Warp and reorient a diffusion tensor image

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

Compute the warp

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.

Apply the transform to the DT image

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

Compose the affine and deformable transforms into a single warp file for ReorientTensorImage

If you are doing a single affine transform only, you can proceed to the next step.

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

Apply the reorientation to the deformed tensor image

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