Minor fixes to configure script to make it (more) compatible with mingw.
Minor fixes to configure script to make it (more) compatible with mingw.

MRtrix3/mrtrix3,MRtrix3/mrtrix3,MRtrix3/mrtrix3,MRtrix3/mrtrix3,MRtrix3/mrtrix3,MRtrix3/mrtrix3