Goals

• An information framework for brain mapping

• Organized around structure– Spatial– Symbolic

• Implemented in a distributed, web-accessible system

• Optimized for language mapping

Photo

Visual Brain Mapper (VBM)

Requirements for visualization-based brain mapping

• Accurate reconstruction of brain surface as seen at neurosurgery

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

Reconstructing the surface

• Isosurface following

• Needs cleanly segmented cortex: the skull-stripping problem

Approaches to skull-stripping

• Manual

• Deformable models

• 3-D region growing/mathematical morphology

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

Representing shape

• Geometric constraint networks

• Set of local constraints

• Interact together to generate a global shape description

Constraint Network

Vi (Vi1, Vi2,…)

Vj (Vj1, Vj2,…)

Cij

Geometric Constraint Network

Vi (Vi1, Vi2,…)

Vj (Vj1, Vj2,…)

Cij

Radial contour modelStructural component

Ri [Ri,inner … Ri,outer ]

Rj [Rj,inner, Rj,outer ]

Cij

Radial contour modelShape component

Ri

Rj

Cij = [Ri/Rjmin … Ri/Rjmax]

Constraint Propagation

Radial surface model

Radial surface model neighbors

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

Mid-sagittal plane

Anterior Commissure

Posterior commissure

Cortical bounding box

Initial model

Initial model - end-on

Initial model - lateral view

Propagation from poles

Define one radial

Propagation from one radial

Error

Correct error

Generate mask

Generate mask

Error in mask

Generate mask

Generate isosurface

Extract veins

Mask veins

Vein isosurface

Extract arteries

Mask arteries

Artery isosurface

Vessels

All

Map

WorkflowSelectPatient

Align

SegmentCortex

SegmentVeins

SegmentArteries

Map

FindEnvelope

MaskVolume

Iso-Surface

SelectModel

DefineLandmarks

Propagate & Search

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 ) ) )

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

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