xiaoerlaigeid / Intracranial-CFD

Intracranial-CFD

A simple tool to perform vessel segmentation based on 3DRA and post contrast CBCT data.

Usage

Workflow

1. Batch conversion of DICOM to NIFTI format
2. Image registration (external process, recommend to use 3D slicer if manual initialization is needed)
3. Located the defected point
4. Crop the image to smaller VOI
5. Vessel segmentation with multiple Otsu thresholding
6. Refinement on the segmented data (optional)
7. Extract surface as VTK file
8. Vessel centerline extraction
9. Crop the defected vessel (with Paraview or other 3D mesh processing software)
   1. Using fiducial point to locate the defected point
   2. Using auto_vessel_seg.py to automatically crop the defected vessel region
10. Extend the inlet and outlet region
11. Remeshing and volume meshing
12. CFD simulation
13. Probe CFD result along centerline
14. Multiplanar reconstruction (MPR) with input image and the centerline to straighten the image data