Bigwarp: export transformation parameters


is there a way to extract the transformation parameters after BigWarp alignment?

E. g. the 7 parameters for scaling and rotation in 3D using a similarity transform?


Hi Chris (@Christoph_Sommer),

Bigwarp uses a thin plate spline transformation model by default, and so has many more than 7 transform parameters. It has ( O( ND ) parameters, where N is the number of landmarks and D is the number of dimensions.

Do you want the affine “part” of the total transformation only? Or did you change the transform model to similarity?

I’m happy to help you achieve what you need, but please explain in more detail what that is exactly.


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Hi John (@bogovicj)

exactly, I would be interested in getting the parameters of the similarity transform: scale, rotation, and translation.


Hi @Christoph_Sommer,

This script may do what you want. Given the csv file storing your landmarks, it prints out the transformation matrix (the affine part of the transform).

It won’t be correct if you changed the transform model in bigwarp when placing landmarks. Is that your use case? Let me know.


Thanks @bogovicj!

My actual use case is the extraction of the scale parameter from the similarity transform.

Your script already gives me a good indication of the scale per axis, yet, in my use case I would need a single scale parameter.

Cheers, Chris


Thanks for clarifying.

In that case, I think this should do the trick:

(It fits a similarity transform using the landmark points, and computes the determinant (volume change) and scale.

Let me know if anything is unclear,



Dear @bogovicj,

thank you very much. That’s exactly what needed!

Cheers, Chris

8 posts were split to a new topic: How to transform points locations (csv) with bigwarp