Thoracic cage coordinate system for recording pathologies in lung CT volume data
View Patent ↗We introduce a thoracic cage coordinate system for recording pathology locations in lung CT volume data. The centerlines of each individual rib are extracted and labeled from top to bottom. For each pair of ribs, a three-dimensional (“3D”) orthogonal basis is computed by eigen-analysis of the rib centerline points, which are taken as the x, y, and z axes. The rib pairs form a set of reference planes. Therefore, there are a set of coordinate systems (x, y, z), each of which is locally valid between two adjacent planes. To define a location globally, a fourth parameter, n, is added to identify the serial number of the reference plane. The complete coordinate is recorded as (n, x, y, z). This system is robust against deformations due to bending and twisting, and is relatively stable over inhalation. Further, this system may be readily adapted in other 3D modalities, such as MRI volume data.
1. A computer-implemented method of creating and using a thoracic cage coordinate system from a thoracic cage, the thoracic cage comprising a plurality of individual rib centerlines, comprising:
grouping pairs of individual rib centerlines into a plurality of rib centerline pairs;
constructing a local coordinate system for each of the plurality of rib centerline pairs;
constructing a global coordinate system using the local coordinate systems of the plurality of rib centerline pairs; and
determining thoracic cage coordinates of a pathological location in the global coordinate system, wherein the pathological location is defined by a patient coordinate system, wherein constructing a local coordinate system for each of the plurality of rib centerline pairs comprises:
computing a covariance matrix on the locations of all points on each of the plurality of rib centerline pairs;
performing eigen-analysis on each of the covariance matrices to obtain three eigenvalues and three eigenvectors for each of the plurality of covariance matrices;
forming a three-dimensional (“3D”) orthogonal basis from the three eigenvectors for each of the covariance matrices; and
defining an origin on a spinal cord.
2. The computer-implemented method of claim 1 , wherein forming a three-dimensional (“3D”) orthogonal basis from the three eigenvectors comprises:
assigning one of the three eigenvectors that corresponds to the smallest of the three eigenvalues as a z-axis of the local coordinate system;
assigning one of the three eigenvectors that corresponds to the middle of the three eigenvalues as a y-axis of the local coordinate system;
assigning one of the three eigenvectors that corresponds to the highest of the three eigenvalues as a x-axis of the local coordinate system; and
forming a transformation matrix using the three eigenvectors for each of the covariance matrices.
3. The computer-implemented method of claim 1 , wherein defining an origin on a spinal cord comprises:
determining a plane whose normal is a z-axis for each of the plurality of local coordinate systems;
obtaining a cross-section of the spinal cord with each of the plurality of planes; and
assigning the cross-section as the origin of the each of the plurality planes.
4. The computer-implemented method of claim 1 , wherein constructing a global coordinate system using the local coordinate systems comprises:
labeling each of the plurality of rib centerline pairs, wherein the global coordinate system comprises all of labeled rib centerline pairs.
5. The-computer-implemented method of claim 4 , wherein labeling each of the plurality of rib centerline pairs comprises labeling each of the plurality of rib centerline pairs from top to bottom.
6. The computer-implemented method of claim 4 , wherein labeling each of the plurality of rib centerline pairs comprises labeling each of the plurality of rib centerline pairs from left to right.
7. The computer-implemented method of claim 4 , wherein labeling each of the plurality of rib centerline pairs comprises labeling each of the plurality of rib centerline pairs in a sequential numerical order.
8. A computer-implemented method of creating and using a thoracic cage coordinate system from a thoracic cage, the thoracic cage comprising a plurality of individual rib centerlines, comprising:
grouping pairs of individual rib centerlines into a plurality of rib centerline pairs;
constructing a local coordinate system for each of the plurality of rib centerline pairs;
constructing a global coordinate system using the local coordinate systems of the plurality of rib centerline pairs; and
determining thoracic cage coordinates of a pathological location in the global coordinate system, wherein the pathological location is defined by a patient coordinate system, wherein determining thoracic cage coordinates of a pathological location in the global coordinate system comprises:
transforming the pathological location into each of the local coordinate systems using a transformation matrix of each of the local coordinate systems;
recording the thoracic cage coordinates in each of the local coordinate systems; and
determining which of the local coordinate systems to use by comparing z-coordinates of the thoracic cage coordinates.
