Table 2.

The various flags and variables for a variety of image registration possibilities. Additional information can be found on the ANTs website (Avants et al., 2009). The variable Δ represents the gradient step length.

	Argument	Flag	Variables / Sample Parameters
Linear	Iterations	--number-of-affine-iterations	N1xN2xN3x…
	Similarity	--affine-metric-type	MI,CC,MSQ
	Affine or Rigid	--do-rigid	true / false
Deform.	Image Similarity	--metric,-m	MI,CC,PR,MSQ [ℐ 𝒥,param, 1]
	Point-Set Similarity	--metric,-m	PSE,JHCT [ℐ 𝒥 X, Y]
	Iterations/Level	--iterations,-i	N1xN2xN3x…
	Regularization	--regularization,-r	Gauss, DMFFD $[{\sigma }_{\mathit{\text{gradient}}}^2,{\sigma }_{\mathit{\text{total}}}^2]$
	Transformation	--transformation,-t	GreedyExp, Elast, SyN, Exp [Δ]
	Transformation	--geodesic	SyN [Δ,# time points,dT]
Misc.	Histogram Match ℐ, 𝒥	--use-histogram-matching	1
	NN Interpolation	--use-NN	0
	Mask Image	--mask,-x	mask.nii
	Output Naming	--output-naming,-o	filename.nii