Hi Thomas:

As Greg already said, the warnings you are seeing are harmless. CMTK tries to reorient all images into "Right-Anterior-Superior" human anatomical orientation, but clearly that isn't possible for non-human images, in which case the images are simply left as they are. So long as your images are oriented approximately the same way (ie., same slice stacking direction) there should be no problem. Otherwise you would have to provide an initial transformation for gross orientation.

Regarding affine.xform - you say you don't get that file. Actually, you should be getting a directory of that name. If you don't, try adding "-v" to the command line; see if that gives you more information.

Best,
  Torsten
Originally posted by Thomas Templier: