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clear
%% Dependencies: brain2mesh, iso2mesh, and zmat (http://github.com/fangq/zmat)
%% Reading in data from c1-c5 SPM segmentations using a 4D array
% the SPM segmentation files are stored in the text-based JNIfTI format
% (.jnii) as defined in the JNIfTI file specification
% https://github.com/fangq/jnifti/
names={'gm','wm','csf','skull','scalp','air'};
for i = 1:5
A = loadjnifti(sprintf('jnii/c%iANTS19-5Years_head.jnii',i));
dim = size(A.NIFTIData);
seg.(names{i}) = A.NIFTIData;
end
%% call brain2mesh to create multi-layered brain mesh; cfg.smooth performs 10-iter. surface smoothing
cfg.dotruncate = 1;
%cfg.smooth=8; % apply smoothing to all surfaces, use a struct to smooth each
%cfg.radbound=struct('scalp',10,'skull',10,'csf',10,'gm',5,'wm',5); % set mesh density per layer
tic
[node,elem,face] = brain2mesh(seg, cfg);
toc
%% call brain1020 to create the 10-5 landmarks on the scalp
initpoints=[
87.4123 188.5120 93.7087
87.4360 5.9213 116.0523
21.1737 93.9561 84.9446
159.6440 89.8472 86.3139
91.2203 104.7490 213.7747];
headsurf=volface(elem(:,1:4));
tic;
[landmarks, curves]=brain1020(node, headsurf, initpoints, 10,5,'cztol',1e-8, 'minangle', 0.75*pi);
toc
view([-0.6 1.5 0.6]);
%% Plotting of the result
plotmesh(node,elem(elem(:,5)==5,:),'FaceColor',[1 1 1]) %%wm
hold on;
plotmesh(node,elem(elem(:,5)==4,:),'x>78| y<110','FaceColor',[0.35 0.35 0.35]) %%pial
plotmesh(node,elem(elem(:,5)==3,:),'x>78 | z<135','FaceColor',[0.2 0.6 1]) %%csf
plotmesh(node,elem(elem(:,5)==2,:),'x>90 | z<130','FaceColor',[1 1 0.9]) %%bone
plotmesh(node,elem(elem(:,5)==1,:),'x>100 | z<125','FaceColor',[1 0.8 0.7]) %%scalp
view([-0.6 1.5 0.6])
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