thoughts.txt

- Threshold data with value which maximizes coverage while minimizing noise
- Isolate a generous portion of the head scan which could contain the CoW
- Find the largest connected component which contains the voxels representing
  the CoW
    - accept multiple largest connected components if their total volumes are
      relatively minimal
- Find medial axis
- Segement medial axis by identifying bifurcation points
    - segement if the angle of bifurcation is greater than some threshold
      for the average angle of the feeding artery
    - if multiple elements satisfy previous condition, accept the path with
      minimal angle
- Align medial axis mesh with a reference via ICP (PCA/SVD) alignment
- Eliminate paths in the medial axis graph which are not represented in the
  reference medial axis graph
- Remove voxels which do not satisfy some minimal proximity threshold with the
  updated medial axis graph
- Label remaining voxels by the corresponding medial axis path
- Correct artifacts caused by eliminating intermediate arteries (this is 
  probably very difficult)



Revised approach

Prerequisites: an averaged ideal CoW mesh with a corresponding medial axis map
with labeled segements

- Threshold and align iteratively until a desired level of correspondence or
  path area is acquired OR prompt for manual threshold selection
- Isolate a generous portion of the thresholded mesh corresponding to the CoW
  to speed up further computation
- Skeletonize mesh, and segment each path by angle deltas at each bifurcation
- Identify nearest neighbor segemented paths on the overlayed ideal medial axis
  map, defining sufficient correspondence as a function of distance from the
  reference and difference between total path lengths
- Remove all path segements from the target skeleton which do not meet some
  correspondence threshold
- Traverse the updated skeleton and identify all voxels on the target mesh
  which are contained within some radius of the skeleton (this radius could
  be a function of the position on the skeleton for the reference mesh,
  interpolated along the paths of the target skeleton)
- Remove all voxels which were not marked previously