Varying cell growth rates, as discussed the tumour appears to be growing far too quickly c.f. clinical examples.  Bottom figure, varying anisotropy by 50% from baseline did not make a noticeable difference.   Bottom code was generated by saving variables after running BrainSim code then loading them inside a new short script as discussed.

Meeting with Zoltan 31/03/2015

Minor Tasks:

1. Run simulation series for different anisotropies, cell growth rates
2. Compare these with papers, values look too high at the moment
3. read biology papers for 2. also (if time).
4. MATLAB: data structures, functions vs scripts, saving variables and data.
5. Plots of series
6. Slices corresponding to time points where tumour is in growth region of interest.

Major Task:

• Write code for calculating 'Centre of mass' of tumour.

0 /leq C(ijk) /leq 1 where C(ijk) is the tumour concentration in voxel ijk

Rcn = (1/N)* Sigma r(ijk) (C(ijk)/K)

r(ijk) = [i-1, j-1, k-1]dx

dx = voxel length

Currently in main loop, voxels labelled m,n,p as i,j,k coords, use this to create r vector then multiply by concentration at voxel i,j,k. 
Try initially using a for loop.  Once this is working, look for more elegant solutions?

• Keep data separated from main code, save variables for each differing parameter run in a labelled folder, call these in separate functions.

Notes for Will's PhD work following meeting 20/03/2015.

Tasks :

1. Plot concentration values for brain sim for varying parameters.
2. Write code to plot concsum=concsum1, concsum2 etc on same set of axes. 

• varying rho (cell growth rate parameter) either side of standard
• varying anisotropy (expecting no major deviation)

1.  Normalise concentration variable for plot, also for further use in 'Moment of inertia' style parameter for mean distance and max distance of tumour spread for varying anisotropy (future work)
2.  Automate labeling of plots
3. rescale time parameter into a real value (days?)
4. visualise 2-d slices corresponding to timepoints on the graph of concentration.
5. read off time point for t = concentration = 1/2 or 1/4 of carrying capacity and visualise slices for clinical correlation of meaningful time points.