Hi,
I would like to automatically extract the brain from CT angiograms using a Python script. I have tested the WrapSolidify extension in 3D Slicer, and it works well (see screenshot). My questions are :
1 - How can I implement such a method directly in Python, without using a GUI?
2 - If WrapSolidify is not possible to use in such a way, what are the best approaches for brain extraction from CT angiograms (without relying on deep learning models)?
Thank you in advance for your help!
Hello @malar563,
Possibly mimic the workflow of the SlicerSwissSkullStripper which doesn’t rely on Deep Learning (DL).
If you lift this restriction, possibly try TotalSegmentator which is DL, but you only need to do inference so no requirements for large dataset for training.
You might be able to run that WrapSolidify extension in a python script using Slicer’s docker container.
Here’s the SlicerDockers repo if you want to try that approach:
@lassoan might want to comment too.
Thank you so much for all your answers, it helps me a lot!
