Hi Dan -

Coordinates are a bit tricky, because they depend on image size as well as (for medical images) standardized orientations.

Your best bet would be to use CMTK's "triplanar" viewer to locate landmarks and then use whatever coordinates the program gives you.

Note that "triplanar" will only be part of your installation if CMTK was build with Qt/GUI support. That should be the case for all binary packages here on NITRC *except* the native Windows package. (On Windows, you can use the Cygwin binaries instead, which do have Qt support enabled.)

Best,
  Torsten