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mkdir -p ../tmp/dwi2response/dhollander && mrconvert BIDS/sub-01/dwi/sub-01_dwi.nii.gz -fslgrad BIDS/sub-01/dwi/sub-01_dwi.bvec BIDS/sub-01/dwi/sub-01_dwi.bval tmp-sub-01_dwi.mif -export_grad_mrtrix tmp-sub-01_dwi.b -strides 0,0,0,1 && dwi2response dhollander tmp-sub-01_dwi.mif ../tmp/dwi2response/dhollander/default_wm.txt ../tmp/dwi2response/dhollander/default_gm.txt ../tmp/dwi2response/dhollander/default_csf.txt -voxels ../tmp/dwi2response/dhollander/default.mif -force && testing_diff_matrix ../tmp/dwi2response/dhollander/default_wm.txt dwi2response/dhollander/default_wm.txt -abs 1e-2 && testing_diff_matrix ../tmp/dwi2response/dhollander/default_gm.txt dwi2response/dhollander/default_gm.txt -abs 1e-2 && testing_diff_matrix ../tmp/dwi2response/dhollander/default_csf.txt dwi2response/dhollander/default_csf.txt -abs 1e-2 && testing_diff_image ../tmp/dwi2response/dhollander/default.mif dwi2response/dhollander/default.mif.gz
dwi2response dhollander BIDS/sub-01/dwi/sub-01_dwi.nii.gz -fslgrad BIDS/sub-01/dwi/sub-01_dwi.bvec BIDS/sub-01/dwi/sub-01_dwi.bval ../tmp/dwi2response/dhollander/fslgrad_wm.txt ../tmp/dwi2response/dhollander/fslgrad_gm.txt ../tmp/dwi2response/dhollander/fslgrad_csf.txt -voxels ../tmp/dwi2response/dhollander/fslgrad.mif -force && testing_diff_matrix ../tmp/dwi2response/dhollander/fslgrad_wm.txt dwi2response/dhollander/default_wm.txt -abs 1e-2 && testing_diff_matrix ../tmp/dwi2response/dhollander/fslgrad_gm.txt dwi2response/dhollander/default_gm.txt -abs 1e-2 && testing_diff_matrix ../tmp/dwi2response/dhollander/fslgrad_csf.txt dwi2response/dhollander/default_csf.txt -abs 1e-2 && testing_diff_image ../tmp/dwi2response/dhollander/fslgrad.mif dwi2response/dhollander/default.mif.gz
dwi2response dhollander BIDS/sub-01/dwi/sub-01_dwi.nii.gz -grad tmp-sub-01_dwi.b ../tmp/dwi2response/dhollander/grad_wm.txt ../tmp/dwi2response/dhollander/grad_gm.txt ../tmp/dwi2response/dhollander/grad_csf.txt -voxels ../tmp/dwi2response/dhollander/grad.mif -force && testing_diff_matrix ../tmp/dwi2response/dhollander/grad_wm.txt dwi2response/dhollander/default_wm.txt -abs 1e-2 && testing_diff_matrix ../tmp/dwi2response/dhollander/grad_gm.txt dwi2response/dhollander/default_gm.txt -abs 1e-2 && testing_diff_matrix ../tmp/dwi2response/dhollander/grad_csf.txt dwi2response/dhollander/default_csf.txt -abs 1e-2 && testing_diff_image ../tmp/dwi2response/dhollander/grad.mif dwi2response/dhollander/default.mif.gz
