Part of ants registration suite
ANTSUseLandmarkImagesToGetBSplineDisplacementField \,fixedImageWithLabeledLandmarks movingImageWithLabeledLandmarks outputDisplacementField meshSize\/[\,0\/]\,xmeshSize\/[\,1\/]\,x\/... \,numberOfLevels \/[\,order=3\/] [\,enforceStationaryBoundaries=1\/] [\,landmarkWeights\/]
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. The optional landmarks weights are read from a text file where each row is either: "label,labelWeight" or "labelWeight" or If the latter format is used, the label weights are assumed to be arranged in ascending order by label.