Transcript gbmimg 1081
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, webaccessible system • Optimized for language mapping Photo Visual Brain Mapper (VBM) Requirements for visualizationbased 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 skullstripping 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,…) Cij Vj (Vj1, Vj2,…) Geometric Constraint Network Vi (Vi1, Vi2,…) Cij Vj (Vj1, Vj2,…) Radial contour model Structural component Ri [Ri,inner … Ri,outer ] Cij Rj [Rj,inner, Rj,outer ] Radial contour model Shape component Ri Cij = [Ri/Rjmin … Ri/Rjmax] Rj 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 Workflow Select Model Align Find Envelope Define Landmarks Segment Cortex Mask Volume Propagate & Search Segment Veins IsoSurface Select Patient Segment Arteries Map Select Patient Align Segment Cortex Segment Veins Segment Arteries Map Workflow Architecture (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 ) ) ) End User Web Interfaces Authoring Programs Symbolic Model Builder Visual Brain Mapper Brain Map Visualizer Experiment Manager Analyzer Internet Knowledge Server Repository Manager Graphics Server Structural Information Servers Symbolic Knowledge Metadata Symbolic Information Images Spatial Knowledge 3-D Models Spatial Information 3-D Maps 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