dwi2response dhollander tmp-sub-01_dwi.mif ../tmp/dwi2response/dhollander/masked_wm.txt ../tmp/dwi2response/dhollander/masked_gm.txt ../tmp/dwi2response/dhollander/masked_csf.txt -voxels ../tmp/dwi2response/dhollander/masked.mif -mask BIDS/sub-01/dwi/sub-01_brainmask.nii.gz -force && testing_diff_matrix ../tmp/dwi2response/dhollander/masked_wm.txt dwi2response/dhollander/masked_wm.txt -abs 1e-2 && testing_diff_matrix ../tmp/dwi2response/dhollander/masked_gm.txt dwi2response/dhollander/masked_gm.txt -abs 1e-2 && testing_diff_matrix ../tmp/dwi2response/dhollander/masked_csf.txt dwi2response/dhollander/masked_csf.txt -abs 1e-2 && testing_diff_image ../tmp/dwi2response/dhollander/masked.mif dwi2response/dhollander/masked.mif.gz
dwi2response dhollander tmp-sub-01_dwi.mif ../tmp/dwi2response/dhollander/fa_wm.txt ../tmp/dwi2response/dhollander/fa_gm.txt ../tmp/dwi2response/dhollander/fa_csf.txt -wm_algo fa -voxels ../tmp/dwi2response/dhollander/fa.mif -mask BIDS/sub-01/dwi/sub-01_brainmask.nii.gz -force && testing_diff_matrix ../tmp/dwi2response/dhollander/fa_wm.txt dwi2response/dhollander/fa_wm.txt -abs 1e-2 && testing_diff_matrix ../tmp/dwi2response/dhollander/fa_gm.txt dwi2response/dhollander/fa_gm.txt -abs 1e-2 && testing_diff_matrix ../tmp/dwi2response/dhollander/fa_csf.txt dwi2response/dhollander/fa_csf.txt -abs 1e-2 && testing_diff_image ../tmp/dwi2response/dhollander/fa.mif dwi2response/dhollander/fa.mif.gz
dwi2response dhollander tmp-sub-01_dwi.mif ../tmp/dwi2response/dhollander/tax_wm.txt ../tmp/dwi2response/dhollander/tax_gm.txt ../tmp/dwi2response/dhollander/tax_csf.txt -wm_algo tax -voxels ../tmp/dwi2response/dhollander/tax.mif -mask BIDS/sub-01/dwi/sub-01_brainmask.nii.gz -force && testing_diff_matrix ../tmp/dwi2response/dhollander/tax_wm.txt dwi2response/dhollander/tax_wm.txt -abs 1e-2 && testing_diff_matrix ../tmp/dwi2response/dhollander/tax_gm.txt dwi2response/dhollander/tax_gm.txt -abs 1e-2 && testing_diff_matrix ../tmp/dwi2response/dhollander/tax_csf.txt dwi2response/dhollander/tax_csf.txt -abs 1e-2 && testing_diff_image ../tmp/dwi2response/dhollander/tax.mif dwi2response/dhollander/tax.mif.gz
dwi2response dhollander tmp-sub-01_dwi.mif ../tmp/dwi2response/dhollander/tournier_wm.txt ../tmp/dwi2response/dhollander/tournier_gm.txt ../tmp/dwi2response/dhollander/tournier_csf.txt -wm_algo tournier -voxels ../tmp/dwi2response/dhollander/tournier.mif -mask BIDS/sub-01/dwi/sub-01_brainmask.nii.gz -force && testing_diff_matrix ../tmp/dwi2response/dhollander/tournier_wm.txt dwi2response/dhollander/tournier_wm.txt -abs 1e-2 && testing_diff_matrix ../tmp/dwi2response/dhollander/tournier_gm.txt dwi2response/dhollander/tournier_gm.txt -abs 1e-2 && testing_diff_matrix ../tmp/dwi2response/dhollander/tournier_csf.txt dwi2response/dhollander/tournier_csf.txt -abs 1e-2 && testing_diff_image ../tmp/dwi2response/dhollander/tournier.mif dwi2response/dhollander/tournier.mif.gz
