File: dwicat

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mrtrix3 3.0.8-1
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mkdir -p ../tmp/dwicat && 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.mif -force && dwiextract tmp.mif tmp01_b1000.mif -shells 0,1000 -force && dwiextract tmp.mif tmp01_b2000.mif -shells 0,2000 -force && dwiextract tmp.mif tmp01_b3000.mif -shells 0,3000 -force && mrcat tmp01_b1000.mif tmp01_b2000.mif tmp01_b3000.mif -axis 3 tmp02.mif -force && mrcalc tmp01_b2000.mif 0.2 -mult tmp03_b2000.mif -force && mrcalc tmp01_b3000.mif 5.0 -mult tmp03_b3000.mif && mrcat tmp01_b1000.mif tmp03_b2000.mif tmp03_b3000.mif -axis 3 tmp03.mif -force && dwicat tmp01_b1000.mif tmp03_b2000.mif tmp03_b3000.mif ../tmp/dwicat/sharedb0_masked.mif -mask BIDS/sub-01/dwi/sub-01_brainmask.nii.gz -force && testing_diff_image ../tmp/dwicat/sharedb0_masked.mif tmp02.mif -frac 1e-6
dwicat tmp01_b1000.mif tmp03_b2000.mif tmp03_b3000.mif ../tmp/dwicat/sharedb0_unmasked.mif -force && testing_diff_image ../tmp/dwicat/sharedb0_unmasked.mif tmp02.mif -frac 1e-6
dwiextract tmp.mif tmp11_b0.mif -shell 0 -force && dwiextract tmp.mif tmp11_b1000.mif -shell 1000 -force && dwiextract tmp.mif tmp11_b2000.mif -shell 2000 -force && dwiextract tmp.mif tmp11_b3000.mif -shell 3000 -force && mrconvert tmp11_b0.mif -coord 3 0,1 - | mrcat - tmp11_b1000.mif tmp12_b1000.mif -axis 3 -force && mrconvert tmp11_b0.mif -coord 3 2,3 - | mrcat - tmp11_b2000.mif tmp12_b2000.mif -axis 3 -force && mrconvert tmp11_b0.mif -coord 3 4,5 - | mrcat - tmp11_b3000.mif tmp12_b3000.mif -axis 3 -force && mrcalc tmp12_b2000.mif 0.2 -mult tmp13_b2000.mif -force && mrcalc tmp12_b3000.mif 5.0 -mult tmp13_b3000.mif -force && mrcat tmp12_b1000.mif tmp12_b2000.mif tmp12_b3000.mif tmp14.mif -axis 3 -force && dwicat tmp12_b1000.mif tmp13_b2000.mif tmp13_b3000.mif ../tmp/dwicat/ownb0_masked.mif -mask BIDS/sub-01/dwi/sub-01_brainmask.nii.gz -force && testing_diff_image ../tmp/dwicat/ownb0_masked.mif tmp14.mif -frac 0.01
dwicat tmp12_b1000.mif tmp13_b2000.mif tmp13_b3000.mif ../tmp/dwicat/ownb0_unmasked.mif -force && testing_diff_image ../tmp/dwicat/ownb0_unmasked.mif tmp14.mif -frac 0.02
dwiextract tmp12_b1000.mif -bzero - | mrconvert - tmp12_b1000_1b0.mif -coord 3 0 -axes 0,1,2 -force && dwicat tmp12_b1000.mif tmp12_b1000_1b0.mif ../tmp/dwicat/3dinput.mif -force