Registration nii volumes

Good morning all,
I cannot finalize a registration between two volumes, representing the same CT reconstruction (.nii). I have one volume smaller than the other, which is even not aligned. These are the steps I follow:

  • I put the markers on the two volumes to identify common points;
  • I create a Similarity transform based on the just created markers;
  • I apply the transform to the volume I want to move (the smaller one);

The result is that the volume rotates in the right way, but it is not scaled (it is still with the same dimensions).

Is the correct way to do what I want to do?
Thanks in advance.

Which modules do you use for this?