All Hands Meeting 2005 AVI Update Morphometry BIRN Analysis, Visualization, and Interpretation
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
Timeline from mBIRN Application AimYear 1Year 2Year 3Year 4Year 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
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
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
Shape Analysis Algorithm and Computation Efforts Progressing Need Clinical Application Targets Need Visualization Use Cases
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
DTI - Interoperability VETSA Datasets 35-Gradient DWI Acquisitions FreeSurfer Analysis of Each Subject ~300 Twin Pairs Needs: Atlas Registration Clinical Hypotheses
Visualization - Interoperability FreeSurfer / Slicer Integration Training Sessions for FreeSurfer Users Held At: MGH BWH BIRN AHM UCSD Collaboration with NA- MIC
Query Atlas Status: Gray Matter Onotology Integration Internet Brain Volume Database Integration To Do: Further Integration with White Matter, Atlases Packaging for Wider Use
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).
Timeline from mBIRN Application AimYear 1Year 2Year 3Year 4Year 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