For the Jacobean, you certainly *don't* want the global translation and rotation included (those are the rigid body parts of the transform).
Sure this is what I thought, but I was confused when you said:
If in subject space... no issues.
do you want the global shear and scaling from the affine, as well as the local displacements from the WARP, or just local displacements themselves?
I will try both. Thank you, but I guess that what is commonly used is _shft_WARP.nii.gz right?
Any thoughts concerning animal_warper issues?
