Morphometry BIRN:Imaging Calibration

Analysis ToolsData Sharing

Imaging Calibration

Structural Data Calibration Effort

• 5 subject, 5 site, 2 session data posted

• Cortical thickness paper published

• Skull stripping paper published

• De-identification paper in press

• Two reproducibility manuscripts in preparation

Imaging Calibration

Diffusion Tensor Imaging Data Calibration Effort

• Single subject, 3 session, 45 scan ~ posted

• 61 normal controls ~ posted

• Single-site variability study completed

• Multi-site variability study ready to go

• “BIRN-approved” protocol underway

DTI Calibration Study: DW Scheme

QUESTION: Which diffusion weighting scheme should you use and why?

TAKE HOME POINT: Use a scheme with many directions ( ~ 30) to get uniform precision and accuracy at all

fiber orientations. BUT…Effect size is small (less than intra and inter scan variability)

ENDPOINT: Paper submitted October 2006

Tools - Image Distortion Correction

• Gradient unwarping of structural data workflow

• DTI eddy-current correction code posted,sequences available for GE, Siemens

• Landmark LDDMM software manuscript in review

Tools – Gradient Unwarping

Portal Version

Tool – Databases

• Open source release

• Additional XNAT sites

• Simplified deployment (BIRN-CC, VMware)

• Integration with end user tools (ex. Slicer)

• Additional features (DICOM, web services, pipelines, compatibility with BIRN-CC

infrastructure)

Duke NIRL Hosted MIRIAD Datahttp://nirlarc.duhs.duke.edu

MIRIAD data in both XNAT and HID

Tools - FreeSurfer

•Subcortical segmentations, •Integration with 3D-Slicer•Automated filling of ventricles and basal ganglia, •Improved skull-stripping and cutting plane definition, •New parcellation (Desikan-Killiany), •Surface-based General Linear Model analysis

Tools - BIRN Query Atlas in Slicer3

• Re-Architecture of the QueryAtlas

– Advanced Label Features Built-In

– Real-Time Interaction with Labels

– “Right Click” on Models and Images to Initiate Queries

– Based on NA-MIC Software Engineering Methodology

– Anatomy-Based Access to Web Resources

• Integrates with BIRN IT Efforts

– Auto Convert and Load BIRN Data

• Leverages mBIRN Data Formats and Analysis (FreeSurfer)

• fBIRN is Building Functional QueryAtlas Integrated with mBIRN QueryAtlas

Tools - CATNAP

GOAL: To simplify and accelerate DTI &

anatomical data processing

HOW IT WORKS: Coregistration with FSL FLIRT Computes DTI gradient table Computes diffusion tensor and

DTI contrasts

DETIALS: Runs in MATLAB Philips data only (so far)

http://www.nbirn.net/downloads/

MBIRN Facilitations: Longitudinal Analysis

UCI - a new Siemens 1.5T after a GE 1.5T: Replicate longitudinal analyses from Han, et al. 2006

Han X, Jovicich J, Salat D, van der Kouwe A, Quinn B, Czanner S, Busa E, Pacheco J, Albert M, Killiany R, Maguire P, Rosas D, Makris N, Dale A, Dickerson B, Fischl B. Reliability of MRI-derived measurements of human cerebral cortical thickness: the effects of field strength, scanner upgrade and manufacturer. Neuroimage. 2006 Aug 1;32(1):180-94. Epub 2006 May 2.

Freesurfer reconstruction using Han’s longitudinal program

Acquire Global mean thickness values and surface thickness measures for variability comparisons

??

BIRN-enabled Collaborations - VETSA

• Vietnam Era Twin Registry (VETSA)– mBIRN Acquisition

• MRI sequences (MGH/UCSD sites)

– mBIRN Image Analysis Workflow• QC of raw data• FreeSurfer cerebral segmentation & QC• FreeSurfer cortical surface reconstruction &

parcellation & QC• Databasing and statistics with clinical information

– Heritability (twin method) statistics • Implemented on cortical surface • Modeling for ROIs in progress

Preliminary Findings of Cortical Heritability (VETSA)

Right HemisphereLeft Hemisphere

Regions in brighter color suggests a stronger genetic component.

The Future… IT

• SRB enabling of tools

– Download pre-existing SRB data into applications

– Applications run on the Apps Server withPortal Interface

– Construct Federated Data Repository of Large Data Sets