Too vague to answer directly, but here are two helpful tips:
1) Whatever you are doing, in the end you need to stack the images on the 3rd dimension not 4th.
2) Do not try to visualize 3D data in MATLAB, unless it is a surface. MATLAB figures (as far as I know) do not support pixel shading, so your figures will look very flat. Instead use Paraview. You can use this function to export your 3D matrix once you have that in MATLAB. Below is an example of a 3D reconstruction I visualized following the same procedure.Notice the depth/shading.