This error is most likely related to incorrect estimation of diffusion brain mask. Can you please check the file <fileprefix>.dwi.RSA.mask.nii.gz and see if looks like reasonable mask for diffusion data (<fileprefix>.dwi.RSA.nii.gz)? I am guessing that it would be highly incorrect.
If that is the case, then please edit the mask manually in BrainSuite to cover brain-area reasonably in diffusion data. Then you should use this mask as input in BDP via –dwi-mask flag.