morphometry birn bruce rosen, m.d. ph.d.. scientific goal methods –multi-site mri calibration,...
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Morphometry BIRN
Bruce Rosen, M.D. Ph.D.
• Scientific Goal
• Methods– Multi-site MRI calibration, acquisition– Integrate advanced image analysis and visualization tools– Data structures to support multi-site structural MRI clinical studies or
trials
• Sites (9) MGH, BWH, Duke, UCLA, UCSD, UCI, JHU, Wash U, MIT
Morphometry BIRN: Overview
Human neuroanatomical data Clinical datacorrelates
Initial Disease Targets:
Unipolar Depression, Alzheimer’s, Mild Cognitive Impairment
“Typical” Imaging Study
Processing
Data Storage
Courtesy: Dan Marcus (WUSTL)
Image Acquisition Investigator
MultiCenter Imaging Study
Non-imaging measures
Other databases
Processing & applications
Collaborators
Data sharing
Central Database
Courtesy: Dan Marcus (WUSTL)
Image Acquisition Investigators
Data Flow Framework
Data Acquisition
Database ManagementDiscover!
Analyze
Visualize
mBIRN Data Flow Framework
Data Acquisition
Database ManagementDiscover!
Analyze
Visualize
Morphometry & DTI
Protocols
LONIPipeline
Workbench
FreesurferQDEC
LDDMM
3-D SlicerMRI StudioBDRXNAT
Data Acquisition
Database ManagementDiscover!
Analyze
Visualize
ls
LONIPipeline
Workbench
FreesurferQDEC
LDDMM
3-D SlicerMRI StudioBDRXNAT
mBIRN Data Flow Framework
Morphometry & DTI
Protocols
Imaging Protocols
Multi-site Structural MRI Data Acquisition & Calibration
Methods: common acquisition protocols, distortion correction, evaluation by scanning human phantoms multiple times at all sites, on GE, Siemens and Philips scanners.
CorrectedUncorrected
Image intensity variability onsame subject scanned at 4 sites(red is > 8% intensity difference)
Goal: develop acquisition & calibration protocols that improve reproducibility, within- and across-sites and platforms, for both
structural and diffusion tensor imaging.
Contact: protocols and distortion corrections softwarecan be obtained from http://www.nbirn.net.Karl Helmer
Data Acquisition
Database ManagementDiscover!
Analyze
Visualize
LONIPipeline
Workbench
FreesurferQDEC
LDDMM
3-D SlicerMRI StudioBDRXNAT
mBIRN Data Flow Framework
Morphometry & DTI
Protocols
mBIRN Analysis Tools
FreeSurfer Automated Segmentation and Parcellation of Brain
StructuresNick Schmansky (MGH)
LDDMMShape Analysis
of Segmented StructuresMichael Miller, Anthony Kolasny (JHU)
QDECGroup Statistical Analysis
of MRI DataNick Schmansky (MGH)
Data Acquisition
Database ManagementDiscover!
Analyze
Visualize
LONIPipeline
Workbench
FreesurferQDEC
LDDMM
3-D SlicerMRI StudioBDRXNAT
mBIRN Data Flow Framework
Morphometry & DTI
Protocols
Workflows
mBIRN Workbench:• Platform independent – java based• Modular environment• Contains a database, +XNAT • Customize to run own applicationsContact: Michael Mendez (MGH)
LONI Pipeline:• Graphical environment; customizable• Includes a diverse set of applications• Parallelizes automatically• Local- and server-based versionsContact: Arthur Toga (LONI)
Data Acquisition
Database ManagementDiscover!
Analyze
Visualize
LONIPipeline
Workbench
FreesurferQDEC
LDDMM
3-D SlicerMRI StudioBDRXNAT
mBIRN Data Flow Framework
Morphometry & DTI
Protocols
mBIRN Visualization Tools
3D Slicer3D Slicer is a multi-platform, free open-source
software for visualization and image computing.Contact: Steve Pieper (BWH)
MRI StudioAllows the Visualization and Analysis of MRI and Diffusion Tensor Imaging
Data – supports LDDMM Contact: Anthony Kolasny(JHU)
mBIRN Data Flow Framework
Data Acquisition
Database ManagementDiscover!
Analyze
Visualize
LONIPipeline
Workbench
FreesurferQDEC
LDDMM
3-D SlicerMRI StudioBDRXNAT
Morphometry & DTI
Protocols
Databases
eXtensible Neuroimaging
Archive Toolkit (XNAT)
• Web application built on an extensible relational / XML database; supports custom tables
• Interoperable with BIRN Data Grid, BDR and fBIRN HID• Interoperable with end-user toolsContact: Dan Marcus, Tim Olsen (WUSTL)
mBIRN Data Flow Framework
Data Acquisition
Database ManagementDiscover!
Analyze
Visualize
LONIPipeline
Workbench
FreesurferQDEC
LDDMM
3-D SlicerMRI StudioBDRXNAT
Morphometry & DTI
Protocols
Application of the mBIRN Tools – MM Project
MGH FreeSurfer
Segmentation
Data DonorSite (WashU)
De-identificationAnd upload
JHUMathematical
Morphometry Project
BIRN DataRepository
BWH3D Slicer
Visualization
Goal: comparison and quantification of structure’s
shape and volumetric differences across patient
populations
1
2
3
4
5
Teragrid
N=45
• Data: 46 hippocampus data sets (2070 comparisons)• Each LDDMM comparison takes about 3 to 8 hours
Improved computational capabilities
Single PC TeraGrid
• 1 comparison • ~431 days
• 60 comparisons simultaneously• ~7 days
MM Project – Use of the TeraGrid
Discover!
1 . 5
2
2 . 5
3
3 . 5
0mm
1.25mm
displacement2.5mm
Results show the ability to differentiate two discinct classes of dementia patients from normal controls using the LDDMM Shape Analysis
BIRN Hypothesis
• Enabling Sharing will Engender Sharing
Links to Further Information
Principal Investigator – Bruce Rosen ([email protected])Project Manager - Karl Helmer ([email protected])
ProtocolsImaging Protocols: http://www.nbirn.net
WorkflowsLONI Pipeline: http://www.loni.ucla.edu/pipeline/Partners Workbench: [email protected]
DatabaseXNAT: http://www.xnat.org/
Analysis and VisualizationFreeSurfer / QDEC : http://surfer.nmr.mgh.harvard.edu/3D Slicer: http://www.slicer.org/MRI Studio: https://www.mristudio.org/LDDMM: http://cis.jhu.edu/software/ldmm/about.htmlDistortion Correction for DTI: http://www.nbirn.net
Karl Helmer mBIRN Project Manager