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

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Interfacing processing and visualization tools
FIPS to Slicer3 and the QueryAtlas
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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

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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

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

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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

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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, aparcaseg.mgz,
  lh.pial, zstat volumes)
• Query using user keywords and anatomical context
• Interactive Exploration

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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

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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

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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