get_mesh_agree: Agreement measures for pairs from a list of 3D meshes

In MeshAgreement: Agreement Measures for 3D Meshes

Agreement measures for pairs from a list of 3D meshes

Description

Calculates distance-based as well as volume-overlap-based agreement measures in each possible pairwise comparison for a list of 3D meshes.

Usage

get_mesh_agree(x, boov=FALSE, do_ui=FALSE, chop=TRUE, ...)

Arguments

x	list of observer/mesh objects as generated by read_mesh.
boov	logical. Use package MeshesUnion / MeshesIntersection instead of the corresponding cgalMesh methods for calculating union/intersection volumes. Depending on the meshes, this may have better performance.
do_ui	logical. Calculate volume-overlap-based measures from union/intersection volumes. More time intensive than distance-based measures.
chop	logical. Delete components from the output of vcgMetro that will not be used later on.
...	Options passed to vcgMetro.

Details

Currently, no mesh can be designated gold standard. get_mesh_agree_pair calculates the agreement for a single pair of meshes. get_mesh_metro calculates the distances. get_mesh_ui calculates the mesh union and intersection. For boov=TRUE, package Boov has to be installed separately.

Value

data.frame with these variables

mesh_1	Name of the first mesh of the pair.
mesh_2	Name of the second mesh of the pair.
group	The grouping variable indicating which pairs belong to the same structure.
vol_1	Volume of the first mesh of the pair.
vol_2	Volume of the second mesh of the pair.
vol_u	Volume of the union.
vol_i	Volume of the intersection.
DCOM	Euclidean distance between the respective center of mass of both meshes.
HD_max	Hausdorff distance - worst case, maximum of both directed Hausdorff distances.
HD_avg	Hausdorff distance - average, arithmetic mean of both directed Hausdorff distancess.
ASD	Average symmetric surface distance.
RMSD	Root mean squared symmetric surface distance.
JSC	Jaccard similarity coefficient.
DSC	Dice similarity coefficient.

References

Fotina et al. Critical discussion of evaluation parameters for inter-observer variability in target definition for radiation therapy. Strahlenther Onkol 2012; 188: 160-167.

Hanna et al. Geometrical Analysis of Radiotherapy Target Volume Delineation: a Systematic Review of Reported Comparison Methods. Clin Oncol 2010; 22, 515-525.

Heimann et al. Comparison and Evaluation of Methods for Liver Segmentation From CT Datasets. IEEE Trans Med Imaging 2009; 28: 1251-1265.

Sherer et al. Metrics to evaluate the performance of auto-segmentation for radiation treatment planning: A critical review. Radiother Oncol 2021; 160: 185-191.

https://www.cgal.org/

http://vcg.isti.cnr.it/vcglib/

See Also

get_mesh_agree_pair, get_mesh_metro, get_mesh_ui

Examples

heartL <- mesh3dL_to_cgalMeshL(data_heart_obsL)
get_mesh_agree(heartL, do_ui=FALSE, nSamples=500L, silent=TRUE)

MeshAgreement documentation built on Nov. 25, 2022, 5:05 p.m.