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All Hands Meeting 2005 Morphometry BIRN - Overview - Scientific Achievements.

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1 All Hands Meeting 2005 Morphometry BIRN - Overview - Scientific Achievements

2 Scientific Goal Methods Support multi-site structural MRI clinical studies or trials Multi-site MRI calibration, acquisition and analysis Integrate advanced image analysis and visualization tools Sites (9) MGH, BWH, Duke, UCLA, UCSD, UCI, JHU, Wash U, MIT Morphometry BIRN: Overview human neuroanatomical data  clinical data correlates Diseases: Unipolar Depression, Alzheimer’s, Mild Cognitive Impairment

3 Multi-site MRI Calibration Integrate Analysis & Visualization Tools Data Management Processing Workflows Morphometry BIRN: Domain Areas Application Cases http://nbirn.net/Publications/Brochures/index.htm fBIRN Mouse BIRN BIRN CC HID XNAT DB Workflows (LONI/Kepler)

4 Morphometry BIRN: manuscripts MacFall et al., Lobar distribution of lesion volumes in late-life depression (Neuropsychopharmacology, submitted) Fennema-Notestine et al., Quantitative evaluation of automatic skull stripping methods (Human Brain Mapping, 2005) Neu et al., The LONI debabeler: a mediator for neuroimaging software (NeuroImage, 2005) Chen et al., Fast correction for direction-dependent distortions in DTI (NeuroImage, in press) Jovicich et al., Reliability in multi-site structural MRI studies: unwarping effects (NeuroImage, in press) Bischoff-Grethe, A Technique for the Deidentification of Structural Brain MRI (NeuroImage, submitted) Farrell et al., Signal to noise ratio effects on fractional anisotropy reproducibility from DTI (to be submitted 2005) Mouse – Morphometry BIRN paper Technical development papers: Ali et al., Automated segmentation of neuroanatomical structures in multispectral mouse MRI (NeuroImage, 2005) Clinical application papers: Han et al., Reliability of MRI-derived measurements of cerebral cortical thickness (NeuroImage, submitted) Fennema-Notestine et al., Multi-site clilnical structural neuroimaging data of legacy data (to be submitted 2005) Beg et al, Pattern classification of hippocampal shape analysis in a study of AD (to be submitted 2006) Marcus et al., The OASIS Project: a publicly available human brain imaging data resource (submitted)

5 Morphometry BIRN: manuscripts MacFall et al., Lobar distribution of lesion volumes in late-life depression (Neuropsychopharmacology, submitted) Fennema-Notestine et al., Quantitative evaluation of automatic skull stripping methods (Human Brain Mapping, 2005) Neu et al., The LONI debabeler: a mediator for neuroimaging software (NeuroImage, 2005) Chen et al., Fast correction for direction-dependent distortions in DTI (NeuroImage, in press) Jovicich et al., Reliability in multi-site structural MRI studies: unwarping effects (NeuroImage, in press) Bischoff-Grethe, A Technique for the Deidentification of Structural Brain MRI (NeuroImage, submitted) Farrell et al., Signal to noise ratio effects on fractional anisotropy reproducibility from DTI (to be submitted 2005) Mouse – Morphometry BIRN paper Technical development papers: Ali et al., Automated segmentation of neuroanatomical structures in multispectral mouse MRI (NeuroImage, 2005) Clinical application papers: Han et al., Reliability of MRI-derived measurements of cerebral cortical thickness (NeuroImage, submitted) Fennema-Notestine et al., Multi-site clilnical structural neuroimaging data of legacy data (to be submitted 2005) Beg et al, Pattern classification of hippocampal shape analysis in a study of AD (to be submitted 2006) Marcus et al., The OASIS Project: a publicly available human brain imaging data resource (submitted)

6 Morphometry BIRN Calibration: Cortical thickness reproducibility across MRI system upgrade Global Thickness variability: Group results (5 subjects) Sonata-Sonata Sonata-Avanto Avanto-Avanto Thickness variability maps: Group results (lh) ~ 6% ~ 3.5%

7 Optimal image can be synthesized from original echo images for better visualization of subcortical structures External Pallidum Internal Pallidum Thalamus To help skull-stripping mBIRN Calibration: sample multi-echo FLASH results Enlarged inset

