Mouse model instabilities 25/08/15

Progress: Simulations with conservative parameters of delta t have still been yielding unstable results.

As proliferation parameter rho is slowed down, the tumours look more real on the visualisation tools, to an extent.  They never grow to fill the whole brain, the ones that look solid even have an instability where they start shrinking and the concentration drops to zero, which implies an unstable data point somewhere in the tensor(?)

e.g.

The simulations are taking now 40+ minutes to run on my desktop PC and are becoming unrunnable apart from for time scales longer than about 23 days on my MacBook.

Data files are very large now due to the higher resolution so until I get stable solutions, I am just saving a record of the parameters I have varied with notes on how the solution behaved. 

Looking at the diffusion tensor variable Mean_Diff, surface plot of slice (:,:,101), I will try running simulations at around (40,40,101) which will be away from the two spikes, although they are only a factor of two or so larger than the surrounding points.

Mouse Brain Simulations part 1:

After meetings at CAI and separately with Nyoman I have been working on processing the mouse brain data to simulate some tumours.  Initial results were flawed, after  a second attempt, where I understood the orientation and data better, I have produced a first simulation.

The anisotropy and diffusion are very apparent in this, presumably due to the much higher resolution images and more defined tracts.

Next step will be to compare this to tractography and make some slices, also repeat the process with the other mouse brain data Nyoman gave me.

A 7T Human image would be fantastic next.

EDIT:  I realised that the max tumour cell concentration was completely wrong as the human value had been used and the voxel size is 11680 times smaller in the mouse scan!

Hence the max tumour cell conc/voxel is around 20 in the mice scan using the same parameters.  Running this data now.

Centre for Advanced Imaging meeting and Mouse Brain Data

1. Following a meeting at CAI on Monday 03/08/2015, they have agreed to work with us and scan some of Simon Puttick's immunodeficient glioblastoma mice for us, to obtain a longitudinal data series. 
2. Nyoman Kurniawan, the small animal imaging expert at CAI has shared a 9.44T mouse brain atlas with us, which I have been working to put into the code and simulate tumours. I have done some of the preliminary processing, extracted the diffusion tensor, now to put in the new scan dimensions into our code.  The mouse brain has much smaller voxels and  is a different shape, the dimensions of the scan are 72x90x170, with the long axis inferior-superior (z-axis) because the mice are scanned vertically with the nose pointing to the sky. The hard bit here is lining up all the data, looking at the way it is organised in mrinfo for example to extract the right coordinates and so on.