Feature extraction from single CT slice

[Bryce]

Hello,

I am trying to extract texture features from the center slice of a segmented lung tumor. Is this possible to do in CERR?

Thanks

[ap...@mskcc.org]

Here is sample code to extract radiomics from the central axial slice. Please pull the latest updates from github to get the correct config file used in the example shown below.

 

% Access PlanC from the viewer or from file

global planC

indexS = planC{end};

% Create a new structure with just the central slice

structNum = 3; % structre for which to obtain the central slice

struct3M = getStrMask(structNum,planC);

numSlcs = size(struct3M,3);

[~,~,~,~,sMin,sMax] = compute_boundingbox(struct3M);

centralSlc = round(median(sMin:sMax));

allSlcNumV = 1:numSlcs;

allSlcNumV(centralSlc) = [];

struct3M(:,:,allSlcNumV) = false;

isUniform = 0;

scanNum = 1;

strName = 'central slice';

planC = maskToCERRStructure(struct3M,isUniform, scanNum, strName, planC);

% Calculate features (required settings can be adjusted in JSON config file. Refer to Wiki for documentation)

paramFileName = fullfile(getCERRPath,'PlanMetrics','heterogenity_metrics','sample_radiomics_extraction_settings.json');

paramS = getRadiomicsParamTemplate(paramFileName);

centralSlcStructNum = length(planC{indexS.structures});

featureS = calcGlobalRadiomicsFeatures(scanNum, centralSlcStructNum, paramS, planC);

disp('Features:')

featureS.shapeS

featureS.Original

featureS.Original.firstOrderS

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