Dear Zhilei,

I see no sign in the output parameters that it was trying to rotate the images. It seems to me that it did a 7.4 µm X displacement and a small Y and Z displacement – now of course that may not be so sensible, but that is what it says. I wonder if your images have any anatomical orientation information in the header, which is resulting in CMTK reorienting the images. Would you like to share the header information from your two input and one output images e.g. what you get by doing Fiji Image ... Show Info?

Best wishes,

Greg.