Anisotropy and Tissue Modelling progress

In the last fortnight I have met with Dr Yonghui Li, who kindly processed the tractography of the diffusion scan we have been working with and gave me a tutorial on the problems involved in doing this task.  Namely, making sure orientation and registration are correct while switching formats to MRTrix friendly files and processing.

I attended a Centre for Advanced Imaging seminar and there met Drs Gary Cowin, Nyoman Kurniawan and Andrew Janke, who showed me around and suggested that we do the deformation of the tissue modelling in a software package called ANTS (Advanced Normalisation of TissueS), which I downloaded and have not managed to compile successfully yet.

Further meeting to follow on Zoltan's return, Gary is the coordinator for imaging research and was very accommodating.

'Anisotropy'

Really we should be referring to surface irregularity?  

Finally got some working code, used the MATLAB \gradient function to calculate the gradient though, then took an absolute value of this. 

Using logical indexing to create a manual isosurface, we can get a matrix of ones, then we could use a nearest neighbours counting approach which I will start work on tomorrow, it should be reasonably straight forward, the question on whether it will provide any greater information than using the built in function is not really clear though.  

I also wrote code to show a movie of the surface plot of tumour evolution in a slice, which shows the traveling wave behaviour nicely.  

Found some code already written to view slice planes of a volume in MATLAB vis3d, which is very handy to have too. 

%% movie of surface plot of tumour cell density evolution in a slice
% if not already defined, make Tumour from cstore
% for i = 1:201
% Tumour(:,:,:,i) =cstore{i};
% end
% then take time point t
% Tumour(t) = Tumour(:,:,:,t)

Slice = Tumour80(:,:,40); %slice at z = 40

%Manually make isosurface matrix
%isoMatrix = Slice > 2e5;
%imagesc(Slice)
%figure
%surf(Slice)
colormap bone
caxis ([0 2.4e5])
colorbar

%make movie of surf plot
writerObj = VideoWriter('surfPlotofSlice.avi');
open(writerObj);
hold off
figure
for kk = 50:120
    Slice = Tumour(:,:,40,kk);
     surf(Slice)
     axis ([0 100 0 100 0 2.5e5])
    pause(0.1)
        frame = getframe;
        writeVideo(writerObj,frame);
colormap gray
caxis ([0 2.4e5])
end
close(writerObj);