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mBIRN Related Activities In and Around BWH

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

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mBIRN Related Activities In and Around BWH

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  1. mBIRN Related ActivitiesIn and Around BWH

  2. BWH Activities and mBIRN • Interconnected Research Efforts • Critical Mass for Infrastructure • Shared Engineering • Research Synergy • Transitional Research • Multiple Targets • Basic Neuroscience, Neurodegeneration, Neuropsychiatric Diseases, Oncology (Brain, Prostate), Targeted Therapy, Intra-operative Robotics…

  3. Surgical Planning Laboratory - Kikinis • Umbrella Organization Providing Infrastructure for Several Researchers and Laboratories • LMI (Westin), CNI (Guttmann), PNL (Shenton), IGT (Jolesz, Wells, Hata)… • Dedicated Laboratory Space • Drop-In Facilities • Training / Meeting Space • High Performance Computing • “Fat Nodes” • Cluster • EMC Disk Array • Multi-Site Fiber, Scanner, and OR Network

  4. NA-MIC - Kikinis • National Alliance for Medical Image Computing • An NIH Roadmap National Center for Biomedical Computing (NCBC) U54 • http://www.na-mic.org • Focus Areas • Algorithm Development • Software Engineering Methodology • Driving Biological Projects • Relies on BIRN for Informatics Infrastructure • “No Strings Attached” Open Source

  5. NCIGT - Jolesz • National Center for Image Guided Therapy • NCRR / NIBIB / NCI U41 • http://www.ncigt.org • Procedures Enhanced by Imaging and Computation • Neurosurgery • Prostate • Cardiac • Focused Ultrasound • Sample Projects • Real Time MR Parallel Imaging • Non-rigid Brain Deformation Monitoring and Simulation • MR Guided Cardiac Ablation

  6. Slicer for IGT • Modular Image Guided Therapy System • Multiple Tracked Instruments • Real Time Imaging + Pre-Op • Intra-Operative Support for Advanced Algorithms • fMRI, DTI, Tractography Resection Guidance • Control of Surgical Robotics • Slicer3 Effort Builds of Experience of Over 1000 Slicer-Guided Craniotomies Courtesy Hata, Liu, Archip, Wells

  7. NAC - Kikinis • Neuroimage Analysis Center • NCRR P41 • http://spl.harvard.edu/nac • Image Post Processing Resources • Novel Algorithms • Integrated Tools • Sophisticated Atlases • Close Collaborations • fMRI Informatics (Wells) • White Matter Architecture (Westin) • Anatomy (Talos) • Visualization (Halle) • Engineering (Pieper) • Time Series (Meier)

  8. Slicer3 • Common Platform • Optimize Engineering Resources • Avoid Duplication of Effort • Leverage Best Practices • Ensure Compatibility • Algorithm -> Laboratory -> Bedside • Improved Architecture • Modules can be used as plugins or executables • BSD-style Open Source License • Ongoing Maintenance, Training Through NA-MIC and Others

  9. How the Pieces Fit (Big Picture) • Mathematics, Algorithm Development, Engineering • NAC (Core Team), NA-MIC (National Collaboration) • Informatics, Calibration, Networking, Databases, Grid • BIRN • Translational Efforts • NCIGT – Surgery and Intervention • fBIRN – Schizophrenia • mBIRN – AD, Depression • NA-MIC DBPs – Schizophrenia, Autism, Prostate, Lesions

  10. Questions…

  11. Slicer3 Usability • Clean, Unified GUI Design • Wendy Plesniak (BWH) and Sebastien Barre (Kitware) • Developed in Close Collaboration with User Community and Trainers • Unified Cross Platform Behavior, Easy Installers • Undo/Redo, Tooltips, Drag ‘n’ Drop… • New Logo!

  12. mBIRN Slicer Goals • Ensure mBIRN Slicer functionality stays current with new Slicer version • FreeSurfer Interoperability • DTI Analysis and Visualization • Provenance • QueryAtlas • BIRNDUP • Protocol Neutral Segmentation (EM Segmenter) • Informatics Interoperability (XNAT, Portal, Grid, Workflows)

  13. FreeSurfer • FreeSurfer Models and Volumes handled as built-in types • Scalar Overlays and Lookup Tables Supported

  14. DTI Analysis and Visualization • Under Active Development but not yet ready • Expected by late 2007 • Developed with NA-MIC, NAC, LMI, and NCIGT • Applications in Image Guided Neurosurgery will Help Drive Development

  15. Provenance • Built in from beginning of Slicer3 • Track Cross-Platform Issues • Windows (XP and soon Vista) • Mac OSX (PPC and X86) • Linux (32 and 64 bit) • Being Integrated with Slicer3 Execution Model • Parameters developed with interactive Slicer environment • Modules can run as independent batch jobs on cluster or grid using those parameters

  16. QueryAtlas • Leverages FreeSurfer and Informatics Interoperability • Interactive Data Exploration for mBIRN and fBIRN • Ongoing Ontology Tie-in Work and Workflow Development

  17. BIRNDUP • Can be ported to Slicer3 • Delayed pending development of mBIRN policy for defacing • Command line tools for DICOM Header Deidentification publicly available and documented

  18. Protocol Neurtral Segementation • EM Segmenter being ported to Slicer3 by MIT and Kitware • Tutorial held January 2007 in Utah • Documentation on the Web • Additional development ongoing • Slicer2 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 Women’s Hospital. Algorithm by Kilian Pohl, MIT/BWH/Isomics

  19. XNAT / Informatics Integration • Current Status: • Query/Browse for Data at XNAT Site (oasis-brains.org) • Download XAR (zip) from XNAT • Tell Browser to “Open With…” Slicer3 • Images Available for Visualization and Analysis • Next Steps • Manifest / Data Description files / XCEDE • FreeSurfer Datasets, DTI Datasets in XNAT • Upload of Processed Data • Direct Database Interface (Improve download performance) • Generalize for BDR

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