dwi2response dhollander tmp-sub-01_dwi.mif -shells 0,3000 ../tmp/dwi2response/dhollander/shells_wm.txt ../tmp/dwi2response/dhollander/shells_gm.txt ../tmp/dwi2response/dhollander/shells_csf.txt -voxels ../tmp/dwi2response/dhollander/shells.mif -mask BIDS/sub-01/dwi/sub-01_brainmask.nii.gz -force && testing_diff_matrix ../tmp/dwi2response/dhollander/shells_wm.txt dwi2response/dhollander/shells_wm.txt -abs 1e-2 && testing_diff_matrix ../tmp/dwi2response/dhollander/shells_gm.txt dwi2response/dhollander/shells_gm.txt -abs 1e-2 && testing_diff_matrix ../tmp/dwi2response/dhollander/shells_csf.txt dwi2response/dhollander/shells_csf.txt -abs 1e-2 && testing_diff_image ../tmp/dwi2response/dhollander/shells.mif dwi2response/dhollander/shells.mif.gz
dwi2response dhollander tmp-sub-01_dwi.mif -lmax 0,2,4,6 ../tmp/dwi2response/dhollander/lmax_wm.txt ../tmp/dwi2response/dhollander/lmax_gm.txt ../tmp/dwi2response/dhollander/lmax_csf.txt -voxels ../tmp/dwi2response/dhollander/lmax.mif -mask BIDS/sub-01/dwi/sub-01_brainmask.nii.gz -force && testing_diff_matrix ../tmp/dwi2response/dhollander/lmax_wm.txt dwi2response/dhollander/lmax_wm.txt -abs 1e-2 && testing_diff_matrix ../tmp/dwi2response/dhollander/lmax_gm.txt dwi2response/dhollander/lmax_gm.txt -abs 1e-2 && testing_diff_matrix ../tmp/dwi2response/dhollander/lmax_csf.txt dwi2response/dhollander/lmax_csf.txt -abs 1e-2 && testing_diff_image ../tmp/dwi2response/dhollander/lmax.mif dwi2response/dhollander/lmax.mif.gz
mkdir -p ../tmp/dwi2response/fa && dwi2response fa tmp-sub-01_dwi.mif ../tmp/dwi2response/fa/default.txt -voxels ../tmp/dwi2response/fa/default.mif -number 20 -force && testing_diff_matrix ../tmp/dwi2response/fa/default.txt dwi2response/fa/default.txt -abs 1e-2 && testing_diff_image ../tmp/dwi2response/fa/default.mif dwi2response/fa/default.mif.gz
dwi2response fa BIDS/sub-01/dwi/sub-01_dwi.nii.gz -fslgrad BIDS/sub-01/dwi/sub-01_dwi.bvec BIDS/sub-01/dwi/sub-01_dwi.bval ../tmp/dwi2response/fa/fslgrad.txt -voxels ../tmp/dwi2response/fa/fslgrad.mif -number 20 -force && testing_diff_matrix ../tmp/dwi2response/fa/fslgrad.txt dwi2response/fa/default.txt -abs 1e-2 && testing_diff_image ../tmp/dwi2response/fa/fslgrad.mif dwi2response/fa/default.mif.gz
dwi2response fa BIDS/sub-01/dwi/sub-01_dwi.nii.gz -grad tmp-sub-01_dwi.b ../tmp/dwi2response/fa/grad.txt -voxels ../tmp/dwi2response/fa/grad.mif -number 20 -force && testing_diff_matrix ../tmp/dwi2response/fa/grad.txt dwi2response/fa/default.txt -abs 1e-2 && testing_diff_image ../tmp/dwi2response/fa/grad.mif dwi2response/fa/default.mif.gz
dwi2response fa tmp-sub-01_dwi.mif ../tmp/dwi2response/fa/masked.txt -voxels ../tmp/dwi2response/fa/masked.mif -mask BIDS/sub-01/dwi/sub-01_brainmask.nii.gz -number 20 -force && testing_diff_matrix ../tmp/dwi2response/fa/masked.txt dwi2response/fa/masked.txt -abs 1e-2 && testing_diff_image ../tmp/dwi2response/fa/masked.mif dwi2response/fa/masked.mif.gz