8 Morphometry BIRN: manuscripts MacFall et al., Lobar distribution of lesion volumes in late-life depression (Neuropsychopharmacology, submitted) Fennema-Notestine et al., Quantitative evaluation of automatic skull stripping methods (Human Brain Mapping, 2005) Neu et al., The LONI debabeler: a mediator for neuroimaging software (NeuroImage, 2005) Chen et al., Fast correction for direction-dependent distortions in DTI (NeuroImage, in press) Jovicich et al., Reliability in multi-site structural MRI studies: unwarping effects (NeuroImage, in press) Bischoff-Grethe, A Technique for the Deidentification of Structural Brain MRI (NeuroImage, submitted) Farrell et al., Signal to noise ratio effects on fractional anisotropy reproducibility from DTI (to be submitted 2005) Mouse – Morphometry BIRN paper Technical development papers: Ali et al., Automated segmentation of neuroanatomical structures in multispectral mouse MRI (NeuroImage, 2005) Clinical application papers: Han et al., Reliability of MRI-derived measurements of cerebral cortical thickness (NeuroImage, submitted) Fennema-Notestine et al., Multi-site clilnical structural neuroimaging data of legacy data (to be submitted 2005) Beg et al, Pattern classification of hippocampal shape analysis in a study of AD (to be submitted 2006) Marcus et al., The OASIS Project: a publicly available human brain imaging data resource (submitted)

9 MGH Segmentation De-identification And upload JHU Shape Analysis of Segmented Structures BIRN Virtual Data Grid BWH Visualization Scientific Goal: correctly classify patient status from morphometric results 1 2 3 4 5 Teragrid N=45 Data Donor Site (WashU) Technical Goal: seamless integration of tools and data flow during processing Morphometry BIRN: Shape Analysis Pipeline Overview

10 Shape Analysis  Algorithm and Computation Efforts Progressing  Need Clinical Application Targets  Need Visualization Use Cases

11 21 control subjects 18 Alzheimer subjects 6 semantic dementia subjects Shape-derived metrics can be used to detect class-specific information Morphometry BIRN: Shape Analysis Pipeline Results

12 Morphometry BIRN: manuscripts MacFall et al., Lobar distribution of lesion volumes in late-life depression (Neuropsychopharmacology, submitted) Fennema-Notestine et al., Quantitative evaluation of automatic skull stripping methods (Human Brain Mapping, 2005) Neu et al., The LONI debabeler: a mediator for neuroimaging software (NeuroImage, 2005) Chen et al., Fast correction for direction-dependent distortions in DTI (NeuroImage, in press) Jovicich et al., Reliability in multi-site structural MRI studies: unwarping effects (NeuroImage, in press) Bischoff-Grethe, A Technique for the Deidentification of Structural Brain MRI (NeuroImage, submitted) Farrell et al., Signal to noise ratio effects on fractional anisotropy reproducibility from DTI (to be submitted 2005) Mouse – Morphometry BIRN paper Technical development papers: Ali et al., Automated segmentation of neuroanatomical structures in multispectral mouse MRI (NeuroImage, 2005) Clinical application papers: Han et al., Reliability of MRI-derived measurements of cerebral cortical thickness (NeuroImage, submitted) Fennema-Notestine et al., Multi-site clilnical structural neuroimaging data of legacy data (to be submitted 2005) Beg et al, Pattern classification of hippocampal shape analysis in a study of AD (to be submitted 2006) Marcus et al., The OASIS Project: a publicly available human brain imaging data resource (submitted)

13 BIRN Virtual Data Grid 1 MGH Freesurfer segmentations 2 BIRN CC Portal Multi-site data queries and statistics Access to visualization and interpretation tools Web AD Project Data Flow 1) Retrospective data upload from UCSD and MGH sites 2) Semi-automated subcortical segmentation (MGH) 3) From any participating site: query, statistical analysiand visualization of the data through the BIRN Portal 3 UCSD Human Imaging DB Data Upload MGH Human Imaging DB 3 3 UCSD N=125 BWH/MGH N=118 MGH Archives UCSD Archives Morphometry BIRN: Multi-site Alzheimer’s Disease Overview

14 Morphometry BIRN: Multi-site Alzheimer’s Disease Results Diagnostic classification of multi-site healthy vs AD Linear and quadratic discriminant analysis applied Classification success rate on test data 90%. Hippocampal volume loss in normal aging from multi-site healthy data Multi-site legacy data, if properly matched and calibrated, can be combined

