dwifslpreproc

These commands depended on the scanner/sequence. The Philips PA sequence required the mrgrid (reslicing to match geometry) command. The Prisma scans did not require this step.

All b values = 100 were manually changed in the bval files to 101. EDDY has problems with b=100. It's possible 100.01 might work but that has not been verified. Alternatively, the b=100 shells could be removed. The commands below are an example run for one participant's data at one time point.

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