Variation in radiomics features

[Kundan Singh Chufal]

I have calculated radiomics feature over a segmented area using original as well as wavelet transformation. For a particular patient i repeated the feature calculation 10 times and each time calculated feature value differ. For many features this difference is quite a bit. Is it normal to have this difference between two calculations performed over the same patient? How reliable is to do any analysis or model building using this calculation algorithm for feature calculation if it changes so much for a same given image or segmentation.

[ap...@mskcc.org]

Its not normal for results to differ between runs. Can you please post your json settings file and the calculation wrapper. In the settings there is an option to use perturbations for image and segmentation. Can you please check whether that setting is left empty. 

Thanks,

Aditya 

On May 23, 2020, at 5:24 AM, Kundan Singh Chufal <kund...@gmail.com> wrote:

I have calculated radiomics feature over a segmented area using original as well as wavelet transformation. For a particular patient i repeated the feature calculation 10 times and each time calculated feature value differ. For many features this difference is quite a bit. Is it normal to have this difference between two calculations performed over the same patient? How reliable is to do any analysis or model building using this calculation algorithm for feature calculation if it changes so much for a same given image or segmentation.

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[kundan]

I have attached my Jason file

and this is the script I am using for calculation

clc;clear;close all;

 

% Directory containing CERR files

dirName =  uigetdir(cd, 'Select directory with CERR formated file');

 

% .json file containing radiomics settings 

% including the names of structures to extract radiomics

paramFileName = 'templeteWavelet.json';

 

% Excel file path to save features(Optional)

outXlsFile = 'E:\QARC-E001R\feature_calculations\features28052020.xlsx';

 

 

% Call batch feature calculator

featureS = batchExtractRadiomics(dirName,paramFileName,outXlsFile);

[Aditya Apte]

The settings include perturbing images and masks. To use the original image and segmentation, please change

 "perturbation": {

      "sequence": "RV",

      "angle2DStdDeg": 7,

      "volScaleStdFraction": 0.1,

      "superPixVol": 0.005

          },

to 

 "perturbation": {

          },

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<templeteWavelet.json>

[ap...@mskcc.org]

Here is more information on perturbations setting:

https://github.com/cerr/CERR/wiki/Global-radiomics-feature-calculation-parameters

You bring up a good point about some features changing a lot between perturbation runs. Ideally, you want to build a model with features that are robust to small perturbations. Robust features can be detected, for example, by testing their robustness to inter reader segmentation. In the absence of multi-reader data, perturbations have been proposed by Zwanenburg et al https://www.nature.com/articles/s41598-018-36938-4. These are the ones implemented in CERR's "perturbations" setting. 

To view this discussion on the web visit https://groups.google.com/d/msgid/cerr-forum/00919F91-A3CF-43D1-8BF2-68421B736219%40gmail.com.

[Kundan Singh Chufal]

Thanks that solved the problem. 

I would like to use all the filters so do we have some universal template for settings 

In 

ImageType

As for original  we use 

“Original”:{}

Can we use same empty curly braces for other filters like LoG, Haralick, Gabor etc 

Or there are some mandatory parameters which we need to fill prior to extracting features. I am aware of parameters for wavelet filters but not for other. Do we have any reading material guiding us how to set parameters to extract features in CERR using these different filters. 

Thanks and regards 

Sent from my iPhone

On 24-May-2020, at 3:24 PM, ap...@mskcc.org wrote:



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<mg_info.txt>

[ap...@mskcc.org]

Hi Kundan,

We need to create more documentation with templates for various filters. Here is existing description of filter parameters.  https://github.com/cerr/CERR/wiki/Texture-calculation

-Aditya 

To view this discussion on the web visit https://groups.google.com/d/msgid/cerr-forum/E364ED5C-BF38-45B0-9F58-8188FC5842BF%40gmail.com.

[kundan]

Thanks  Aditya

Actually we are doing some work related to response prediction modeling using deep learning CNN algorithm and wanted to compare that model performance with radiomics model.

So we need to have as many features as possible prior to feature selection and model building. We plan to do feature stability and selection based on test retest, inter and intraobserver segmentation and two CT acquisition protocols. 

