AHM2010:DiffusionDatatypesBreakout

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 of new diffusion datatypes in future. They agree Slicer3 generic data model should enable plugins of new data for diffusion visualization. This will be very useful. Suggested approach is below in meeting notes.
• 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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