How do you use elastix?

[ntatsisk]

It would be helpful if people share info related to their application of elastix. For example, such knowledge can be directly incorporated in the collection of jupyter notebooks and the model zoo of parameter files benefiting the rest of the community!

So, how do you use elastix?

Additionally, you can comment on:

• elastix flavor: executable, C++ API, ITK-Elastix/other wrapping, elastix-napari napari plugin, SlicerElastix 3D Slicer plugin, etc
• dataset: private or public
• result visualization
• availability of shareable code/notebook/parameter file/tips & tricks
• anything else really

Feel free to reply below. Thanks! 🙏

[cnmy-ro]

I'm using elastix as a tool in my MRI reconstruction project mainly to perform cross-contrast registration on clinical MRI scans of the brain. My research focuses on multi-contrast reconstruction which requires the contrasts to be perfectly aligned. The aforementioned registration step is used to correct for any inter-scan motion.

• Elastix flavor: ITK-Elastix, because my workflow is entirely in Python.
• Dataset: Private
• Results, notebooks, tips & tricks: I'm still in the beginner stage in exploring elastix's capabilities in my project. I hope to share some of these contents soon!