QueryAtlas

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QueryAtlas
Steve Pieper, Greg Brown, David Kennedy, Maryanne
Martone, Jyl Boline, Burak Ozyurt, Wendy
Plesniak, Michael Halle, Anna Tang, and Florin
Talos
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QueryAtlas a Slicer3 module
The Query Atlas is a 3D Slicer module that uses
atlas-based anatomical representations, linked to
underlying semantic descriptions, as an
interactive 3D spatial reference for viewing
experimental results and for performing
information searches to study and interpret them.
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Slicer3

• Slicer3
• Cross-Platform Integrated Visualization and
  Analysis Structure / Function
• Multi-Site Development BWH, MIT, GE, Kitware,
  Isomics, UCSD, JHU, MGH
• Multi-Project Scope fBIRN, mBIRN, NAC, NA-MIC,
  NCIGT, RO1s
• Impact
• fBIRN and mBIRN Informatics (XNAT) and Data
  (XCEDE) Compatibility
• Leverage Active Dissemination and Training
  Efforts of Partner Grants

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Slicer3

• Slicer3 Complete re-design using
  Community-centered approach
• Considers user experience for diverse
  community
• End-users of the desktop application
• Developers working on core software, using
  different programming styles
• Contributors of algorithms who want a
  light-weight API

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Slicer3
GUI designed with input from application
scientists for improved usability
Toolbar with module navigation
Module GUI panel
Slice viewer control
3D viewer control
Status progress
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QueryAtlas Overview

• Use the QueryAtlas to
• Load volumetric analyses from XCEDE compliant or
  XNAT databases
• Visualize volumes, models and parametric map
  overlays.
• Annotate models and labelmaps with anatomy labels
• Formulate queries in the context of particular
  study results (fMRI activations or group
  statistics, for example)
• View and manage collections of query results

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QueryAtlas Overview

• Target Audiences
• Neuroscientists Address Information Overload
  with Ontology-Aware Tools
• Tool Builders Provide Reference Implementation
  of XCEDE Compliant Application Software
• Non-Specialists Educational Tool and Compelling
  Demonstration of Data Richness
• Leverages Cross-Testbed BIRN Resources

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QueryAtlas Overview

• Complete QueryAtlas Xcede 2.0 Catalog
• To support BIRN research, the QueryAtlas is Xcede
  2.0 catalog compliant. A complete QueryAtlas
  Xcede catalog describes and contains uris for
• an anatomical volume (brain.mgz)
• results of a FreeSurfer morphological analysis (
  a label map, aparcaseg.mgz and models, lh.pial
  and/or rh.pial)
• the model's annotataion overlay (lh.aparc.annot
  and/or rh.aparc.annot) derived from the
  anatomical
• results of the FIPS processing (an
  example_functional.nii dataset and brain
  activation statistics volume datasets of
  interest, zstatX.nii, zfstatX.nii) and
• a FreeSurfer matrix (anat2exf.register.dat) to
  register the anatomical to the example functional
  volume.
• The anatomical volume, the example functional
  volume and the matrix that registers them in
  FreeSurfer are required when the catalog is
  parsed in order to compute the registration
  matrix in Slicer's coordinate system that
  correctly aligns all statistics volumes with the
  scene's anatomical information.

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QueryAtlas Overview
Relationship to BIRN informatics efforts
distortion correction tools
acquisition protocols
local databases
PubMed
(.xcat)
XNAT
visualization Interpretation (Slicer3/QueryAtlas
)
(.xar)
IBVD
. . .
workflows analysis tools
BrainInfo
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Supported data

• Currently, the QueryAtlas supports
• Annotated FreeSurfer datasets (aparcaseg.mgz,
  lh/rh.aparc.annot)
• Xcede 2.0 catalog .xcat files for fBIRN
  FIPS/FreeSurfer data
• XNAT archive .xar files for mBIRN Qdec data
• Can be extended to include other atlas-based
  annotated label maps or model files (requires
  extending readers and data handling methods, and
  the controlled vocabulary)

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Overview
Supported workflows
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Interface Overview
1. Scene loading and Annotation setup 2.
Annotation and Display options 3. Ontology
Mapping and Browsing 4. Define Search Terms 5.
Build queries, View Manage and Save Results
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Bookmark file read/write for Firefox
Set Mozilla Firefox 2 location through the
Application Settings Interface
View -gt ApplicationSettings -gt Slicer Settings
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Loading Qdec data

• Load an XNAT .xar archive from command-line,
• or load a .qdec file from the GUI
• Set up annotations
• Select among
• population statistics overlays

