If you type median to the search box in the SimpleFilters, you should see the filters: BinaryMedianFilter is the first one shown, but the drop down should list the others. Same for Gaussian too.
You probably should have done the crop volume with interpolation and isotropic spacing prior to starting the segmentation. If you only want to resample in the Z direction, ResampleScalarVolume can give you what you want. (just leave x and y values as 0,0 and enter whatever spacing you want for Z).
Rest of what you are trying to achieve is not clear to me.