Okay - I looked at your data, and here is what is happening:

- Your input images are confocal microscopies and as such do not live in one of the typical, medical (human) coordinate systems, e.g. "LPS" for DICOM.
- You are trying to reformat into a NIFTI file - but NIFTI requires that physical image coordinates are in RAS space.
- Since your input images have no valid anatomical coordinate space, conversion of the coordinate system to RAS fails

Coincidentally, you only saw the error you observed because you are using a Debug build - the Release build would have silently ignored the problem.

Now, I just checked a bug fix into the SVN repository, which will be part of the next CMTK release. This fix will issue a warning when your situation occurs, but will continue to write a NIFTI file (albeit one that violates the standard with respect to the meaning of its coordinates).

In the meantime, I strongly recommend for performance reasons that you compile MCTK in "Release" mode (run "ccmake ." in your build directory and set CMAKE_BUILD_TYPE to "Release").

Also, you should be able to write output in NRRD format (reformat.nrrd or reformat.nhdr) rather than NIFTI to avoid the problem - NRRD does not require any specific coordinate space, so CMTK will write without attemtping to change the coordinate system.

Hope this solves your problem.

Torsten