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Interactive annotations on Qdec data
way-finding with interactive annotations on the
FreeSurfer inflated brain mapped with different
population statistics
Does the correlation between thickness and Left
NonWM Hypointensities differ from zero?
Does the average thickness differ from zero?
Does the average thickness differ from zero?
click to play movie
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Loading FIPS/FreeSurfer data
(XCEDE 2.0 catalog descriptions)

• Close any currently loaded scene.
• Load an XCEDE catalog (.xcat file)
• from command-line or from the GUI
• (example phII BIRN SIRP paradigm, combined
  morphology and functional analyses)
• Set up Slice layers for convenient display
• Set up annotations

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Loading FIPS/FreeSurfer data
(XCEDE 2.0 catalog descriptions)

• Select among brain activation overlays included
  in the catalog (zstat.nii, zfstat.nii)

C7 C14 C17
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Loading FIPS/FreeSurfer data
(Go to Volumes Module to control data display)

• Select brain as the active volume, and set its
  threshold to Auto
• Select each statistics
• file as the active
• volume and set its
• threshold and window/
• level to adjust the
• display appropriately
• Navigate back to the QueryAtlas

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Interactive annotations
Combined structural image data and functional
statistics informed by local or formal anatomical
annotations

• In the annotation and Display Options GUI Panel,
  select the termset used for annotations
• Toggle LH and RH model visibility
• In the three Slice Viewers, toggle Slice Plane
  visibility

click to play movie
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Controlled vocabulary

• Extensible mechanism for linking atlas-based
  labels in various local naming systems to
  symantically compatible terms used in the larger
  biomedical informatics community
• CSV format files, leverages current BIRNLex
  ontology and mapping to other termsets and
  NeuroNames resources from BrainInfo
• Specifically provides mapping between local
  termsets (FreeSurfer) and BIRNLex, NeuroNames,
  UMLS, IBVD
• Extensible to include other local and formal
  termsets
• Distributed with Slicers QueryAtlas module
• TBD Authoring/editing policy and mechanisms,
  means of tracking BIRNLex changes

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Features Quick translation search
3D Viewers Context menu (right click) provides a
quick jump to ontology mapping and quick search.
Ontology Mapping structure term selection
panel Controlled vocabulary leverages current
BIRNLex ontology and mapping to other termsets
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Features SPL Ontology browser
3D Viewers Context menu launches SPL Ontology
Browser if local term maps to BIRNLex term or
NeuroNames term (requires Java 1.5) Interactive
tree view of BIRNLex and NeuroNames structures
entry
matching terms
f.o.v
Tree view pan, zoom, expand, collapse
info
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Features SPL Ontology browser

• SPL Ontology browser
• information visualization tool
• written in Java using Jython scripting language
• based on open-source Prefuse toolkit
• contains subset of BIRNlex ontology (root
  Regional part of Organ)
• contains all of NeuroNames, including synonyms
• converted to JSON format for simplified parsing
  and better human readability
• NeuroNames CSV file to JSON is python script
• BIRNlex to JSON uses Jython and Jena ontology
  toolkit
• Slicer sends commands using a socket-based
  mechanism
• (Currently, communication is one-way)

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Features Detailed search
Select terms of interest and pass to structure
search terms in the Search Terms GUI panel
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Features Detailed search

• Select among structure terms to use
• Specify additional (group, species, other) terms
  
• Select search target, and inspect resulting
  links
• Reserve and accumulate useful links

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Features Detailed search

• Save useful links to Firefox bookmark file (or
  load past results)

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Example data more information

• FIPS/FreeSurfer example dataset
• http//wiki.na-mic.org/Wiki/index.php/Slicer3Modu
  leQueryAtlasExample_data
• Qdec example dataset
• http//www.na-mic.org/Slicer/Download/Data/TEST4.q
  dec
• Simple tutorial describing features and use
• http//wiki.na-mic.org/Wiki/index.php/Slicer3Modu
  leQueryAtlas

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Future work

• Ability to query richer information repositories
  and infrastructure using available web services
• Information display tools for intuitive
  inspection and integrated comprehension of search
  results (images, data tables, text)
• Tools for transacting with BIRN HID and other
  XCEDE-compliant data resources
• Extending software and controlled vocabulary to
  include new atlas information
• Adding experimental natural language parsing
  tools for query formulation
• Developing mechanisms for tracking BIRNLex and
  approach to community authoring and editing of
  controlled vocabulary

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Acknowledgement
This research was supported by Grant 5 MOI RR
000827 to the FIRST BIRN and Grant 1 U24 RR021992
to the FBIRN Biomedical Informatics Research
Network (BIRN, http//www.nbirn.net), that is
funded by the National Center for Research
Resources (NCRR) at the National Institutes of
Health (NIH). This work was also supported by
NA-MIC, NAC, NCIGT. NeuroNames ontology and URI
resources are provided courtesy of BrainInfo,
University of Washington.