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Back to NA-MIC Collaborations, Harvard DBP 2, DBP2:Harvard:Brain_Segmentation_Roadmap

Stochastic Tractography Progress

Status

Stochastic tractography requires careful maintenance and on-going development improving its usability and performance. 

To get latest documentation goes on the link Slicer 3.4 documentation

A - Development of tractography workflow 

• DWI image preprocessing
  • denoising
  • Eddy currents corrections
• WM mask & ROIs creation
• tensor estimation & visualization
• tracts reconstruction & visualization (should be useful to see tracts and not only the connectivity map)
• connectivity maps creation & visualization

B - Visualization of diffusion properties - test utilities 

• 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) 

• 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 

• initial skeleton incorporating already existing stochastic tractography components (done)
• 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)
  • multiprocessing (and clustering) supported (done)
  • roi filtering from region A to region B and B to A (done)
• module release ready (done)
• bugfix (in progress)

B - Visualization of diffusion properties 

• 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 (done)

C – Study of limit cases (tract reconstruction issue) 

• 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
• 04/2009 - Module release ready for Slicer 3.4