Dear Jacek,
By the looks of it, I would say that, although the BET mask you obtained
looks good, it is not coregistered with the image you are using in DTIFIT
but I have never used the MRtrix3 software so maybe there is something
there also.
Could you check the coregistration between the BET mask and the image
you are using in the dtifit? And share the commands that you executed?
Hope this helps,
aran
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