Setting an Initial Transform for Elastix

lschuring
Tue, 19 Mar 2024 19:06:04 +0000
Beginner Questions

Hi ITK community!

I am setting up a pipeline in python to register MRI image stacks which tend to have poor initial alignment. I would like to provide an elastix image filter (sitk.ElastixImageFilter()) an initial transform determined via manual inspection (I have an 1x6 array of euler rotations, followed by translations).

I can see that I need to provide my elastixImageFilter a text file in a specific format that will define the initial transform (SetInitialTransformParameterFileName), but I am finding it difficult to find information on what the content/formatting of that file should be. And in the Elastix manual it states, “The transformation is defined as a mapping from the fixed image to the moving image.” Does that still apply to the initial transform that I will provide it in the required text file?

Eventually, I aim to remove the need for manual initial alignment, but for now, I want to focus on improving the elastix transform filter portion of my pipeline before I tackle initial alignment automation.

Thank you!

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