How to generate transform at Elastix rigid registration

Jason_chen · January 5, 2025, 3:37am

Hi, I am using 3D slicer to register a CT volume into MR volume and transform node labels on CT into MR coordinates.

Through Elastix in 3D slicer I can do the registration and output the transform to do the job, which is done successfully. However, I want to make that pipeline in Python scripts, with ITK-Elastix to register the volume.

The problem here is that the way to transform the nodes in moving image(CT) into fixed image(MR) with reference to the registration transform parameters is not clear in ITK-Elastix.

So I want to know how this is done in Slicer-Elastix. In another word, how is it done to get a transform matrix from rigid registration result parameters?

If there is any function or algorithm, it is welcomed to introduce.
Thanks a lot!

muratmaga · January 5, 2025, 6:09pm

This is more of ITK-Elastix question than Slicer one. Did you look at their repository for documentation: GitHub - InsightSoftwareConsortium/ITKElastix: An ITK Python interface to elastix, a toolbox for rigid and nonrigid registration of images

Specifically, this example I think shows what you want to do:

github.com

InsightSoftwareConsortium/ITKElastix/blob/main/examples/ITK_Example01_SimpleRegistration.ipynb

{
 "cells": [
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## 1. Simple Elastix"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Registration"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {},

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How to generate transform at Elastix rigid registration

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