That's not the way indexing works. It will go through every possible permutation of x, y, and z and then will expect to set it to a SINGLE value. Essentially you are specifying a rectangular block in the 3D matrix - a chunk out of the larger full 3D block. See this small demo:
m=rand(6,6,6)
m(1:3,2:4,3:5) = 0
Look where it put the zeros - not in just 3 elements, but in a whole block. So each element (in imaging we call it a voxel) should have one value, but you're trying to set three values equal to that value, not 1. If you don't want all permutations, use a for loop to take just one element from values and set it to the same index from x, y, and z, like this:
for k = 1 : length(x)
matrix(x(k), y(k), z(k)) = values(k);
end
