No, this is not related to the mask for T1w/MPRAGE image. For registration, BDP needs to use an approximate brain-mask for diffusion data. This mask can be defined via
--dwi-mask flag. When it not defined then BDP shows this message.
It is recommended to check the automatically estimated mask after processing, as large inaccuracies in the DWI-mask can affect the registration and distortion correction. In case of inaccurate estimation, the DWI-mask should be manually edited and BDP should be re-run with