This sounds suspiciously like this issue, which seems specific to MRtrix3 version 3.0_RC2. Which version are you using? In 3.0_RC3, the default parameters for the ants algorithm were adjusted, so it might work better in that version. In addition, support was added for overriding them on the command line, which should at least allow you to tweak the parameters to the underlying ANTs command, N4BiasFieldCorrection, to hopefully get a decent result.
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