dwi2response fa tmp-sub-01_dwi.mif ../tmp/dwi2response/fa/threshold.txt -voxels ../tmp/dwi2response/fa/threshold.mif -mask BIDS/sub-01/dwi/sub-01_brainmask.nii.gz -threshold 0.7 -force && testing_diff_matrix ../tmp/dwi2response/fa/threshold.txt dwi2response/fa/threshold.txt -abs 1e-2 && testing_diff_image ../tmp/dwi2response/fa/threshold.mif dwi2response/fa/threshold.mif.gz
dwi2response fa tmp-sub-01_dwi.mif ../tmp/dwi2response/fa/lmax.txt -voxels ../tmp/dwi2response/fa/lmax.mif -mask BIDS/sub-01/dwi/sub-01_brainmask.nii.gz -lmax 6 -number 20 -force && testing_diff_matrix ../tmp/dwi2response/fa/lmax.txt dwi2response/fa/lmax.txt -abs 1e-2 && testing_diff_image ../tmp/dwi2response/fa/lmax.mif dwi2response/fa/lmax.mif.gz
dwi2response fa tmp-sub-01_dwi.mif ../tmp/dwi2response/fa/shells.txt -voxels ../tmp/dwi2response/fa/shells.mif -mask BIDS/sub-01/dwi/sub-01_brainmask.nii.gz -shells 0,2000 -number 20 -force && testing_diff_matrix ../tmp/dwi2response/fa/shells.txt dwi2response/fa/shells.txt -abs 1e-2 && testing_diff_image ../tmp/dwi2response/fa/shells.mif dwi2response/fa/shells.mif.gz
mkdir -p ../tmp/dwi2response/manual && dwi2response manual tmp-sub-01_dwi.mif dwi2response/fa/default.mif.gz ../tmp/dwi2response/manual/default.txt -force && testing_diff_matrix ../tmp/dwi2response/manual/default.txt dwi2response/manual/default.txt -abs 1e-2
dwi2response manual BIDS/sub-01/dwi/sub-01_dwi.nii.gz -fslgrad BIDS/sub-01/dwi/sub-01_dwi.bvec BIDS/sub-01/dwi/sub-01_dwi.bval dwi2response/fa/default.mif.gz ../tmp/dwi2response/manual/fslgrad.txt -force && testing_diff_matrix ../tmp/dwi2response/manual/fslgrad.txt dwi2response/manual/default.txt -abs 1e-2
dwi2response manual BIDS/sub-01/dwi/sub-01_dwi.nii.gz -grad tmp-sub-01_dwi.b dwi2response/fa/default.mif.gz ../tmp/dwi2response/manual/grad.txt -force && testing_diff_matrix ../tmp/dwi2response/manual/grad.txt dwi2response/manual/default.txt -abs 1e-2
dwi2tensor tmp-sub-01_dwi.mif - -mask BIDS/sub-01/dwi/sub-01_brainmask.nii.gz | tensor2metric - -vector tmp.mif -force && dwi2response manual tmp-sub-01_dwi.mif dwi2response/fa/default.mif.gz -dirs tmp.mif ../tmp/dwi2response/manual/dirs.txt -force && testing_diff_matrix ../tmp/dwi2response/manual/dirs.txt dwi2response/manual/dirs.txt -abs 1e-2
dwi2response manual tmp-sub-01_dwi.mif dwi2response/fa/default.mif.gz ../tmp/dwi2response/manual/lmax.txt -lmax 0,2,4,6 -force && testing_diff_matrix ../tmp/dwi2response/manual/lmax.txt dwi2response/manual/lmax.txt -abs 1e-2
dwi2response manual tmp-sub-01_dwi.mif dwi2response/fa/default.mif.gz ../tmp/dwi2response/manual/shells.txt -shells 0,3000 -force && testing_diff_matrix ../tmp/dwi2response/manual/shells.txt dwi2response/manual/shells.txt -abs 1e-2