15 Morphometry BIRN: manuscripts MacFall et al., Lobar distribution of lesion volumes in late-life depression (Neuropsychopharmacology, submitted) Fennema-Notestine et al., Quantitative evaluation of automatic skull stripping methods (Human Brain Mapping, 2005) Neu et al., The LONI debabeler: a mediator for neuroimaging software (NeuroImage, 2005) Chen et al., Fast correction for direction-dependent distortions in DTI (NeuroImage, in press) Jovicich et al., Reliability in multi-site structural MRI studies: unwarping effects (NeuroImage, in press) Bischoff-Grethe, A Technique for the Deidentification of Structural Brain MRI (NeuroImage, submitted) Farrell et al., Signal to noise ratio effects on fractional anisotropy reproducibility from DTI (to be submitted 2005) Mouse – Morphometry BIRN paper Technical development papers: Ali et al., Automated segmentation of neuroanatomical structures in multispectral mouse MRI (NeuroImage, 2005) Clinical application papers: Han et al., Reliability of MRI-derived measurements of cerebral cortical thickness (NeuroImage, submitted) Fennema-Notestine et al., Multi-site clilnical structural neuroimaging data of legacy data (to be submitted 2005) Beg et al, Pattern classification of hippocampal shape analysis in a study of AD (to be submitted 2006) Marcus et al., The OASIS Project: a publicly available human brain imaging data resource (submitted)

16 All Hands Meeting 2005 Morphometry BIRN Tool Dissemination

17 Recommendation for MRI acquisition protocols Software Processing and Visualization Tools MRI data Tutorials Morphometry BIRN: Tool Dissemination Domains for public dissemination

18 Recommendation for MRI acquisition protocols Scanner Upgrade Calibration Protocol: http://www.na-mic.org/Wiki/index.php/MGH-BWH_Mini-BIRN_Standard_Upgrade_Protocol GE/Siemens diffusion MRI acquisition with phase maps Software Processing and Visualization Tools: Gradient non-linearities distortion correction code Distortion correction code for DTI (Bo and eddy currents effects) Tool for de-identifying structural MRI Freesurfer: tool for automated segmentation of neuroanatomical structures LDMM: tool for shape analyses LONI Pipeline: tool for controlling processing workflows 3D Slicer: visualization tool MRI data: Open Access Structural Imaging Series Multi-site mBIRN calibration study (5 subjects, 5 sites, 2 visits) DTI calibration data (2 subjects scanned multiple times) Tutorials: 3D Slicer and Freesufer (Thu Oct 20) Morphometry BIRN: Tool Dissemination

19 Recommendation for MRI acquisition protocols Scanner Upgrade Calibration Protocol: http://www.na-mic.org/Wiki/index.php/MGH-BWH_Mini-BIRN_Standard_Upgrade_Protocol GE/Siemens diffusion MRI acquisition with phase maps Software Processing and Visualization Tools Gradient non-linearities distortion correction code Distortion correction code for DTI (Bo and eddy currents effects) Tool for de-identifying structural MRI Freesurfer: tool for automated segmentation of neuroanatomical structures LDMM: tool for shape analyses LONI Pipeline: tool for controlling processing workflows 3D Slicer: visualization tool MRI data: Open Access Structural Imaging Series Multi-site mBIRN calibration study (5 subjects, 5 sites, 2 visits) DTI calibration data (2 subjects scanned multiple times) Tutorials: 3D Slicer and Freesufer (Thu Oct 20) Morphometry BIRN: Tool Dissemination

20 Uncorrected ImagesCorrected Images Siemens Sonata (1.5T) Siemens AC88 (7T) Morphometry BIRN: gradient unwarping code

21 Recommendation for MRI acquisition protocols Scanner Upgrade Calibration Protocol: http://www.na-mic.org/Wiki/index.php/MGH-BWH_Mini-BIRN_Standard_Upgrade_Protocol GE/Siemens diffusion MRI acquisition with phase maps Software Processing and Visualization Tools Gradient non-linearities distortion correction code Distortion correction code for DTI (Bo and eddy currents effects) Tool for de-identifying structural MRI Freesurfer: tool for automated segmentation of neuroanatomical structures LDMM: tool for shape analyses LONI Pipeline: tool for controlling processing workflows 3D Slicer: visualization tool MRI data: Open Access Structural Imaging Series Multi-site mBIRN calibration study (5 subjects, 5 sites, 2 visits) DTI calibration data (2 subjects scanned multiple times) Tutorials: 3D Slicer and Freesufer (Thu Oct 20) Morphometry BIRN: Tool Dissemination

22 Distortion corrections with phase-maps for each diffusion-encoding direction Morphometry BIRN: DTI correction code http://wiki.na-mic.org/Wiki/index.php/Mbirn:_B0_and_eddy_current_correction_code_for_diffusion_MRI

