Shape features
These features are computed according to the definitions in IBSI section 4.1. Shape features describe geometric aspects of a region of interest (ROI), such as area and volume. Marching Cubes algorithm is used to build the outer surface mesh.
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max3dDiameter: The largest pairwise Euclidean distance between surface voxels in the ROI
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max2dDiameterAxialPlane: The largest pairwise Euclidean distance between axial-plane surface voxels in the ROI.
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max2dDiameterSagittalPlane: The largest pairwise Euclidean distance between sagittal-plane surface voxels in the ROI.
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max2dDiameterCoronalPlane: The largest pairwise Euclidean distance between coronal-plane surface voxels in the ROI.
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global planC
% Define the structure index
structNum = 1;
% Call the shape calculator
shapeS = getShapeParams(structNum,planC)
Mesh calculation might run out of memory in case of very fine resolution. Downsampling helps in such situations. Just provide the additional input which specifies the number of rows/columns/slices to downsample the region of interest. For example,
rcsV = [30,30,20];
shapeS = getShapeParams(structNum,planC,rcsV);
Shape calculation also accepts binary matrix containing the structure segmentation. The following example demonstrates such a calculation.
% mask3M is the binary mask containing the structure segmentation. It can be passed from an external application or obtained from CERR as follows:
mask3M = getUniformStr(structNum,planC);
% Get the associated scan index
scanNum = getStructureAssociatedScan(structNum, planC)
% Get the x,y,z grid spacing
[xValsV, yValsV, zValsV] = getUniformScanXYZVals(planC{indexS.scan}(scanNum));
yValsV = fliplr(yValsV);
xValsV = xValsV(minc:maxc);
yValsV = yValsV(minr:maxr);
zValsV = zValsV(mins:maxs);
% Crop the mask
[minr, maxr, minc, maxc, mins, maxs] = compute_boundingbox(mask3M);
maskBoundingBox3M = mask3M(minr:maxr,minc:maxc,mins:maxs);
% call the shape calculator
shapeS = getShapeParams(mask3M, {xValsV, yValsV, zValsV});