I went through this documentation  https://github.com/cerr/CERR/wiki/Texture-calculation

and accordingly tried to calculate texture feature using 

Haralick

my jason setting was

"HaralickCooccurance": {
                "NumLevels":64,
                "PatchSize":"[2 2 0]",
                "Directionality":2,
                "Type":"All"
                  }

and i got this error

--- Texture Calculation for Slice # 67 ----
Elapsed time is 7967.295615 seconds.
Unrecognized function or variable 'fieldName'.
Error in createFieldNameFromParameters (line 59)
fieldName = strrep(fieldName,' ','');
Error in calcRadiomicsForImgType (line 88)
    outFieldName = createFieldNameFromParameters...
Error in calcGlobalRadiomicsFeatures (line 24)
featureS = calcRadiomicsForImgType(volToEval,maskBoundingBox3M,paramS,gridS);
Error in batchExtractRadiomics (line 48)
        featS.(structFieldName) = calcGlobalRadiomicsFeatures...
Error in newBatchExtractorEso (line 15)
featureS = batchExtractRadiomics(dirName,paramFileName,outXlsFile); 

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Dr Kundan Singh Chufal

Sr Consultant Radiation Oncology

Chief Breast and Thorax Radiation Services

Rajiv Gandhi Cancer Institute and Research Centre

Sector-5, Rohini 110085, Delhi, India 

[Aditya Apte]

Sounds great. We will look into your reported error and provide you with template settings. 

-Aditya

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[Kundan Singh Chufal]

Once again thanks Aditya

one more thing to add 

Wavelets name "Haar" is recognized but when i try to use different name like "Coiflets" or  any other name it is not recognizing that name.

I did check the file called wavemngr.m and used mavemngr('tfsn') and it prints the wavelet name but some how when i want to extract feature using that listed names i am unable to do so and there is a message stating that name not found.

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<templeteWavelet.json>

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Dr Kundan Singh Chufal

Sr Consultant Radiation Oncology

Chief Breast and Thorax Radiation Services

Rajiv Gandhi Cancer Institute and Research Centre

Sector-5, Rohini 110085, Delhi, India 

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[iy...@mskcc.org]

Hi Kundan,

 

We have expanded the documentation to include examples using derived images: https://github.com/cerr/CERR/wiki/Example1-batch-calculate-global-radiomics-features-for-the-patient-cohort.

 

Also re. wavelet calculations, the supported classes are 'db','haar','coif','fk','sym','dmey','bior','rbio' (‘coif’ , in your case). Further details are available at https://github.com/cerr/CERR/wiki/Texture-calculation.

 

Hope this helps,

Aditi

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[kundan]

thanks for the documentation

but when we are calculating class coif for wavelet this is the error

Error in wavDecom3D (line 19)

[loD,hiD] = wfilters(wavType,'d');

Error in processImage (line 184)

            out3M = wavDecom3D(vol3M,dir,wavType);

Error in calcRadiomicsForImgType (line 49)

        outS = processImage(imageTypeC{k}.imageType,volOrig3M,maskBoundingBox3M,...

Error in calcGlobalRadiomicsFeatures (line 24)

featureS = calcRadiomicsForImgType(volToEval,maskBoundingBox3M,paramS,gridS);

Error in batchExtractRadiomics (line 55)

        featS.(structFieldName) = calcGlobalRadiomicsFeatures...

Error in newBatchExtractorEso (line 20)

featureS1 = batchExtractRadiomics(dirName,paramFileName1,outXlsFile1);

Also when we are calculating LAWSCONVOLUTION

this is the error

Error in doseHist (line 67)

    [volsHistV] = accumulate(volsHistV, volsV, indV);

Error in getIvhParams (line 72)

[scanBinsV, volsHistV] = doseHist(scansV, volsV, IVHBinWidth);

Error in calcRadiomicsForImgType (line 208)

            featureS.(outFieldName).ivhFeaturesS = getIvhParams(scanV, volV, IVHBinWidth,...

Error in calcGlobalRadiomicsFeatures (line 24)

featureS = calcRadiomicsForImgType(volToEval,maskBoundingBox3M,paramS,gridS);

Error in batchExtractRadiomics (line 55)

        featS.(structFieldName) = calcGlobalRadiomicsFeatures...

Error in newBatchExtractorEso (line 20)

featureS1 = batchExtractRadiomics(dirName,paramFileName1,outXlsFile1);

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[iy...@mskcc.org]

Can you please share your JSON settings file so we can help identify the issue?

Also, we recently posted an update for Laws texture calculation. Could you make sure you’re using the latest version of CERR?

 

Thanks,

Aditi

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