ITK Registration Framework Help Needed for Multimodal Image Analysis

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Hello Everyone :hugs:,

For my current research, which involves multimodal image processing, I need some help understanding how to use the ITK registration framework.

For my project, I align brain CT and MRI pictures so that I can compare them. I am having trouble with a few things even though I have been following the documentation’s basic ITK registration examples:

Initial Alignment: The images’ initial alignment is not good even with a stiff transform and shared data as the metric. In order to guarantee comparable intensity ranges, I pre-processed the photos and used a histogram equalisation method.

Should I take into account any further pre-processing measures or starting parameter configurations to enhance the initial alignment? :thinking:

Parameter tuning: I’m having trouble deciding which of the optimizer’s parameters—such as the learning rate and the number of iterations—is best. Is there a recommended method for adjusting these settings in ITK that is particular to multimodal registration? :thinking:

Convergence Problems: When utilising a high number of iterations, the registration process frequently fails to converge. Despite my attempts to modify the convergence criteria, the outcomes are still erratic. Has anyone had such problems? If so, how did you handle them? :thinking:

3D Registration: I’m thinking about employing a multiresolution strategy because both modalities are 3D volumes. Could someone please give me a thorough example or suggest some resources that I can use to learn how to use ITK for multiresolution registration? :thinking:

Post-Processing: Are there particular post-processing methods advised to confirm and improve the alignment after the registration is finished? :thinking: Although I’ve heard of employing checkerboard overlays and different images, I would need additional information about efficient verification techniques.

I’m working in C++ and using ITK version 5.2. It would be very beneficial to have any devops code snippets, examples, or pointers to pertinent material.

Thank You :pray: in advance.

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Greetings, Kelvin.

To learn how to use the ITK registration framework I’d say you may want to get started with The ITK Software Guide (https://itk.org/ItkSoftwareGuide.pdf) — it is a treasure house of knowledge to give you confidence in driving ITK.

To begin with, ITK’s API can be a bit of a maze, but the initial chapters will help you get a good overview, and then, you’d need to find an example that suits your registration scenario. Based on what you said, Section 3.5 of the ITK Software Guide, Multi-Modality Registration, is a good starting point.

The aspects you list, such as parameter tuning, convergence problems, etc. — many of those are covered in the registration framework overview and specific examples.

There’s a bit of a learning curve, but soon you are likely to find yourself in a comfortable place writing your own scripts, whether it’s in C++ or Python.

I hope this helps.

Kind regards,
Constantine

P.S. And then, there will be specific questions, which can be posted here, for the experts to help with.

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You might want to consider using an existing registration package instead of trying to piece together your own ITK-based pipeline. That’d probably save you quite a bit of time and frustration as many of these questions have been considered. Both ANTs and Elastix are derived from ITK components and you probably won’t go wrong with either one.

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