AHM2010:DiffusionDatatypesBreakout

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Agenda

  • How should the NAMIC-Kit handle new upcoming diffusion datatypes?
  • Discussion of
    • Varieties of diffusion datatypes
    • Slicer data model for visualization of new datatypes
    • File formats for interoperability of analysis tools

Overall Conclusions

  • All attendees want to use Slicer3 for visualization in future. They agree Slicer3 generic data model should enable plugins of new data for diffusion visualization. This will be very useful.
  • All attendees agree vtkPolyData for fibers, and nrrd for volumes, are sufficiently generic to store all datatypes we can imagine.
  • See below for meeting notes.

Logistics:

  • Wednesday January 6, 12:30 pm - 1:30 pm
  • Location: Amethyst 1

Meeting Notes

DATA TYPES LIST (not exhaustive, includes data used by attendees and other well-known models)

  • real spherical harmonic coefficients: vectors but of varying lengths 6 to 100 components, tied to a basis
  • two-tensor or mixtures of tensors, of watson functions
  • mixture models in general
  • PAS vector of coefficients, basis
  • Gaussian mixture models - Fisher basis gaussian on sphere
  • ball and stick model (Tim Behrens)
  • probabilistic tracking -- scalar map
  • DSI - volumes full FT of signal
  • qball
  • (various scalar measures from the above)

FRAMEWORK IDEAS (to enable development of slicer visualization for new data)

  • Visualization issue: difficult to implement in current framework (Luke Bloy experience involved duplicating all code from tensors for spherical harmonics).
  • Everyone would like to use slicer to look at their data in future
  • Data Model Class Abstraction Idea
    • overloaded methods/ plugin idea
    • API for new data - how to view it in slicer
      • implement the following methods i.e. display node, scalar computation
      • at this point give me a glyph
      • at this point give me scalars that are relevant
    • Use polydata and add arrays to it for multicomponent data
    • Each data model class knows how to deal with its data
    • Model should ideally be used for volumes/models/fibers

INTEROPERABILITY (file types for cross-program diffusion data I/O)

  • current file type is vtkPolyData - named arrays can tag datatypes for future datatype expansion.
  • nrrd for volumes - for future, allows arbitrary strings/fields if we need to store metadata
  • Conclusion is these formats are sufficiently general and can remain the standard for NAMIC interoperability

Attendees

  • Anuja Sharma
  • Alex Yarmarkovitch
  • Mahnaz Maddah
  • Deepika Mahalingam
  • Yundi Shi
  • Zohara Cohen
  • Martin Styner
  • Gopal Veni
  • James Malcolm
  • Luke Bloy
  • Sonia Pujol
  • Lauren O'Donnell

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