DTI preprocessing with MRtrix3

1

Hi I have been trying to do the preprocessing of DTI scan which has just one phase encoding direction AP.

  1. mrconvert input.nii -fslgrad dti.bvec dti.bval AP_DTI.mif
  2. dwidenoise AP_DTI.mif den_dti_AP.mif
  3. mrdegibbs den_dti_AP.mif unr_den_dti_AP.mif -axes 0,1
  4. dwifslpreproc unr_den_dti_AP.mif preproc_unr_den_AP.mif -rpe_none -pe_dir AP -eddy_options " --slm=linear"
    5.dwi2mask preproc_unr_den_AP.mif mask_dti.nii
    i skipped the distortion correction since I have just one phase encoding direction. But the mask came out really bad including the non brain tissue.
    What I could have done wrong you think.
    Thanks,
    Sanjida