1. 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
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
Aim
Year 1
Year 2
Year 3
Year 4
Year 5
2.1 Segmentation and Parcellation
Face Segmenter for Deidentification
Grid Enabled Analysis
QA Tools; Portal Integration
Integration with DTI Tools
Large-Scale Application to Clinical Collaborator Data
2.2 Shape Analysis
Multiple Sub-structure Analysis
Grid Portal Enabled Analysis
DTI Registration
Hemisphere Analysis
Full-brain Analysis
2.3 DTI Analysis
Deploy 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 Visualization
Shape Analysis Visualization
DTI Tractography Visualization
Parallel Visualization
Grid Enabled Visualization
Integrated Population Visualization
2.5 Query Atlas
Integration of Gray Matter Ontologies
White Matter Ontologies
Cellular Imaging Queries
Genomic / Proteomic Queries
Integrated Multi-Scale / Multi-Species
2.6 Machine Learning
Refine 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: To Do: 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 To Do:
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
Aim
Year 1
Year 2
Year 3
Year 4
Year 5
2.1 Segmentation and Parcellation
Face Segmenter for Deidentification
Grid Enabled Analysis
QA Tools; Portal Integration
Integration with DTI Tools
Large-Scale Application to Clinical Collaborator Data
2.2 Shape Analysis
Multiple Sub-structure Analysis
Grid Portal Enabled Analysis
DTI Registration
Hemisphere Analysis
Full-brain Analysis
2.3 DTI Analysis
Deploy 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 Visualization
Shape Analysis Visualization
DTI Tractography Visualization
Parallel Visualization
Grid Enabled Visualization
Integrated Population Visualization
2.5 Query Atlas
Integration of Gray Matter Ontologies
White Matter Ontologies
Cellular Imaging Queries
Genomic / Proteomic Queries
Integrated Multi-Scale / Multi-Species
2.6 Machine Learning
Refine Models for BIRN Data
Hypothesis Generation Tool
Incorporation of a priori Hypotheses
Visualization of Hypotheses
Integrated Portal-Based Tool