mkdir -p ../tmp/dwi2response/msmt_5tt && dwi2response msmt_5tt tmp-sub-01_dwi.mif BIDS/sub-01/anat/sub-01_5TT.nii.gz ../tmp/dwi2response/msmt_5tt/default_wm.txt ../tmp/dwi2response/msmt_5tt/default_gm.txt ../tmp/dwi2response/msmt_5tt/default_csf.txt -voxels ../tmp/dwi2response/msmt_5tt/default.mif -pvf 0.9 -force && testing_diff_matrix ../tmp/dwi2response/msmt_5tt/default_wm.txt dwi2response/msmt_5tt/default_wm.txt -abs 1e-2 && testing_diff_matrix ../tmp/dwi2response/msmt_5tt/default_gm.txt dwi2response/msmt_5tt/default_gm.txt -abs 1e-2 && testing_diff_matrix ../tmp/dwi2response/msmt_5tt/default_csf.txt dwi2response/msmt_5tt/default_csf.txt -abs 1e-2 && testing_diff_image ../tmp/dwi2response/msmt_5tt/default.mif dwi2response/msmt_5tt/default.mif.gz
dwi2response msmt_5tt BIDS/sub-01/dwi/sub-01_dwi.nii.gz -fslgrad BIDS/sub-01/dwi/sub-01_dwi.bvec BIDS/sub-01/dwi/sub-01_dwi.bval BIDS/sub-01/anat/sub-01_5TT.nii.gz ../tmp/dwi2response/msmt_5tt/fslgrad_wm.txt ../tmp/dwi2response/msmt_5tt/fslgrad_gm.txt ../tmp/dwi2response/msmt_5tt/fslgrad_csf.txt -voxels ../tmp/dwi2response/msmt_5tt/fslgrad.mif -pvf 0.9 -force && testing_diff_matrix ../tmp/dwi2response/msmt_5tt/fslgrad_wm.txt dwi2response/msmt_5tt/default_wm.txt -abs 1e-2 && testing_diff_matrix ../tmp/dwi2response/msmt_5tt/fslgrad_gm.txt dwi2response/msmt_5tt/default_gm.txt -abs 1e-2 && testing_diff_matrix ../tmp/dwi2response/msmt_5tt/fslgrad_csf.txt dwi2response/msmt_5tt/default_csf.txt -abs 1e-2 && testing_diff_image ../tmp/dwi2response/msmt_5tt/fslgrad.mif dwi2response/msmt_5tt/default.mif.gz
dwi2response msmt_5tt BIDS/sub-01/dwi/sub-01_dwi.nii.gz -grad tmp-sub-01_dwi.b BIDS/sub-01/anat/sub-01_5TT.nii.gz ../tmp/dwi2response/msmt_5tt/grad_wm.txt ../tmp/dwi2response/msmt_5tt/grad_gm.txt ../tmp/dwi2response/msmt_5tt/grad_csf.txt -voxels ../tmp/dwi2response/msmt_5tt/grad.mif -pvf 0.9 -force && testing_diff_matrix ../tmp/dwi2response/msmt_5tt/grad_wm.txt dwi2response/msmt_5tt/default_wm.txt -abs 1e-2 && testing_diff_matrix ../tmp/dwi2response/msmt_5tt/grad_gm.txt dwi2response/msmt_5tt/default_gm.txt -abs 1e-2 && testing_diff_matrix ../tmp/dwi2response/msmt_5tt/grad_csf.txt dwi2response/msmt_5tt/default_csf.txt -abs 1e-2 && testing_diff_image ../tmp/dwi2response/msmt_5tt/grad.mif dwi2response/msmt_5tt/default.mif.gz
dwi2response msmt_5tt tmp-sub-01_dwi.mif BIDS/sub-01/anat/sub-01_5TT.nii.gz ../tmp/dwi2response/msmt_5tt/masked_wm.txt ../tmp/dwi2response/msmt_5tt/masked_gm.txt ../tmp/dwi2response/msmt_5tt/masked_csf.txt -voxels ../tmp/dwi2response/msmt_5tt/masked.mif -mask BIDS/sub-01/dwi/sub-01_brainmask.nii.gz -pvf 0.9 -force && testing_diff_matrix ../tmp/dwi2response/msmt_5tt/masked_wm.txt dwi2response/msmt_5tt/masked_wm.txt -abs 1e-2 && testing_diff_matrix ../tmp/dwi2response/msmt_5tt/masked_gm.txt dwi2response/msmt_5tt/masked_gm.txt -abs 1e-2 && testing_diff_matrix ../tmp/dwi2response/msmt_5tt/masked_csf.txt dwi2response/msmt_5tt/masked_csf.txt -abs 1e-2 && testing_diff_image ../tmp/dwi2response/msmt_5tt/masked.mif dwi2response/msmt_5tt/masked.mif.gz
