Hi Developers, 

I have another question: I always got the warning "image does not have valid orientation meta information; cannot reorient" when I apply a cmtk tool on my image files. I have re-oriented my data in the RAS coordinate as suggested in the user guide, but the warning message remains. Should I just ignore the warning?Thanks!

Best,
Dan

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.