OK, no issue with your directions then, it’s just a matter of supplying them to any command that needs to know, including dwi2mask. Since the gradient table isn’t stored in the NIfTI header, it needs to be supplied explicitly every time - which is why we recommend MRtrix3’s own mif format.
In your case, you should only need to type:
$ dwi2mask DTI.nii -fslgrad DTI_bvecs.bvecs DTI_bvals.bvals DTI_mask.nii
to get this working… (don’t forget the filename suffix for the output, otherwise MRtrix3 won’t know what format you want for your output).