Super simple question about fixed/moving/transformix

[John Malone]

Hello everyone

Many people reading this will know the answer to this immediately. 

I wonder if I have the terminology and Transformix correct. 

So I have a volume, called it 'volume_marked.nii', and a companion volume 'volume_marked_regionA.nii' of the same size that contains just an outline of (anatomical) region A.

I want to register volume_marked.nii with another volume ' volume_empty.nii ' and then use the transformation to map volume_marked_regionA.nii onto  volume_empty.nii to see regionA in volume_empty.nii.

Basic stuff right. So I read the manual. In Section 2.6 of manual it says:

"A frequent confusion about the transformation is its direction. In elastix the transformation is defined as a coordinate mapping from the fixed image domain to the moving image domain"

(and in Section 4.2 confirming this, it says  

"Besides using transformix for deforming images, you can also use transformix to evaluate the trans formation Tµ(x) at some points x ∈ ΩF . This means that the input points are specified in the fixed image domain")

I figure I want to eventually pass volume_marked_regionA.nii to transformix to get it in the transformed space, so I have no choice but to make volume_marked.nii my fixed image and  volume_empty.nii the moving image.

So I do this, I look at the result.nii in the output folder, it looks good.

I then pass volume_marked_regionA.nii to transformix, but I don't get the right answer.

Experimenting, I swap the fixed and moving around ie. I pass volume_marked.nii as the MOVING image and  volume_empty nii the FIXED image.

Again I look at the result.nii from elastix, and it works (different to the first time around of course).

This time when I pass the volume_marked_regionA.nii to Transformix, I get the correct output - regionA is mapped correctly.

So, my conclusion is that Transformix maps from the moving space to the fixed space - which contradicts the documentation?!

Do I have this right? So do I have a bug in my code?

Many thanks in advance

John