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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.

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Presentation on theme: "Morphometry BIRN Bruce Rosen, M.D. Ph.D.. Scientific Goal Methods –Multi-site MRI calibration, acquisition –Integrate advanced image analysis and visualization."— Presentation transcript:

1 Morphometry BIRN Bruce Rosen, M.D. Ph.D.

2 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 data correlates Initial Disease Targets: Unipolar Depression, Alzheimer’s, Mild Cognitive Impairment

3 “Typical” Imaging Study Processing Data Storage Courtesy: Dan Marcus (WUSTL) Image Acquisition Investigator

4 MultiCenter Imaging Study Non-imaging measures Other databases Processing & applications Collaborators Data sharing Central Database Courtesy: Dan Marcus (WUSTL) Image Acquisition Investigators

5 Data Flow Framework Data Acquisition Database Management Discover! Analyze Visualize

6 mBIRN Data Flow Framework Data Acquisition Database Management Discover! Analyze Visualize Morphometry & DTI Protocols LONI Pipeline Workbench Freesurfer QDEC LDDMM 3-D Slicer MRI Studio BDRXNAT

7 Data Acquisition Database Management Discover! Analyze Visualize ls LONI Pipeline Workbench Freesurfer QDEC LDDMM 3-D Slicer MRI Studio BDRXNAT mBIRN Data Flow Framework Morphometry & DTI Protocols

8 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. Corrected Uncorrected Image intensity variability on same 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 software can be obtained from http://www.nbirn.nethttp://www.nbirn.net. Karl Helmer

9 Data Acquisition Database Management Discover! Analyze Visualize LONI Pipeline Workbench Freesurfer QDEC LDDMM 3-D Slicer MRI Studio BDRXNAT mBIRN Data Flow Framework Morphometry & DTI Protocols

10 mBIRN Analysis Tools FreeSurfer Automated Segmentation and Parcellation of Brain Structures Nick Schmansky (MGH) LDDMM Shape Analysis of Segmented Structures Michael Miller, Anthony Kolasny (JHU) QDEC Group Statistical Analysis of MRI Data Nick Schmansky (MGH)

11 Data Acquisition Database Management Discover! Analyze Visualize LONI Pipeline Workbench Freesurfer QDEC LDDMM 3-D Slicer MRI Studio BDRXNAT mBIRN Data Flow Framework Morphometry & DTI Protocols

12 Workflows mBIRN Workbench: Platform independent – java based Modular environment Contains a database, +XNAT Customize to run own applications Contact: Michael Mendez (MGH) LONI Pipeline: Graphical environment; customizable Includes a diverse set of applications Parallelizes automatically Local- and server-based versions Contact: Arthur Toga (LONI)

13 Data Acquisition Database Management Discover! Analyze Visualize LONI Pipeline Workbench Freesurfer QDEC LDDMM 3-D Slicer MRI Studio BDRXNAT mBIRN Data Flow Framework Morphometry & DTI Protocols

14 mBIRN Visualization Tools 3D Slicer 3D Slicer is a multi-platform, free open-source software for visualization and image computing. Contact: Steve Pieper (BWH) MRI Studio Allows the Visualization and Analysis of MRI and Diffusion Tensor Imaging Data – supports LDDMM Contact: Anthony Kolasny(JHU)

15 mBIRN Data Flow Framework Data Acquisition Database Management Discover! Analyze Visualize LONI Pipeline Workbench Freesurfer QDEC LDDMM 3-D Slicer MRI Studio BDRXNAT Morphometry & DTI Protocols

16 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 tools Contact: Dan Marcus, Tim Olsen (WUSTL)

17 mBIRN Data Flow Framework Data Acquisition Database Management Discover! Analyze Visualize LONI Pipeline Workbench Freesurfer QDEC LDDMM 3-D Slicer MRI Studio BDRXNAT Morphometry & DTI Protocols

18 Application of the mBIRN Tools – MM Project MGH FreeSurfer Segmentation Data Donor Site (WashU) De-identification And upload JHU Mathematical Morphometry Project BIRN Data Repository BWH 3D Slicer Visualization Goal: comparison and quantification of structure’s shape and volumetric differences across patient populations 1 2 3 4 5 Teragrid N=45

19 Data: 46 hippocampus data sets (2070 comparisons) Each LDDMM comparison takes about 3 to 8 hours Improved computational capabilities Single PCTeraGrid 1 comparison ~431 days 60 comparisons simultaneously ~7 days MM Project – Use of the TeraGrid

20 Discover! 0mm 1.25mm displacement 2.5mm Results show the ability to differentiate two discinct classes of dementia patients from normal controls using the LDDMM Shape Analysis

21 BIRN Hypothesis Enabling Sharing will Engender Sharing

22 Links to Further Information Principal Investigator – Bruce Rosen (bruce@nmr.mgh.harvard.edu) Project Manager - Karl Helmer (helmer@nmr.mgh.harvard.edu) Protocols Imaging Protocols: http://www.nbirn.net Workflows LONI Pipeline: http://www.loni.ucla.edu/pipeline/ Partners Workbench: snmurphy@partners.org Database XNAT: http://www.xnat.org/ Analysis and Visualization FreeSurfer / 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.html Distortion Correction for DTI: http://www.nbirn.net Karl Helmer mBIRN Project Manager

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