CoLlAGe - cerr/CERR GitHub Wiki

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.

Filter parameters

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

Usage

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);

Generating filtered images

global planC
strNum = 1;
scanNum = [];  % leave empty when passing structNum to automatically identify associated scan index
planC = generateTextureMapFromPlanC(planC,scanNum,strNum,paramS)

Extracting radiomic features

global planC
scanNum  = 1;
strNum = 2; 
featureS = calcGlobalRadiomicsFeatures(scanNum, structNum, paramS, planC);

Reference

Prasanna, P., Tiwari, P., & Madabhushi, A. (2016). Co-occurrence of local anisotropic gradient orientations (CoLlAGe): a new radiomics descriptor. Scientific reports, 6, 37241.