CMTK ignores units. So long as your image data and the parameters you set have values that are consistent with your implicit units, you will be fine. So there is no need to resave.

Just set the grid spacing to values that are consistent with your FOV and the degree of warping that may be necessary. I would imagine that an initial spacing of order 100 and final spacing of 10 might be plausible - normally they are powers of two so perhaps 128 ... 8. Torsten is the expert on that of course and it is specimen dependent.

Best,

Greg.