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Interfacing processing and visualization tools: FIPS to Slicer3 and the QueryAtlas

Interfacing processing and visualization tools: FIPS to Slicer3 and the QueryAtlas. Goals for 3D Slicer fBIRN Query Atlas. Rich Data Exploration Environment Functional / Structural 3D Visualization Morphometry Results: Surface/Volume ROIs Access to Experiment Data (HID)

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Interfacing processing and visualization tools: FIPS to Slicer3 and the QueryAtlas

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  1. Interfacing processing and visualization tools: FIPS to Slicer3 and the QueryAtlas

  2. Goals for 3D Slicer fBIRN Query Atlas • Rich Data Exploration Environment • Functional / Structural 3D Visualization • Morphometry Results: Surface/Volume ROIs • Access to Experiment Data (HID) • Subject ID, Demographics, Diagnoses… • Acquisition Paradigms • Analysis Design, Contrasts… • Data Analysis Provenance • Scientific Literature and Web Searches • Data Loaded by Queries • BIRN DBs • Local Cache / Analysis Directories

  3. Versions of QueryAtlas • First Version in Slicer2 • Multiple ROI Search Terms • Web Targets • UMLS, Talaraich, FreeSurfer Anatomy Terms • Drawbacks • Awkward Programming Interface • Slow Response to Selections • Not Tightly Integrated with Application • No Link to BIRN Study Databases • Now Being Reimplemented in Slicer3 • New Programming Model • Better Performance • Explicit Links to BIRN Informatics

  4. Overall Pipeline HID FIPS FIPS2MRML Query Atlas Local disk Visualization screenshot Tools to Streamline Retrieval of FIPS Processing Data for Visualization and Analysis

  5. Information & Infrastructure for FIPS Users HID FIPS FIPS2MRML Query Atlas Local disk USE: • Environment Variables for FIPS FreeSurfer and Slicer • known directory structure for BIRN and FreeSurfer Data • automatically generated FIPS files (fips.database.dat, FSBIRNID.dat)

  6. Searches based on keyword, value HID FIPS FIPS2MRML Query Atlas Local disk • User specifies search criteria • Currently returns matches for BIRN FirstLevel analysis datasets on local disk • (Same principles can be used to query HID) • Generates Slicer MRML scenes (Medical Reality Markup Language – XML description) • FIPS2MRML Included with QueryAtlas in Slicer3 Development Version

  7. Searches based on keyword, value HID FIPS FIPS2MRML Query Atlas Local disk Visualization screenshot • Scene loaded into Slicer3 • Query Atlas used to visualize FIPS and FreeSurfer analyses: (brain.mgz, aparc+aseg.mgz, lh.pial, zstat volumes) • Query using user keywords and anatomical context • Interactive Exploration

  8. Prototype QueryAtlas in Slicer3 • Direct Access to Anatomical Labels • Hardware Assisted Anatomy Picking • Context Menu Access • Quick Access to Searches • Build Complex Queries • Integrated with Modernized Slicer Architecture

  9. Objectives for Next Iteration of Query Atlas • Collect and Implement User Scenarios • Integration with BIRN Databases • FIPS2MRML tie to HID, SRB • Incorporate Terms for Paradigm, Diagnosis… • Improved Ontologies • Gray and White Matter • Experiment and Subject Information • Suitable for Literature Searches • Refine Coordinate Systems • Functional / Structural • First Level / Group (linear, nonlinear, flattened) • Group Level Analysis

  10. Timeline for QueryAtlas • Leverage Slicer3 efforts of Collaborations • NAC, NA-MIC plan for Slicer3 Release in January, 2007 • mBIRN Query Atlas with Freesurfer Interoperability in Slicer3, March 2007 • Slicer3-based fBIRN QueryAtlas release for next fBIRN Meeting, April 2007 • Identify User Scenarios at this Meeting • Determine Target Implementation Features

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