Stochastic Tractography Progress

Status

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

To get the latest module 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)

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)

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