dwifslpreproc

mrconvert COLON02_POST_dwi.nii.gz -fslgrad COLON02_POST_dwi.bvec COLON02_POST_dwi.bval dwi.mif

dwidenoise dwi.mif dwi_den.mif -noise noise.mif

dwiextract dwi_den.mif - -bzero | mrmath - mean mean_b0_AP.mif -axis 3

fslroi COLON02_POST_dwi_PA.nii.gz dwi_b0_PA.nii.gz 0 1

mrconvert dwi_b0_PA.nii.gz -fslgrad dwi_b0_PA.bvec dwi_b0_PA.bval dwi_b0_PA.mif

mrgrid dwi_b0_PA.mif regrid -template mean_b0_AP.mif b0_PA_resampled.mif

mrcat mean_b0_AP.mif b0_PA_resampled.mif -axis 3 b0_pair.mif

dwifslpreproc dwi_den.mif dwi_den_preproc.mif -nocleanup -pe_dir AP -rpe_pair -se_epi b0_pair.mif -eddy_options " --slm=linear --data_is_shelled"

dwibiascorrect ants dwi_den_preproc.mif dwi_den_preproc_unbiased.mif -bias bias.mif

dwi2mask dwi_den_preproc_unbiased.mif mask.mif

mrview dwi_den_preproc_unbiased.mif