23 Recommendation for MRI acquisition protocols Scanner Upgrade Calibration Protocol: http://www.na-mic.org/Wiki/index.php/MGH-BWH_Mini-BIRN_Standard_Upgrade_Protocol GE/Siemens diffusion MRI acquisition with phase maps Software Processing and Visualization Tools Gradient non-linearities distortion correction code Distortion correction code for DTI (Bo and eddy currents effects) Tool for de-identifying structural MRI Freesurfer: tool for automated segmentation of neuroanatomical structures LDMM: tool for shape analyses LONI Pipeline: tool for controlling processing workflows 3D Slicer: visualization tool MRI data: Open Access Structural Imaging Series Multi-site mBIRN calibration study (5 subjects, 5 sites, 2 visits) DTI calibration data (2 subjects scanned multiple times) Tutorials: 3D Slicer and Freesufer (Thu Oct 20) Morphometry BIRN: Tool Dissemination

24 Morphometry BIRN: defacing code http://wiki.na-mic.org/Wiki/index.php/Mbirn:_Defacer_for_structural_MRI

25 Recommendation for MRI acquisition protocols Scanner Upgrade Calibration Protocol: http://www.na-mic.org/Wiki/index.php/MGH-BWH_Mini-BIRN_Standard_Upgrade_Protocol GE/Siemens diffusion MRI acquisition with phase maps Software Processing and Visualization Tools Gradient non-linearities distortion correction code Distortion correction code for DTI (Bo and eddy currents effects) Tool for de-identifying structural MRI Freesurfer: tool for automated segmentation of neuroanatomical structures LDMM: tool for shape analyses LONI Pipeline: tool for controlling processing workflows 3D Slicer: visualization tool MRI data: Open Access Structural Imaging Series Multi-site mBIRN calibration study (5 subjects, 5 sites, 2 visits) DTI calibration data (2 subjects scanned multiple times) Tutorials: 3D Slicer and Freesufer (Thu Oct 20) Morphometry BIRN: Tool Dissemination

26 Freesurfer (MGH) (surfer.nmr.mgh.harvard.edu) 3D Slicer (BWH) (www.slicer.org )www.slicer.org LDMM JHU (www.cis.jhu.edu/software/ldmm )www.cis.jhu.edu/software/ldmm LONI Pipeline (UCLA) (www.loni.ucla.edu )www.loni.ucla.edu Morphometry BIRN: supported tools

27 Recommendation for MRI acquisition protocols Scanner Upgrade Calibration Protocol: http://www.na-mic.org/Wiki/index.php/MGH-BWH_Mini-BIRN_Standard_Upgrade_Protocol GE/Siemens diffusion MRI acquisition with phase maps Software Processing and Visualization Tools Gradient non-linearities distortion correction code Distortion correction code for DTI (Bo and eddy currents effects) Tool for de-identifying structural MRI Freesurfer: tool for automated segmentation of neuroanatomical structures LDMM: tool for shape analyses LONI Pipeline: tool for controlling processing workflows 3D Slicer: visualization tool MRI data Open Access Structural Imaging Series Multi-site mBIRN calibration study (5 subjects, 5 sites, 2 visits) DTI calibration data (2 subjects scanned multiple times) Tutorials: 3D Slicer and Freesufer (Thu Oct 20) Morphometry BIRN: Tool Dissemination

28 Open Access Structural Imaging Series project www.oasis-brains.org Rich structural & functional MRI dataset (WashU) Open access user agreement means free & unrestricted use of data Part I (November, 2005): 400 cross-sectional acquisitions across lifespan, including 100 demented individuals Extensions throughout 2006: longitudinal, DTI, fMRI, calibration…

29 The OASIS project Data set includes 3-4 raw T1- weighted scan, averaged, atlas- registered, and FSL- segmented. Data can be searched, downloaded, and viewed via the web site.

30 Recommendation for MRI acquisition protocols Scanner Upgrade Calibration Protocol: http://www.na-mic.org/Wiki/index.php/MGH-BWH_Mini-BIRN_Standard_Upgrade_Protocol GE/Siemens diffusion MRI acquisition with phase maps Software Processing and Visualization Tools Gradient non-linearities distortion correction code Distortion correction code for DTI (Bo and eddy currents effects) Tool for de-identifying structural MRI Freesurfer: tool for automated segmentation of neuroanatomical structures LDMM: tool for shape analyses LONI Pipeline: tool for controlling processing workflows 3D Slicer: visualization tool MRI data Open Access Structural Imaging Series Multi-site mBIRN calibration study (5 subjects, 5 sites, 2 visits) DTI calibration data (2 subjects scanned multiple times) Tutorials 3D Slicer and Freesufer (Thu Oct 20) Morphometry BIRN: Tool Dissemination

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