File: dwinormalise

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mkdir -p ../tmp/dwinormalise/group && mkdir -p tmp-dwi && mkdir -p tmp-mask && mrconvert BIDS/sub-02/dwi/sub-02_dwi.nii.gz -fslgrad BIDS/sub-02/dwi/sub-02_dwi.bvec BIDS/sub-02/dwi/sub-02_dwi.bval tmp-dwi/sub-02.mif -force && mrconvert BIDS/sub-02/dwi/sub-02_brainmask.nii.gz tmp-mask/sub-02.mif -force && mrconvert BIDS/sub-03/dwi/sub-03_dwi.nii.gz -fslgrad BIDS/sub-03/dwi/sub-03_dwi.bvec BIDS/sub-03/dwi/sub-03_dwi.bval tmp-dwi/sub-03.mif -force && mrconvert BIDS/sub-03/dwi/sub-03_brainmask.nii.gz tmp-mask/sub-03.mif -force && dwinormalise group tmp-dwi/ tmp-mask/ ../tmp/dwinormalise/group/ ../tmp/dwinormalise/group/fa.mif ../tmp/dwinormalise/group/mask.mif -force && testing_diff_image ../tmp/dwinormalise/group/sub-02.mif dwinormalise/group/sub-02.mif.gz -frac 1e-5 && testing_diff_image ../tmp/dwinormalise/group/sub-03.mif dwinormalise/group/sub-03.mif.gz -frac 1e-5 && testing_diff_image ../tmp/dwinormalise/group/fa.mif dwinormalise/group/fa.mif.gz -abs 1e-5 && testing_diff_image ../tmp/dwinormalise/group/mask.mif dwinormalise/group/mask.mif.gz
mkdir ../tmp/dwinormalise/individual && dwinormalise individual 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/dwi/sub-01_brainmask.nii.gz ../tmp/dwinormalise/individual/out.mif -force && testing_diff_image ../tmp/dwinormalise/individual/out.mif dwinormalise/individual/out.mif.gz -frac 1e-5
dwinormalise individual 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/dwi/sub-01_brainmask.nii.gz ../tmp/dwinormalise/individual/percentile.mif -percentile 40 -force && testing_diff_image ../tmp/dwinormalise/individual/percentile.mif dwinormalise/individual/percentile.mif.gz -frac 1e-5