If your image data always has the same orientation with respect to your specimen's world coordinate system (i.e. Body axis) you can safely ignore this.

When saving a nrrd file you can specify a coordinate system in the header but the Fiji/IMAGEJ plugin does not support this IIRC. If the coordinate system is specified CMTK, will look after reorienting the images to a consistent orientation for you.

Best,

Greg.