configure: use -idirafter rather than -isystem
configure: use -idirafter rather than -isystem

This should avoid issues such as #1390

(cherry-picked from dev)

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