dwi2tensor tmp-sub-01_dwi.mif - -mask BIDS/sub-01/dwi/sub-01_brainmask.nii.gz | tensor2metric - -vector tmp-dirs.mif -force && dwi2response msmt_5tt tmp-sub-01_dwi.mif BIDS/sub-01/anat/sub-01_5TT.nii.gz ../tmp/dwi2response/msmt_5tt/dirs_wm.txt ../tmp/dwi2response/msmt_5tt/dirs_gm.txt ../tmp/dwi2response/msmt_5tt/dirs_csf.txt -voxels ../tmp/dwi2response/msmt_5tt/dirs.mif -dirs tmp-dirs.mif -pvf 0.9 -force && testing_diff_matrix ../tmp/dwi2response/msmt_5tt/dirs_wm.txt dwi2response/msmt_5tt/default_wm.txt -abs 1e-2 && testing_diff_matrix ../tmp/dwi2response/msmt_5tt/dirs_gm.txt dwi2response/msmt_5tt/default_gm.txt -abs 1e-2 && testing_diff_matrix ../tmp/dwi2response/msmt_5tt/dirs_csf.txt dwi2response/msmt_5tt/default_csf.txt -abs 1e-2 && testing_diff_image ../tmp/dwi2response/msmt_5tt/dirs.mif dwi2response/msmt_5tt/default.mif.gz
dwi2response msmt_5tt tmp-sub-01_dwi.mif BIDS/sub-01/anat/sub-01_5TT.nii.gz ../tmp/dwi2response/msmt_5tt/tax_wm.txt ../tmp/dwi2response/msmt_5tt/tax_gm.txt ../tmp/dwi2response/msmt_5tt/tax_csf.txt -voxels ../tmp/dwi2response/msmt_5tt/tax.mif -wm_algo tax -pvf 0.9 -force && testing_diff_matrix ../tmp/dwi2response/msmt_5tt/tax_wm.txt dwi2response/msmt_5tt/tax_wm.txt -abs 1e-2 && testing_diff_matrix ../tmp/dwi2response/msmt_5tt/tax_gm.txt dwi2response/msmt_5tt/tax_gm.txt -abs 1e-2 && testing_diff_matrix ../tmp/dwi2response/msmt_5tt/tax_csf.txt dwi2response/msmt_5tt/tax_csf.txt -abs 1e-2 && testing_diff_image ../tmp/dwi2response/msmt_5tt/tax.mif dwi2response/msmt_5tt/tax.mif.gz
dwi2response msmt_5tt tmp-sub-01_dwi.mif BIDS/sub-01/anat/sub-01_5TT.nii.gz ../tmp/dwi2response/msmt_5tt/sfwmfa_wm.txt ../tmp/dwi2response/msmt_5tt/sfwmfa_gm.txt ../tmp/dwi2response/msmt_5tt/sfwmfa_csf.txt -voxels ../tmp/dwi2response/msmt_5tt/sfwmfa.mif -sfwm_fa_threshold 0.7 -pvf 0.9 -force && testing_diff_matrix ../tmp/dwi2response/msmt_5tt/sfwmfa_wm.txt dwi2response/msmt_5tt/sfwmfa_wm.txt -abs 1e-2 && testing_diff_matrix ../tmp/dwi2response/msmt_5tt/sfwmfa_gm.txt dwi2response/msmt_5tt/sfwmfa_gm.txt -abs 1e-2 && testing_diff_matrix ../tmp/dwi2response/msmt_5tt/sfwmfa_csf.txt dwi2response/msmt_5tt/sfwmfa_csf.txt -abs 1e-2 && testing_diff_image ../tmp/dwi2response/msmt_5tt/sfwmfa.mif dwi2response/msmt_5tt/sfwmfa.mif.gz
dwi2response msmt_5tt tmp-sub-01_dwi.mif BIDS/sub-01/anat/sub-01_5TT.nii.gz ../tmp/dwi2response/msmt_5tt/lmax_wm.txt ../tmp/dwi2response/msmt_5tt/lmax_gm.txt ../tmp/dwi2response/msmt_5tt/lmax_csf.txt -voxels ../tmp/dwi2response/msmt_5tt/lmax.mif -lmax 0,2,4,6 -pvf 0.9 -force && testing_diff_matrix ../tmp/dwi2response/msmt_5tt/lmax_wm.txt dwi2response/msmt_5tt/lmax_wm.txt -abs 1e-2 && testing_diff_matrix ../tmp/dwi2response/msmt_5tt/lmax_gm.txt dwi2response/msmt_5tt/lmax_gm.txt -abs 1e-2 && testing_diff_matrix ../tmp/dwi2response/msmt_5tt/lmax_csf.txt dwi2response/msmt_5tt/lmax_csf.txt -abs 1e-2 && testing_diff_image ../tmp/dwi2response/msmt_5tt/lmax.mif dwi2response/msmt_5tt/lmax.mif.gz
