Error in radiomics feature calculations

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Kundan Singh Chufal

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May 21, 2020, 5:24:10 AM5/21/20
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I am using batch extraction method for feature calculation as explained in wiki page
https://github.com/cerr/CERR/wiki/Example1-batch-calculate-global-radiomics-features-for-the-patient-cohort

I am getting this error

CERR>> Loading 126627.mat...
CERR>> Loaded 126627.mat...
Reference to non-existent field 'minClipIntensity'.

Error in calcRadiomicsForImgType (line 39)
minClipIntensity = paramS.textureParamS.minClipIntensity;

Error in calcGlobalRadiomicsFeatures (line 24)
featureS = calcRadiomicsForImgType(volToEval,maskBoundingBox3M,paramS,gridS);

Error in batchExtractRadiomics (line 48)
featS.(structFieldName) = calcGlobalRadiomicsFeatures...

Error in newBatchExtractorEso (line 12)
featureS = batchExtractRadiomics(dirName,paramFileName,outXlsFile);

iy...@mskcc.org

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May 21, 2020, 10:31:40 AM5/21/20
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Hi Kundan,

We have pushed a fix to handle missing/empty values for the minClipIntensity & maxClipIntensity parameters. Can you please try again with the latest version on Github?

These parameters were added recently to specify the intensity limits for quantization. When unspecified, the min & max intensities within the region of interest are used by default. For more information on all available calculation settings, please see https://github.com/cerr/CERR/wiki/Global-radiomics-feature-calculation-parameters.

Best,
Aditi
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kundan

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May 21, 2020, 12:13:43 PM5/21/20
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thanks for yur help. minclipintensity error has gone but now i am getting other error.

Index exceeds the number of array elements (1).

Error in radiomics_first_order_stats (line 118)
edgeV = edgeMinV(k):binWidth:edgeMaxV(k);

Error in calcRadiomicsForImgType (line 92)
        featureS.(outFieldName).firstOrderS = radiomics_first_order_stats...


Error in calcGlobalRadiomicsFeatures (line 24)
featureS = calcRadiomicsForImgType(volToEval,maskBoundingBox3M,paramS,gridS);

Error in batchExtractRadiomics (line 48)
        featS.(structFieldName) = calcGlobalRadiomicsFeatures...

Error in newBatchExtractorEso (line 12)
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 

iy...@mskcc.org

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May 21, 2020, 3:48:01 PM5/21/20
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Thanks for pointing this out.

We have updated the code on GitHub to fix this. Can you please pull the latest changes and give it a try?

 

Best,

Aditi

Myrediff

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May 21, 2020, 11:47:11 PM5/21/20
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Thanks 
Now it’s calculating as expected. Just an additional question. Does this calculation preprocess the image prior to feature extraction. 
Resampling, normalization, zero centering 
Or these preprocessing steps if required has to be done separately before executing feature calculation.

Sent from my iPhone

On 22-May-2020, at 1:18 AM, iy...@mskcc.org wrote:



Kundan Singh Chufal

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May 24, 2020, 7:21:54 AM5/24/20
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I am not able to calculate features using filter Haralick and also for other features

my jason settings is :

"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 

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