Summary of current issues:

Working on segmenting T1 and T2 images from Simon to export to MATLAB and try to quantify difference in tumour spread for boundary.  

1. Need a different tool?  Check is FSL or MRTrix will do it, but I think they will only make a mask and brain extraction for diffusion data?  
2. analysis of the data in MATLAB, converting scalar field to meaning
3. differentiating between tumour and (say) bone of other dense material with same image value.
4. Maybe using FreeSurfer and/or 3D Slicer to do segmentatin and extraction.

Growing tumours:

Have found optimal values for stable solutions generally seem to exist at around Stability condition =  0.02 or thereabouts. Can simulate tumours quite effectively when parameters are right.

Simulation issues:  

1. Need to confirm how anisotropic the in vivo tumours are, scaling anisotropy appears to make things 'jagged' but still more like a spiky ball as opposed to strictly following any structures.  Investigate this further and visually compare with images.