Provided by: ants_1.9.2+svn680.dfsg-4_amd64
ANTSUseLandmarkImagesToGetAffineTransform - part of ANTS registration suite
ANTSUseLandmarkImagesToGetAffineTransform FixedImageWithLabeledLandmarks.nii.gz MovingImageWithLabeledLandmarks.nii.gz [rigid | affine] OutAffine.txt
we expect the input images to be (1) N-ary (2) in the same physical space as the images you want to register and (3 ) to have the same landmark points defined within them ... landmarks will be defined from the center of mass of the labels in the input images . You can use ITK-snap to generate the label images.