mBIRN Related Activities In and Around BWH

Spring Meeting 2007 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 - PowerPoint PPT Presentation

Transcript of mBIRN Related Activities In and Around BWH

Spring Meeting 2007

mBIRN Related ActivitiesIn and Around BWH

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…

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

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

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

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


Hata, Liu,



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)


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

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


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!

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,



FreeSurfer Models and Volumes handled as built-in types

Scalar Overlays and Lookup Tables Supported

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


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


Leverages FreeSurfer and Informatics Interoperability

Interactive Data Exploration for mBIRN and fBIRN

Ongoing Ontology Tie-in Work and Workflow Development


Can be ported to Slicer3• Delayed pending development of mBIRN policy for


Command line tools for DICOM Header Deidentification publicly available and documented

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

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