1. Spring Meeting 2007 mBIRN Related Activities In 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.  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 NA-MIC - Kikinis

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