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Stochastic Tractography Progress
Status
Stochastic tractography requires careful maintenance and on-going development improving its usability and performance.
- A - Development of tractography workflow
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- DWI image preprocessing
- denoising
- Eddy currents corrections
- WM mask & ROIs creation
- tensor estimation & visualization (this step is somewhat hidden)
- tracts reconstruction & visualization (should be useful to see tracts and not only the connectivity map)
- connectivity maps creation & visualization
- DWI image preprocessing
- B - Visualization of diffusion properties - test utilities
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- reveal more features related to diffusion - develop visualization
- finalize batch - testing different parameters of the stochastic tractography with different datasets - wrap up of the results
- C – Study of limit cases (tract reconstruction issue)
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- sensitivity to inputs (WM/ROIs) if exist - needing criteria definition and algorythmic extensions
- further algorythmic extensions if needed for dealing with specific reconstruction cases (tracts with multiple branches)
Updates/Progress
- A - Development of tractography workflow
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- initial skeleton incorporating already existing stochastic tractography components (in progress)
- test Slicer GUI access with python (done)
- implement tractography algorythm in python (based on Ola Friman Matlab implementation) (done)
- test based on sample dataset show identical computational results between Matlab and python implementation (done)
- B - Visualization of diffusion properties
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- create visual map showing regions defined by WM mask where FA (fractional anisotropy is upper the defined threshold e.g. 0.3) and where the mask forbids (defining as a non white matter region) the stochastic algorythm to go in
- C – Study of limit cases (tract reconstruction issue)
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- relate C to B
Schedule
- 08/2008 - Introduction to tractography, Slicer software, articles related to tractography.
- 09/2008 - Setup of Slicer3, first tests with stochastic tractography, algorythm implementation, work with training datasets
- 10/2008 - Introduction of python interpreter for implementation of batch utility + diffusion features visualization
- 11/2008 - Completion of batch utility, testing for NAMIC meeting preparation, tractography workflow first prototype ready
- 12/2008 - wrap up, finalization of NAMIC meeting presentation for the stochastic tractography module