Warp and reorient a diffusion tensor image

Moving image: dt.nii.gz Fixed image: fixed.nii.gz

1. Run antsRegistration or antsRegistrationSyN[quick].sh, registering the DT (by proxy, eg using FA, B0, or some other scalar image in the DT space) to the fixed image. This produces the warps movingDT_ToFixed1Warp.nii.gz and movingDT_ToFixed0GenericAffine.mat.

2. Apply these transforms to deform the tensor image. After this the tensors will be correctly located in the fixed space, but they retain their original orientation.

antsApplyTransforms -d 3 -e 2 -r fixed.nii.gz -i dt.nii.gz \
-o dtDeformed.nii.gz -t movingDT_ToFixed1Warp.nii.gz \
-t movingDT_ToFixed0GenericAffine.mat -r fixed.nii.gz

3. Compose the warps into a single warp file for ReorientTensorImage

antsApplyTransforms -d 3 -r fixed.nii.gz -o [dtCombinedWarp.nii.gz,1] \
-t movingDT_ToFixed1Warp.nii.gz -t movingDT_ToFixed0GenericAffine.mat \
-r fixed.nii.gz

4. Apply the reorientation to the deformed tensor image

ReorientTensor 3 dtDeformed.nii.gz dtReoriented.nii.gz \
dtCombinedWarp.nii.gz