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)

• 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

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

Overall Pipeline

HID

Local disk

FIPS FIPS2MRML Query Atlas

Visualization screenshot

Tools to Streamline Retrieval ofFIPS Processing Data forVisualization and Analysis

Information & Infrastructure for FIPS Users

HID

Local disk

FIPS FIPS2MRML Query Atlas

• Environment Variables for FIPS FreeSurfer and Slicer• known directory structure for BIRN and FreeSurfer Data• automatically generated FIPS files (fips.database.dat, FSBIRNID.dat)

USE:

Searches based on keyword, value

HID

Local disk

FIPS FIPS2MRML Query Atlas

• 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

Searches based on keyword, value

HID

Local disk

FIPS FIPS2MRML Query Atlas

• 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

Visualization screenshot

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

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

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