Tool	options	description
cmtk registration	--Initxlate	Calculate affine transformation
	--dofs 6,9,12
	--sampling 3
	--coarsest 25
	--omit-original-data
	--accuracy 3
	--exploration 25.6
cmtk warp	-v	Use affine transformation as initialization
	--fast
	--grid-spacing 40
	--refine 2
	--jacobian-weight 0.001
	--coarsest 6.4
	--sampling 3.2
	--accuracy 3.2
	--omit-original-data
reformatx		Apply transformation to other stacks
cmtk streamxform		To apply a found transformation to coordinates of segmented neurons