Hello,
I am using the following commands to correct for b0 inhomogeneities by warping the post eddy corrected b0 volume to a subjects T1 and then applying that warp to the diffusion weighted image as discussed in this paper https://www.frontiersin.org/articles/10.3389/fninf.2017.00017/full#supplementary-material.
antsIntermodalityIntrasubject.sh -d 3 -i ${dwi_dir}/${subj}/dmri/lowb_brain.nii.gz -r ${SUBJECTS_DIR}/${subj}/mri/brainmask.mgz -x ${SUBJECTS_DIR}/${subj}/mri/brainmask.mgz -w template -o ${dwi_dir}/${subj}/dmri/B0toT1SmallWarp -t 2
antsApplyTransforms -d 3 -e 3 -i ${dwi_dir}/${subj}/dmri/dwi.nii.gz -n BSpline -r ${SUBJECTS_DIR}/${subj}/mri/brainmask.mgz -o ${dwi_dir}/${subj}/dmri/dwi_corrected.nii.gz -t ${dwi_dir}/${subj}/dmri/B0toT1SmallWarp1Warp.nii.gz -t ${dwi_dir}/${subj}/dmri/B0toT1SmallWarp0GenericAffine.mat
dtifit -k ${dwi_dir}/${subj}/dmri/dwi_corrected.nii.gz -m ${dwi_dir}/${subj}/dmri/B0toT1SmallWarpanatomical.nii.gz -r ${dwi_dir}/${subj}/dmri/bvecs -b ${dwi_dir}/${subj}/dmri/bvals -o ${dwi_dir}/${subj}/dmri/dtifit
My question is are there any modifications to the tensors or b-values that I have to make before estimating the tensor values with dtifit? Are there any other factors I should take into consideration or be wary of? The technique seems to have greatly improved the b0 inhomogeneities in my dwi images.
Best,
Daniel Callow