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

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Presentation transcript:

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

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 V i (V i1, V i2,…) V j (V j1, V j2,…) C ij

Geometric Constraint Network V i (V i1, V i2,…) V j (V j1, V j2,…) C ij

Radial contour model Structural component R i [R i,inner … R i,outer ] R j [R j,inner, R j,outer ] C ij

Radial contour model Shape component RiRi RjRj C ij = [Ri/Rj min … Ri/Rj max ]

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

Error in mask

Generate mask

Generate isosurface

Extract veins

Mask veins

Vein isosurface

Extract arteries

Mask arteries

Artery isosurface

Vessels

All

Map

Workflow Select Patient Align Segment Cortex Segment Veins Segment Arteries Map Find Envelope Mask Volume Iso- Surface Select Model Define Landmarks Propagate & Search

Workflow Architecture Select Patient Align Segment Cortex Segment Veins Segment Arteries Map

Spatial Knowledge 3-D Models Images 3-D Maps Symbolic Model Builder Visual Brain Mapper Authoring Programs Spatial Information Internet Experiment Manager End User Web Interfaces Brain Map Visualizer Analyzer Graphics Server Knowledge Server Structural Information Servers Repository Manager Symbolic Knowledge 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