Position of the 3D image and its cross section do not match

[cpinter (Csaba Pinter)]

In your case it seems that you have three volumes of the same thing, at the same resolutions (not isotropic), but sliced differently. I don’t quite understand why. I think you can use any of them, there should be no difference. This also means that there is no sense in using more than one. I’d use the XY one given that the standard “slicing” is that you have the same spacing within the slice and lower resolution along Z, and you can see the gantry shape in the slice.