1. All Hands Meeting 2005 AVI Update Morphometry BIRN Analysis, Visualization, and Interpretation

2. Aims Reminder: Adapt and Apply  Segmentation Protocol Specific Protocol Neutral Defacing Protocol Specific QA  Shape Analysis Interoperability with Segmentation Port to Grid Shape-Based Metrics In-Context Visualization  Diffusion Analysis Interoperability with Segmentation Forebrain Atlas Atlases to Improve Tractography Expert Review of Automated Tractography  Integrated Visualization Integration with Data Grid and Informatics Combined Structure, Connectivity, Population  Query Atlas Numerical/Ontological Linkage Interactive Composite Queries Visualization of Query Results  Machine Learning Hypothesis Generation Integrate a priori hypotheses Hypothesis Visualization Portal Integration

3. Timeline from mBIRN Application AimYear 1Year 2Year 3Year 4Year 5 2.1 Segmentation and Parcellation Face Segmenter for Deidentification Grid Enabled AnalysisQA Tools; Portal Integration Integration with DTI Tools Large-Scale Application to Clinical Collaborator Data 2.2 Shape AnalysisMultiple Sub-structure Analysis Grid Portal Enabled Analysis DTI RegistrationHemisphere AnalysisFull-brain Analysis 2.3 DTI AnalysisDeploy Current DTI Tools to Clinical Sites Define DTI File Formats for Scans and Results; Reliability Analysis Expert Atlas Construction Integrate Atlases with Morphometry Tools Comparison and Refinement of Automated Tractography; Tensor STAPLE 2.4 VisualizationShape Analysis Visualization DTI Tractography Visualization Parallel VisualizationGrid Enabled Visualization Integrated Population Visualization 2.5 Query AtlasIntegration of Gray Matter Ontologies White Matter Ontologies Cellular Imaging Queries Genomic / Proteomic Queries Integrated Multi-Scale / Multi-Species 2.6 Machine LearningRefine Models for BIRN Data Hypothesis Generation Tool Incorporation of a priori Hypotheses Visualization of Hypotheses Integrated Portal- Based Tool

4. Segmentation and Parcellation  FreeSurfer being applied widely to multi-site data analysis (WashU, VETSA…)  New Protocol-Neutral EMSegment tools integrated in Slicer (see next slide)  Defacing Manuscript Prepared, Reviewed by Co- Authors  Segmentation QA Proceeding in Close Collaboration with Calibration

5. Protocol Neurtral Segmentation Example  “UK Brothers” Case UCI/MGH/BWH collaboration  Routine Clinical Protocol not optimized for segmentation  Enlarged Ventricles Captured by Joint Registration/Segmentation difficult to capture by registration alone

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

7. DTI Analysis - Atlas  JHU (Mori) Multi- Subject White Matter Labeled Tensor Atlas Available in Slicer  Improved Atlases in Development Labels – JHU Tracts – UCI  Registration Techniques being Tested/Refined

8. DTI - Interoperability  VETSA Datasets 35-Gradient DWI Acquisitions FreeSurfer Analysis of Each Subject ~300 Twin Pairs  Needs: Atlas Registration Clinical Hypotheses

9. Visualization - Interoperability  FreeSurfer / Slicer Integration Training Sessions for FreeSurfer Users Held At:  MGH  BWH  BIRN AHM UCSD Collaboration with NA- MIC

10. Query Atlas  Status: Gray Matter Onotology Integration Internet Brain Volume Database Integration  To Do: Further Integration with White Matter, Atlases Packaging for Wider Use

11. Machine Learning  Very General Classification Program Available Binary/ASCII Multi- Subject Input Output is Classifier Function Installed at MGH (Golland, Fischl) Available for Other Sites  To Do: Identify Clinical Scenarios MIT to Work with Sites to Adapt and Test Normal Control Examples Schizophrenia Patients Examples Detected Shape Differences. The differences are represented as a deformation of a normal hippocampus (from blue - inwards defomration, to green - no deformation, to red - outward deformation).

12. Timeline from mBIRN Application AimYear 1Year 2Year 3Year 4Year 5 2.1 Segmentation and Parcellation Face Segmenter for Deidentification Grid Enabled AnalysisQA Tools; Portal Integration Integration with DTI Tools Large-Scale Application to Clinical Collaborator Data 2.2 Shape AnalysisMultiple Sub-structure Analysis Grid Portal Enabled Analysis DTI RegistrationHemisphere AnalysisFull-brain Analysis 2.3 DTI AnalysisDeploy Current DTI Tools to Clinical Sites Define DTI File Formats for Scans and Results; Reliability Analysis Expert Atlas Construction Integrate Atlases with Morphometry Tools Comparison and Refinement of Automated Tractography; Tensor STAPLE 2.4 VisualizationShape Analysis Visualization DTI Tractography Visualization Parallel VisualizationGrid Enabled Visualization Integrated Population Visualization 2.5 Query AtlasIntegration of Gray Matter Ontologies White Matter Ontologies Cellular Imaging Queries Genomic / Proteomic Queries Integrated Multi-Scale / Multi-Species 2.6 Machine LearningRefine Models for BIRN Data Hypothesis Generation Tool Incorporation of a priori Hypotheses Visualization of Hypotheses Integrated Portal- Based Tool