dwi2response msmt_5tt tmp-sub-01_dwi.mif BIDS/sub-01/anat/sub-01_5TT.nii.gz ../tmp/dwi2response/msmt_5tt/shells_wm.txt ../tmp/dwi2response/msmt_5tt/shells_gm.txt ../tmp/dwi2response/msmt_5tt/shells_csf.txt -voxels ../tmp/dwi2response/msmt_5tt/shells.mif -shells 0,2000 -pvf 0.9 -force && testing_diff_matrix ../tmp/dwi2response/msmt_5tt/shells_wm.txt dwi2response/msmt_5tt/shells_wm.txt -abs 1e-2 && testing_diff_matrix ../tmp/dwi2response/msmt_5tt/shells_gm.txt dwi2response/msmt_5tt/shells_gm.txt -abs 1e-2 && testing_diff_matrix ../tmp/dwi2response/msmt_5tt/shells_csf.txt dwi2response/msmt_5tt/shells_csf.txt -abs 1e-2 && testing_diff_image ../tmp/dwi2response/msmt_5tt/shells.mif dwi2response/msmt_5tt/shells.mif.gz
mkdir -p ../tmp/dwi2response/tax && dwi2response tax tmp-sub-01_dwi.mif ../tmp/dwi2response/tax/default.txt -voxels ../tmp/dwi2response/tax/default.mif -force && testing_diff_matrix ../tmp/dwi2response/tax/default.txt dwi2response/tax/default.txt -abs 1e-2 && testing_diff_image ../tmp/dwi2response/tax/default.mif dwi2response/tax/default.mif.gz
dwi2response tax BIDS/sub-01/dwi/sub-01_dwi.nii.gz -fslgrad BIDS/sub-01/dwi/sub-01_dwi.bvec BIDS/sub-01/dwi/sub-01_dwi.bval ../tmp/dwi2response/tax/fslgrad.txt -voxels ../tmp/dwi2response/tax/fslgrad.mif -force && testing_diff_matrix ../tmp/dwi2response/tax/fslgrad.txt dwi2response/tax/default.txt -abs 1e-2 && testing_diff_image ../tmp/dwi2response/tax/fslgrad.mif dwi2response/tax/default.mif.gz
dwi2response tax BIDS/sub-01/dwi/sub-01_dwi.nii.gz -grad tmp-sub-01_dwi.b ../tmp/dwi2response/tax/grad.txt -voxels ../tmp/dwi2response/tax/grad.mif -force && testing_diff_matrix ../tmp/dwi2response/tax/grad.txt dwi2response/tax/default.txt -abs 1e-2 && testing_diff_image ../tmp/dwi2response/tax/grad.mif dwi2response/tax/default.mif.gz
dwi2response tax tmp-sub-01_dwi.mif ../tmp/dwi2response/tax/masked.txt -voxels ../tmp/dwi2response/tax/masked.mif -mask BIDS/sub-01/dwi/sub-01_brainmask.nii.gz -force && testing_diff_matrix ../tmp/dwi2response/tax/masked.txt dwi2response/tax/masked.txt -abs 1e-2 && testing_diff_image ../tmp/dwi2response/tax/masked.mif dwi2response/tax/masked.mif.gz
dwi2response tax tmp-sub-01_dwi.mif ../tmp/dwi2response/tax/lmax.txt -voxels ../tmp/dwi2response/tax/lmax.mif -lmax 6 -force && testing_diff_matrix ../tmp/dwi2response/tax/lmax.txt dwi2response/tax/lmax.txt -abs 1e-2 && testing_diff_image ../tmp/dwi2response/tax/lmax.mif dwi2response/tax/lmax.mif.gz
