Revision as of 15:47, 3 November 2008

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Stochastic Tractography Progress

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

A - Development of tractography workflow

 :* 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

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 (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

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 algorithm to go in

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, 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

@@ Line 8: / Line 8: @@
 ; A - Development of tractography workflow :
-:*  DWI image loading
+:*  DWI image preprocessing
+  :* denoising
+  :* Eddy currents corrections
 :*  WM mask & ROIs creation
 :*  tensor estimation & visualization (this step is somewhat hidden)
@@ Line 25: / Line 27: @@
 == Updates/Progress ==
 ; A - Development of tractography workflow :
-:* initial skeleton incorporating already existing stochastic tractography components
+:* initial skeleton incorporating already existing stochastic tractography components (in progress)
-:* test Slicer GUI access with python
+:* 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 :
 :* 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 algorithm to go in
+:*
 ; C – Study of limit cases (tract reconstruction issue) :