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CoLlAGe
Co-occurrence of Local Anisotropic Gradient Orientations (CoLlAGe) is a radiomic descriptor for capturing local anisotropic differences in voxel-level gradient orientations. It is computed by assigning every image voxel an entropy value associated with the co-occurrence matrix of gradient orientations computed around every voxel.
Dimension : 1- 2D 2- 3D
Dominant_Dir_Radius: Patch size [numRows, numCols, numSlices]
Cooccur_Radius: Patch size [numRows, numCols, numSlices]
Number_Gray_Levels: No. gray levels
Filters can be applied by manually creating a dictionary of parameters or passing them via JSON-format configuration files.
- Dictionaries are created using the syntax:
paramS.<parameter_name>.val = <value>;
where parameter_name
is one of the supported filter parameters listed above and value
, one of the associated arguments.
-
Sample filter configuration
The following settings can be used to (1) obtain a CoLlage-filtered after cropping around the specified structure and padding by M voxel widths, and (2) calculate first-order statistics from the filtered image.
{
"structures": ["ROI"],
"imageType": {
"CoLlage": {
"Dimension ": 2,
"Dominant_Dir_Radius": [N N N],
"Cooccur_Radius": [P P P],
"Number_Gray_Levels": 64
}
},
"settings": {
"padding": {
"cropToMaskBounds": "yes",
"method": "mirror",
"size": [M M M]
},
"firstOrder": {
"offsetForEnergy": 0,
"binNumEntropy":64
}
}
}
Configurations are parsed and converted to parameter dictionaries using
paramFile = 'Path/to/config_file.json'
paramS = getRadiomicsParamTemplate(paramFile);
global planC
strNum = 1;
scanNum = []; % leave empty when passing structNum to automatically identify associated scan index
planC = generateTextureMapFromPlanC(planC,scanNum,strNum,paramS)
global planC
scanNum = 1;
strNum = 2;
featureS = calcGlobalRadiomicsFeatures(scanNum, structNum, paramS, planC);
- Prasanna, P., Tiwari, P., & Madabhushi, A. (2016). Co-occurrence of local anisotropic gradient orientations (CoLlAGe): a new radiomics descriptor. Scientific reports, 6, 37241.