All Hands Meeting 2005

Morphometry BIRN- Overview- Scientific Achievements

• 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 datacorrelates

Diseases: Unipolar Depression, Alzheimer’s, Mild Cognitive Impairment

Multi-site MRI

Calibration

Integrate Analysis &

Visualization Tools

Data Management

Processing Workflows

Morphometry BIRN: Domain Areas

Application Caseshttp://nbirn.net/Publications/Brochures/index.htm

• fBIRN• Mouse BIRN• BIRN CC

HID

XNAT

DB

Workflows (LONI/Kepler)

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)

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)

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%

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

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)

MGH Segmentation

De-identificationAnd upload

JHUShape Analysis

of Segmented Structures

BIRNVirtual

Data Grid

BWHVisualization

Scientific Goal: correctly classify patient status from

morphometric results

1

2

3

4

5

Teragrid

N=45

Data DonorSite (WashU)

Technical Goal: seamlessintegration of tools and

data flow during processing

Morphometry BIRN: Shape Analysis Pipeline Overview

Shape Analysis

Algorithm and Computation Efforts Progressing Need Clinical Application Targets Need Visualization Use Cases

21 control subjects18 Alzheimer subjects 6 semantic dementia subjects

Shape-derived metrics can be used to detect class-specific information

Morphometry BIRN: Shape Analysis Pipeline Results

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)

BIRNVirtual Data

Grid

1

MGH Freesurfer

segmentations

2

BIRN CC PortalMulti-site data queries

and statisticsAccess to visualization and interpretation tools

0.3 0.4 0.5 0.6 0.7 0.8 0.9 1.0CVLT Discriminability Score

1000

2000

3000

4000

5000

6000

Le

ft H

ipp

oca

mp

al V

olu

me

BWH/MGH and UCSD Data

WebWeb

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

UCSDHuman Imaging

DB

Data Upload

MGHHuman Imaging

DB

3 3

UCSDN=125

BWH/MGHN=118

MGHArchives

UCSDArchives

Morphometry BIRN: Multi-site Alzheimer’s Disease Overview

UCSDMGH/BWH

WashU

Site

60 70 80 90

AGE

2000

3000

4000

5000

Lef

t-H

ipp

oca

mp

us

Hippocampal Volume Loss in Normal Aging

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

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)

All Hands Meeting 2005

Morphometry BIRN Tool Dissemination

• Recommendation for MRI acquisition protocols

• Software Processing and Visualization Tools

• MRI data

• Tutorials

Morphometry BIRN: Tool Dissemination

Domains for public dissemination

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

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

Uncorrected Images Corrected Images

Siemens Sonata(1.5T)

Siemens AC88(7T)

Morphometry BIRN: gradient unwarping code

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

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

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

Morphometry BIRN: defacing code

http://wiki.na-mic.org/Wiki/index.php/Mbirn:_Defacer_for_structural_MRI

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

Freesurfer (MGH) (surfer.nmr.mgh.harvard.edu)

3D Slicer (BWH)(www.slicer.org )

LDMM JHU(www.cis.jhu.edu/software/ldmm )

LONI Pipeline (UCLA)(www.loni.ucla.edu )

Morphometry BIRN: supported tools

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

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…

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.

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