matlab - padding the 3D images for deformation -

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i trying pad 3d image deformation process. want know if padding 3d images of dimension 256*256*150 , after applying padding dimension become 656*656*150 . should try pad third dimension i.e 150 before applying process on padded image?

i using matlab padding 

mask_im=padarray(image_mask,[2*window_size_pad 2*window_size_pad],'both');

if necessary pad third dimension , should use pad ..i have seen matlab pad array dimension , doesn't third dimension.

if apply rotation along third axis, no need pad third dimension... should pad every dimension wish apply frequency domain transform. best way pad them permute axis

b = permute(a,[1,3,2])

pad, permute 

a = permute(b,[1,3,2])

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