Hi Gordon:

I am going to check with the NeuroDebian maintainer, who is the one making this particular build. One possible explanation is that CMTK may be configured without FFTW support, which would also make the phantom detection tool disappear.

Will let you know once I hear back from them.

In the meantime, you could build CMTK from source, which should be fairly straightforward. Just make sure FFTW (CMTK_USE_FFTW) support is turned on in CMake.

Best,
  Torsten