Using transformix and a deformation field to transform an image

[artoews]

Hi, I have a deformation field in numpy array format and want to use Transformix to apply this deformation field to an image. Basically I want to adapt this python example script, replacing the TranslationTransform with a DeformationFieldTransform. How can this be done?

[N-Dekker]

@artoews Very good question, thanks!

First of all, the transform you specify to itk.TransformixFilter must be an "ITK transform". In ITK the deformation field transform type is named itk.DisplacementFieldTransform. Before passing it to itk.TransformixFilter, you must set the DisplacementField of this itk.DisplacementFieldTransform.

itk.DisplacementFieldTransform cannot be passed to itk.TransformixFilter.SetTransform, because it cannot be "converted" internally to an elastix/transformix representation. So instead, you should pass it to itk.TransformixFilter.SetExternalTransform

See also

• Allow ITK DisplacementFieldTransform as input to library interface #874

I'm sorry we did not yet make a Python example for this use case 🤷