Incorrect registered image

I have moving image of size 256x256x11 and fixed image of 512x512x512 which is the template image. I just want to register the moving to fixed space. I am getting improper registered image. The sample of the output is given below.

I also did the down sampling of the template to match size of moving image using c3d but still got the same result.

For reference. template image
fixed image

How could I get properly registered moving image to template. I need to transform the mask of fixed image using the result transformation of this registration.

All the help and suggestions are greatly appreciated!

Hello @pratibha,

Before you try to register the images programmatically, please read about the ITK registration framework, see the itk book. If using SimpleITK, go over the online tutorial and fundamental concepts, conventions and registration overview. In any case, there is no need to resample the volumes prior to registration.

Another much easier, non programmatic, solution is to use Slicer and its general registration.

Thank you for the resources, I’ll look into them. Just an additional question, Is the result image image due to bad parameters initialization? I just used the default affine in itk-elastix.

Your images seem to require non-linear deformation, which means you should try BSpline, and more likely, two-stage registration with affine followed by BSpline.

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