3D Shape Descriptors for Human Peripheral Nerves

Undergraduate Student: Jennard Dy
Principal Investigator: Faisal Beg

This project is a collaboration with Dr. Andy Hoffer of the SFU School of Kinesiology. We are working on developing shape descriptors for peripheral nerves. One way to describe them are through their skeletons or centerlines. Skeletons are useful representations for nerves as they contain most of the information that one would want like length and the number of bifurcations. Various skeletonization programs were researched and tested to find how good they are when applied to our datasets. A suitable program that uses Voronoi diagrams to get the medial axis was found and it was run using the isosurfaces of the nerve objects.

The datasets are sets of MR images of the thigh and these were manually segmented to isolate the sciatic nerve from the rest of the cross-section of the thigh.  The input to the sketonization programs that were found is the 3D dataset formed from the segmented slices or the isosurface of the 3D dataset.

The diagram below shows the centerlines produced by the Vascular Modeling Toolkit (VMTK) Centreline Extraction program.  The VMTK centerline is visualized using ParaView.  The red dots represent the intersection of the centerline with the slices of the original object.

The diagram below shows the manually generated centerline created by connecting all the centroid points using a spline program.  Some preprocessing of the points needs to be done because the program tries to fit a line across all the points without knowing how many branches the object has.  To get these centroid points, each slice of the original dataset is investigated and the centroid of the slice is determined by eye.  The manually generated centerline is visualized using Matlab.

Dr. Faisal Beg's website (http://www.ensc.sfu.ca/~mfbeg)
Dr. Andy Hoffer's website (http://fas.sfu.ca/kin/Faculty/Hoffer.html)

Site by Faculty of Applied Science web team, Simon Fraser University