Cortical vessel segmentation

I am trying to segment cortical vessels fro gadolinium enhanced t1 MRI images. I tried using local thresholding as well as vessleness filtering, however, scalp and even white matter interfere with the segmentation.

I don’t know how to get a clean segmentation of vessels and I think the vessels are visible enough in the images, as given below.
Do you have any suggestions on what could help?


That’s a hard problem and I don’t think there’s anything automated. Eventually there will be a deep learning solution I’m sure. If you don’t find anything you could try training something using MONAI Label or nnU-Net.

The best approach is manual segmentation, or if you want to speed up, do a treshold and then manual corrections (used with treshold settings also) but it won’t work for small structures.

If you have good quality T1-pre images (without motion) using the same protocol, doing subtraction of T1post - T1pre can give you the vasculature map and then you can clean that up as needed.