Could someone please explain how the voxels in a 3D image in Matlab relate to a normal (i.e. positive) coordinate system? I assumed that the 1st, 2nd and 3rd indices of the image matrix corresponded to x-, y- and z-coordinates respectively, but that is clearly not the case. The following example illustrates the issue I am having...
I have a 3D model of a right hand which is defined by the variables 'vertices' and 'faces':
p=patch('Vertices',vertices,'Faces',faces);
p.FaceColor = [0 1 0];
xlabel('X'); ylabel('Y'); zlabel('Z')
With the following code I can create a 3D image of the hand simply by counting the number of vertices within a voxel:
xedges = 0:0.5:30;
yedges = 0:0.5:30;
zedges = 0:0.5:15;
Img = zeros(numel(xedges)-1, numel(yedges)-1, numel(zedges)-1);
for iZ = 1:numel(zedges)-1
bZ = vertices(:,3)>=zedges(iZ) & vertices(:,3)<zedges(iZ+1);
Img(:,:,iZ) = histcounts2(vertices(bZ,1),vertices(bZ,2),xedges,yedges);
end
When I plot this image with volshow I get a left hand!
When I plot the image with orthosliceViewer the x and y dimensions are swapped:
I cannot find any documentation on if the orthosliceViewer coordinate system is positive or negative, but if it is positive I am looking at a left hand again.
Is the solution simply to do permute(Img, [2 1 3])?
