Can you try adding masks for structural and diffusion data and try running the BDP command.
There are two flags I want you to add and let me know if the error still persists:
1. –dwi-mask <filename.nii.gz> : Specifies the filename of the brain-mask file for diffusion data.
2. –t1-mask <filename.nii.gz> : Specifies the filename of the brain-mask file for input T1-weighted image.This mask can be same as the brain mask generated during BrainSuite extraction sequence.
More details of flags can be found at http://brainsuite.org/processing/diffusion/flags/