dwi2tensor uses all available images (i.e. across all shells).
If you wish to only use the images corresponding to specific b-values you have to select them yourself in a separate command, typically dwiextract.
E.g. to fit the diffusion tensor to the b<=800 data only, discarding the b=2800 data you would run:
dwiextract -shells 0,800 dwi.mif dwi_lowb.mif
dwi2tensor -mask mask.mif dwi_lowb.mif dt.mif
or you could string these commands together using pipes as:
dwiextract -shells 0,800 dwi.mif - | dwi2tensor -mask mask.mif - dt.mif
To get a list of the b-value shells available in your dataset, you could use:
mrinfo dwi.mif -shell_bvalues