2010 CCA Retreat

Introduction

This is a one-day retreat for the clinical computational anatomy project of NAC. The purpose is to review the state of this project, learn about related external ontological efforts, and formulate strategic plans for the rest of the funding cycle.

Date and Location:

• June 18 2010
• 1249 Boylston St. 2nd floor demo room
• Start at 8.30

Agenda

Introduction

• CCA specific aims: See non-public Feb 2010 presentation
• MRI image-based atlas
  • Structural data and rough segmentation on pubdb
  • DWI needs to be re-acquired
  • Anatomical Hierarchy still in development
• linking imaging and ontological data
  • model hierarchy from February no longer being used
  • new label map color table being used to drive the model naming and hierarchy
  • some freesurfer labels are not well defined or organized
• brain function ontology
• data visualization

Current Progress

• 2009-10 brain atlas (Ron Kikinis, Michael Halle, Daniel Rubin)
  • data acquisition
  • labeling
  • thalamus labeling

• naming and color assignment
  • wiki-based slicer color files
  • CCA brain hierarchy
  • new default slicer LUT

• extracting data from ontologies
  • JSONTO data format and embedded sqlite database
  • FMA, RadLex, NIFstd conversion
  • example uses

• Ontology visualization
  • java-based ontology visualization tool (Jim Miller)

• Integration with Slicer
  • QueryAtlas (Steve Pieper)

Discussion

• Current state of relevant ontologies and tools (Daniel Ruben)

• Making ontologies useable
  • How do we factor out complete and useful information from relevant ontologies and present it do developers/researchers/users?
  • How can this information be integrated into the Slicer/NA-MIC infrastructure?
    • JSONTO reader
    • VTK infovis
    • Query atlas extensions
    • Segmentation
  • What's the best way to encourage researchers to use and create knowledge in machine-readable format?
  • (Your questions here!)

Final discussion and wrap up

• Possible Anatomist Collaborators

Participants

• Ron Kikinis
• Michael Halle
• Florin Talos
• Daniel Rubin
• Jim Miller
• Steve Pieper
• Wendy Plesniak
• Nicole Aucoin
• Dominik Meier