As @mikebind said, VMTK has been functioning nicely for years. You have really a lot of endpoints, do you really need so many centerlines ?
Try simply with two endpoints that you manually place in the aorta itself, and increase progressively focusing on your project’s end goals.
If you don’t get any centerline at all, you can use ‘Smoothing’ effect in ‘Segment editor’, with ‘Fill holes’ options. The default kernel size is 3mm, it should be suitable. But sometimes, it has to be increased to 6 or 9, rarely more. Then restart creating simple centerlines.
In the ‘Advanced’ section of ‘Extract centerline’, ‘Subdivide’ often helps, as well as reducing ‘Decimation aggressiveness’. Disabling ‘Preprocess input surface’ may be useful too.
Explore further, an aorta should be processed successfully.