diff --git a/bash/get_dw_response b/bash/get_dw_response index 63c4066..a448c68 100755 --- a/bash/get_dw_response +++ b/bash/get_dw_response @@ -38,7 +38,7 @@ gen_WM_mask $dwi_file ${pfx}mask.mif - | threshold - ${pfx}wm_mask.mif -abs $WM_ dwi2tensor $dwi_file - | tensor2FA - - | mrmult - ${pfx}wm_mask.mif - | threshold - ${pfx}sf_mask.mif -abs $SF_FA_THRESHOLD # Mask single_fibre mask with whole brain mask -#estimate_response $dwi_file ${pfx}sf_mask.mif $output -lmax 8 -normalise +#estimate_response $dwi_file ${pfx}sf_mask.mif $output -lmax 8 # Save the average b0 to file for use in scaling the base intensity of the expected image get_b0 $dwi_file ${pfx}sf_mask.mif -method median > ${output_base}.b0.$output_ext