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My goal: How to (1) construct 3D image for visualization. (2) how to write 3D array or image into binary raw file.

Is there a way to accomplish this in Mathematica?

Alternative_Answer for: (1)

slices={1,2,3,4,5}; ss = Map[ImageData, slices]; ListContourPlot3D[ss, Mesh -> None, Contours -> Automatic]
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As to your first question:

There's a very nice example of volume rendering with medical images in the documentation (Applications section, item Volume Rendering) that seems to be applicable.

Mathematica graphics

Mathematica graphics

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  • $\begingroup$ I'm wondering how to make this. $\endgroup$ Commented May 30, 2012 at 21:10
  • $\begingroup$ Alternative approach: I was able to use an example by "halirutan": filenames = FileNames[]; ch[i_] := ImageData[Import[filenames[[i]]], "Bit"]; ss = Table[ch[i], {i, 1, 20}]; ListContourPlot3D[ss, Mesh -> Automatic] $\endgroup$ Commented May 30, 2012 at 21:29
  • $\begingroup$ @Szabolcs, here is my extremely slow volume rendered in mathematica, coordinates are slightly offset, gist.github.com/2840409. enjoy. $\endgroup$ Commented May 31, 2012 at 2:10