Dear FSL users,
suppose you computed the jacobian of a non linear transformation, to match the image A on the atlas B. I know the corpus-callosum mask in the atlas B.
For computing the mean value of the jacobian in that mask, do I have to apply the non linear warping field to the jacobian before computing the mean?
Ex.:
fnirt --ref=atlas_B --in=A --config=config.cnf --cout=nonLinear
fnirtfileutils --in=nonLinear --ref=atlas_B --jac=jacobian --out=nonLinear_warpField
applywarp --ref=atlas_B --in=jacobian --warp=nonLinear_warpField --rel --out=jacobian_warped
Do I have to use "jacobian" or "jacobian_warped" to compute the mean of jacobian in the corpus-callosum mask drawn in atlas_B?
Thank you for help
Giovanni
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