mbirn related activities in and around bwh

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mBIRN Related Activities In and Around BWH. BWH Activities and mBIRN. Interconnected Research Efforts Critical Mass for Infrastructure Shared Engineering Research Synergy Transitional Research Multiple Targets - PowerPoint PPT Presentation


  • BWH Activities and mBIRNInterconnected Research EffortsCritical Mass for InfrastructureShared EngineeringResearch SynergyTransitional ResearchMultiple TargetsBasic Neuroscience, Neurodegeneration, Neuropsychiatric Diseases, Oncology (Brain, Prostate), Targeted Therapy, Intra-operative Robotics

  • Surgical Planning Laboratory - KikinisUmbrella Organization Providing Infrastructure for Several Researchers and LaboratoriesLMI (Westin), CNI (Guttmann), PNL (Shenton), IGT (Jolesz, Wells, Hata)Dedicated Laboratory SpaceDrop-In FacilitiesTraining / Meeting SpaceHigh Performance ComputingFat NodesClusterEMC Disk ArrayMulti-Site Fiber, Scanner, and OR Network

  • NA-MIC - KikinisNational Alliance for Medical Image ComputingAn NIH Roadmap National Center for Biomedical Computing (NCBC) U54http://www.na-mic.orgFocus AreasAlgorithm DevelopmentSoftware Engineering MethodologyDriving Biological ProjectsRelies on BIRN for Informatics InfrastructureNo Strings Attached Open Source

  • NCIGT - JoleszNational Center for Image Guided TherapyNCRR / NIBIB / NCI U41http://www.ncigt.orgProcedures Enhanced by Imaging and ComputationNeurosurgeryProstateCardiacFocused UltrasoundSample ProjectsReal Time MR Parallel ImagingNon-rigid Brain Deformation Monitoring and SimulationMR Guided Cardiac Ablation

  • Slicer for IGTModular Image Guided Therapy SystemMultiple Tracked InstrumentsReal Time Imaging + Pre-OpIntra-Operative Support for Advanced AlgorithmsfMRI, DTI, Tractography Resection GuidanceControl of Surgical RoboticsSlicer3 Effort Builds of Experience of Over 1000 Slicer-Guided CraniotomiesCourtesy Hata, Liu, Archip, Wells

  • NAC - KikinisNeuroimage Analysis CenterNCRR P41http://spl.harvard.edu/nacImage Post Processing ResourcesNovel AlgorithmsIntegrated ToolsSophisticated AtlasesClose CollaborationsfMRI Informatics (Wells)White Matter Architecture (Westin)Anatomy (Talos)Visualization (Halle)Engineering (Pieper)Time Series (Meier)

  • Slicer3Common PlatformOptimize Engineering ResourcesAvoid Duplication of EffortLeverage Best PracticesEnsure CompatibilityAlgorithm -> Laboratory -> BedsideImproved ArchitectureModules can be used as plugins or executablesBSD-style Open Source LicenseOngoing Maintenance, Training Through NA-MIC and Others

  • How the Pieces Fit (Big Picture)Mathematics, Algorithm Development, EngineeringNAC (Core Team), NA-MIC (National Collaboration)Informatics, Calibration, Networking, Databases, GridBIRNTranslational EffortsNCIGT Surgery and InterventionfBIRN SchizophreniamBIRN AD, DepressionNA-MIC DBPs Schizophrenia, Autism, Prostate, Lesions

  • Questions

  • Slicer3 UsabilityClean, Unified GUI DesignWendy Plesniak (BWH) and Sebastien Barre (Kitware)Developed in Close Collaboration with User Community and TrainersUnified Cross Platform Behavior, Easy InstallersUndo/Redo, Tooltips, Drag n DropNew Logo!

  • mBIRN Slicer GoalsEnsure mBIRN Slicer functionality stays current with new Slicer versionFreeSurfer InteroperabilityDTI Analysis and VisualizationProvenanceQueryAtlasBIRNDUPProtocol Neutral Segmentation (EM Segmenter)Informatics Interoperability (XNAT, Portal, Grid, Workflows)

  • FreeSurferFreeSurfer Models and Volumes handled as built-in typesScalar Overlays and Lookup Tables Supported

  • DTI Analysis and VisualizationUnder Active Development but not yet readyExpected by late 2007Developed with NA-MIC, NAC, LMI, and NCIGTApplications in Image Guided Neurosurgery will Help Drive Development

  • ProvenanceBuilt in from beginning of Slicer3Track Cross-Platform IssuesWindows (XP and soon Vista)Mac OSX (PPC and X86)Linux (32 and 64 bit)Being Integrated with Slicer3 Execution ModelParameters developed with interactive Slicer environmentModules can run as independent batch jobs on cluster or grid using those parameters

  • QueryAtlasLeverages FreeSurfer and Informatics InteroperabilityInteractive Data Exploration for mBIRN and fBIRNOngoing Ontology Tie-in Work and Workflow Development

  • BIRNDUPCan be ported to Slicer3Delayed pending development of mBIRN policy for defacingCommand line tools for DICOM Header Deidentification publicly available and documented

  • Protocol Neurtral SegementationEM Segmenter being ported to Slicer3 by MIT and KitwareTutorial held January 2007 in UtahDocumentation on the WebAdditional development ongoingSlicer2 version successfully used in MS Lesion segmentation Included in the current 3D Slicer 2.6 Applied to white matter lesion segmentation in Multiple Sclerosis. MPRAGE and FLAIR Available to support BELL Data courtesy Istvan Csapo, Charles Guttmann, Center for Neurological Imaging, Brigham and Womens Hospital. Algorithm by Kilian Pohl, MIT/BWH/Isomics

  • XNAT / Informatics IntegrationCurrent Status:Query/Browse for Data at XNAT Site (oasis-brains.org)Download XAR (zip) from XNATTell Browser to Open With Slicer3Images Available for Visualization and AnalysisNext StepsManifest / Data Description files / XCEDEFreeSurfer Datasets, DTI Datasets in XNATUpload of Processed DataDirect Database Interface (Improve download performance)Generalize for BDR