I'm receiving the same error.  Tsvet, I'm curious.  Do you have more than two TEs for your magnitude and phase maps? 

Preparing functional Creation of voxel-displacement map (VDM) for Susceptibility Distortion Correction
Please wait...
ERROR DESCRIPTION:

Scalar structure required for this assignment.
Error in FieldMap (line 1476)
V.dt(1)=4;
Error in conn_setup_preproc (line 2786)
scphase=FieldMap('Scale',fmap{1});
Error in conn (line 1143)
ok=conn_setup_preproc('',varargin{2:end});
Error in conn_menumanager (line 121)
feval(CONN_MM.MENU{n0}.callback{n1}{1},CONN_MM.MENU{n0}.callback{n1}{2:end});