9. A machine-readable medium having instructions stored thereon for execution by a processor to perform method of creating and using a thoracic cage coordinate system from a thoracic cage, the thoracic cage comprising a plurality of individual rib centerlines, comprising:
grouping pairs of individual rib centerlines into a plurality of rib centerline pairs;
constructing a local coordinate system for each of the plurality of rib centerline pairs;
constructing a global coordinate system using the local coordinate systems of the plurality of rib centerline pairs; and
determining thoracic cage coordinates of a pathological location in the global coordinate system, wherein the pathological location is defined by a patient coordinate system, wherein constructing a local coordinate system for each of the plurality of rib centerline pairs comprises:
computing a covariance matrix on the locations of all points on each of the plurality of rib centerline pairs;
performing eigen-analysis on each of the covariance matrices to obtain three eigenvalues and three eigenvectors for each of the plurality of covariance matrices;
forming a three-dimensional (“3D”) orthogonal basis from the three eigenvectors for each of the covariance matrices; and
defining an origin on a spinal cord.
10. The machine readable medium of claim 9 , wherein forming a three-dimensional (“3D”) orthogonal basis from the three eigenvectors comprises:
assigning one of the three eigenvectors that corresponds to the smallest of the three eigenvalues as a z-axis of the local coordinate system;
assigning one of the three eigenvectors that corresponds to the middle of the three eigenvalues as a y-axis of the local coordinate system; assigning one of the three eigenvectors that corresponds to the highest of the three eigenvalues as a x-axis of the local coordinate system; and
forming a transformation matrix using the three eigenvectors for each of the covariance matrices.
11. The machine readable medium of claim 9 , wherein defining an origin on a spinal cord comprises:
determining a plane whose normal is a z-axis for each of the plurality of local coordinate systems;
obtaining a cross-section of the spinal cord with each of the plurality of planes; and
assigning the cross section as the origin of the each of the plurality planes.
12. The machine readable medium of claim 9 , wherein constructing a global coordinate system using the local coordinate systems comprises:
labeling each of the plurality of rib centerline pairs, wherein the global coordinate system comprises all of the labeled rib centerline pain.
13. The machine readable medium of claim 12 , wherein labeling each of the plurality of rib centerline pairs comprises labeling each or the plurality of rib centerline pairs from top to bottom.
14. The machine readable medium of claim 12 , wherein labeling each of the plurality of rib centerline pairs comprises labeling each of the plurality of rib centerline pairs from left to right.
15. The machine readable medium of claim 12 , wherein labeling each of the plurality of rib centerline pairs comprises labeling each of the plurality of rib centerline pairs in a sequential numerical order.
16. A machine-readable medium having instructions stored thereon for execution by a processor to perform method of creating and using a thoracic cage coordinate system from a thoracic cage the thoracic cage comprising a plurality of individual rib centerlines, comprising:
grouping pairs of individual rib centerlines into a plurality of rib centerline pairs;
constructing a local coordinate system for each of the plurality of rib centerline pairs;
constructing a global coordinate system using the local coordinate systems of the plurality of rib centerline pairs: and
determining thoracic cage coordinates of a pathological location in the global coordinate system, wherein the pathological location is defined by a patient coordinate system, wherein determining thoracic cage coordinates of a pathological location in the global coordinate system comprises:
transforming the pathological location into each of the local coordinate systems using a transformation matrix of each of the local coordinate systems;
recording the thoracic cage coordinates in each of the local coordinate systems; and
determining which of the local coordinate systems to use by comparing z-coordinates of the thoracic cage coordinates.