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It seems that a 3D dft can be performed using 1D dft on each axis.
http://www.inf.ufsc.br/~visao/khoros/html-dip/c5/s2/front-page.html
Maybe it is possible to use the DFT_ROWS flag to perform the dft in one dimension and a 2D dft to perform the dft in the other 2 dimensions. Some rearranging of pixels will maybe have to be performed too, to get the proper MAT input for the dft.
