Difference between revisions of "AHM2010:DiffusionDatatypesBreakout"
From NAMIC Wiki
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| − | Agenda | + | '''Agenda''' |
*How should the NAMIC-Kit handle new upcoming diffusion datatypes? | *How should the NAMIC-Kit handle new upcoming diffusion datatypes? | ||
*Discussion of | *Discussion of | ||
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** File formats for interoperability of analysis tools | ** File formats for interoperability of analysis tools | ||
| − | Overall Conclusions | + | '''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 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. | * All attendees agree vtkPolyData for fibers, and nrrd for volumes, are sufficiently generic to store all datatypes we can imagine. | ||
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* Lauren O'Donnell | * Lauren O'Donnell | ||
| − | Meeting Notes | + | '''Meeting Notes''' |
| − | DATA TYPES LIST (not exhaustive, includes data used by attendees and other well-known models) | + | '''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 | * 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 | *two-tensor or mixtures of tensors, of watson functions | ||
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*(various scalar measures from the above) | *(various scalar measures from the above) | ||
| − | FRAMEWORK IDEAS (to enable development of slicer visualization for new data) | + | '''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). | * 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 | * Everyone would like to use slicer to look at their data in future | ||
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** Model should ideally be used for volumes/models/fibers | ** Model should ideally be used for volumes/models/fibers | ||
| − | INTEROPERABILITY (file types for cross-program diffusion data I/O) | + | '''INTEROPERABILITY''' (file types for cross-program diffusion data I/O) |
*current file type is vtkPolyData - named arrays can tag datatypes for future datatype expansion. | *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 | *nrrd for volumes - for future, allows arbitrary strings/fields if we need to store metadata | ||
Revision as of 21:37, 6 January 2010
Home < AHM2010:DiffusionDatatypesBreakoutAgenda
- 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
Attendees
- Anuja Sharma
- Alex Yarmarkovitch
- Mahnaz Maddah
- Deepika Mahalingam
- Yundi Shi
- Zohara Cohen
- Martin Styner
- Gopal Veni
- James Malcolm
- Luke Bloy
- Lauren O'Donnell
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
