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This does not work with Python 3.12, as ITK 5.3 is not compiled for it. Python 3.11 or earlier is required.
Use https://github.com/uncbiag/uniGradICON for registration.
That will make visualization of results in Slicer more convenient. Current situation is depicted here:
Case `9021791-right-96 MONTH` causes a crash. Minimal reproduction image is tracked here: https://github.com/InsightSoftwareConsortium/ITKCuberille/pull/80. If we don't end up fixing the crash, we should consider changing [the parameters](https://github.com/uncbiag/OAI_analysis_2/blob/da8644197948719c59adb31935802086a1abb627/oai_analysis/mesh_processing.py#L380-L383).
Visually inspect the 2D maps and identify potentially problematic ones, then take a deeper look into some of them. Images with `v3-` prefix in `Y:\krs-3121-scratch\collections\oai\all-images\`.
We could interpret `*_thickness.npy` numpy array as a grayscale image, and use ITK image comparison filter to regress to known good output.
Red intersection is original mesh, colored intersection is the smoothed mesh. There is some visible shrinking which is expected, and twice as big translation to the screen left (patient right)....
Currently, `analysis_pipeline` function takes a single image as input. Change this function, or add an additional function, to allow processing multiple images in a tight loop. This should allow more...
The current ITK from PyPI is missing libtbb on Linux, see [ITK#4713](https://github.com/InsightSoftwareConsortium/ITK/issues/4713). We want to switch to the newer version of ITK/Cuberille as soon as this is fixed, in order...
This is a less aggressive rework of #437.