Get Your Brain Together Hackathons

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Tutorial: itk-elastix and MONAI

Instructors

• Konstantinos Ntatsis (Leiden University Medical Center)
• Niels Dekker (Leiden University Medical Center)

Tutorial Description

We will start with a general introduction of the elastix image registration toolbox. The tutorial itself will be about itk-elastix, a python wrapping of the elastix. We will demonstrate how to register and transform (brain) images, and how itk-elastix can be used together with the medical deep learning library MONAI.

Duration: 0.5 hours.

Learning Outcomes

1. Outcome 1. Get an overview of elastix
2. Outcome 2. Use itk-elastix to register and transform brain images
3. Outcome 3. Find additional documentation, example notebooks and parameter file zoo
4. Outcome 4. Bridge images and transforms between ITK/Elastix and MONAI

Approach and Materials

Interactive tutorial based on:

• Slides + a jupyter notebook

Background and References

• itk-elastix repo
• jupyter examples
• ITK-MONAI bridge
• elastix discussions