(Registration) Understanding exported similarity/affine transforms

[hmk...@yahoo.dk]

Hi,
I just recently realized that a registration module was added, and have now had a little time (and a relevant project) to play around with it. I am already a big fan - it is very nice, intuitive, and something that I have really been missing - well done!

I would like to be able to export manually set transformation parameters (rigid/affine) - import them in into matlab/python - and use them constructively in various processing scripts, and to perform various customized image operations etc. The translation and rotation part of the transform (so rigid), I understand and can work with quite nicely.

However, when scaling is added (so similarity transforms) I cannot seem to grasp how the transforms are applied. I noticed that the translation parameters are actually modified during export when scalings are non-zero.
Suppose, that I have manually set translation parameters to [t_x, t_y, t_z] and also applied a scaling in y, s_y. Then the translation vector is not exported/stored as [t_x, t_y, t_z], but rather [t_x, y', t_z]. I can't get my head around how that modification of t_y relates to the scaling parameter, s_y.
An explanation or some further references to how the transforms work would be much appreciated :)

Best,
Martin

[Paul Yushkevich]

Hi Martin,

Try using c3d_affine_tool on the transforms exported from ITK-SNAP (it's a binary shipped with SNAP) and the -info-full command. It breaks the transformation into rigid and scaling components.

Hope that's helpful

Paul

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Paul A. Yushkevich, Ph.D.
Professor of Radiology
Penn Image Computing and Science Laboratory
University of Pennsylvania Perelman School of Medicine