dwi2response tax tmp-sub-01_dwi.mif ../tmp/dwi2response/tax/shell.txt -voxels ../tmp/dwi2response/tax/shell.mif -shell 2000 -force && testing_diff_matrix ../tmp/dwi2response/tax/shell.txt dwi2response/tax/shell.txt -abs 1e-2 && testing_diff_image ../tmp/dwi2response/tax/shell.mif dwi2response/tax/shell.mif.gz
mkdir -p ../tmp/dwi2response/tournier && dwi2response tournier tmp-sub-01_dwi.mif ../tmp/dwi2response/tournier/default.txt -voxels ../tmp/dwi2response/tournier/default.mif -number 20 -iter_voxels 200 -force && testing_diff_matrix ../tmp/dwi2response/tournier/default.txt dwi2response/tournier/default.txt -abs 1e-2 && testing_diff_image ../tmp/dwi2response/tournier/default.mif dwi2response/tournier/default.mif.gz
dwi2response tournier BIDS/sub-01/dwi/sub-01_dwi.nii.gz -fslgrad BIDS/sub-01/dwi/sub-01_dwi.bvec BIDS/sub-01/dwi/sub-01_dwi.bval ../tmp/dwi2response/tournier/fslgrad.txt -voxels ../tmp/dwi2response/tournier/fslgrad.mif -number 20 -iter_voxels 200 -force && testing_diff_matrix ../tmp/dwi2response/tournier/fslgrad.txt dwi2response/tournier/default.txt -abs 1e-2 && testing_diff_image ../tmp/dwi2response/tournier/fslgrad.mif dwi2response/tournier/default.mif.gz
dwi2response tournier BIDS/sub-01/dwi/sub-01_dwi.nii.gz -grad tmp-sub-01_dwi.b ../tmp/dwi2response/tournier/grad.txt -voxels ../tmp/dwi2response/tournier/grad.mif -number 20 -iter_voxels 200 -force && testing_diff_matrix ../tmp/dwi2response/tournier/grad.txt dwi2response/tournier/default.txt -abs 1e-2 && testing_diff_image ../tmp/dwi2response/tournier/grad.mif dwi2response/tournier/default.mif.gz
dwi2response tournier tmp-sub-01_dwi.mif ../tmp/dwi2response/tournier/masked.txt -voxels ../tmp/dwi2response/tournier/masked.mif -mask BIDS/sub-01/dwi/sub-01_brainmask.nii.gz -number 20 -iter_voxels 200 -force && testing_diff_matrix ../tmp/dwi2response/tournier/masked.txt dwi2response/tournier/masked.txt -abs 1e-2 && testing_diff_image ../tmp/dwi2response/tournier/masked.mif dwi2response/tournier/masked.mif.gz
dwi2response tournier tmp-sub-01_dwi.mif ../tmp/dwi2response/tournier/lmax.txt -voxels ../tmp/dwi2response/tournier/lmax.mif -lmax 6 -number 20 -iter_voxels 200 -force && testing_diff_matrix ../tmp/dwi2response/tournier/lmax.txt dwi2response/tournier/lmax.txt -abs 1e-2 && testing_diff_image ../tmp/dwi2response/tournier/lmax.mif dwi2response/tournier/lmax.mif.gz
dwi2response tournier tmp-sub-01_dwi.mif ../tmp/dwi2response/tournier/shell.txt -voxels ../tmp/dwi2response/tournier/shell.mif -shell 2000 -number 20 -iter_voxels 200 -force && testing_diff_matrix ../tmp/dwi2response/tournier/shell.txt dwi2response/tournier/shell.txt -abs 1e-2 && testing_diff_image ../tmp/dwi2response/tournier/shell.mif dwi2response/tournier/shell.mif.gz
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