Progress:

Monday July 06:

Working on anisotropy measures and visualisation of data. 

The simulation runs well now, I need to collect a new lot of data sets with the new boundary that includes the falx, but these can be ran as needed.

Exploration of the isosurface function in MATLAB has been productive, and 3D visualisation techniques have been explored and movies rendered.  

Dr Yonghui Li has provided me with a data set of processed tractography and given me a tutorial on how to do this myself, although I have not yet done so, nor was I able to open the data on my immediate attempt this morning.  

Next steps will be to explore the tractographic data and imaging tools associated with this and to produce a real anisotropy quantitative measure. 

Anisotropy:

A 2D toy model using a random grid was easily able to be implemented, however I have not yet been able to extend this to the 3D isosurface data produced.  

Tasks:  

1. Get a quantitative measure for the anisotropy of an isosurface.
2. Get a measure for total cell concentration within a given isosurface.
3. Measure the volume of the isosurface to compare with the surface area as a measure of smoothness.