Gray Level Co-ocurrence matrix (GLCM)

[laurar2022]

In order to obtain the GLCM I need to quantize the scan matrix and specify a number of gray levels or bins. However I don't know how to obtain them or if I have to use the number of gray levels specified in the github wiki (https://github.com/cerr/CERR/wiki/Quantize-scan-matrix).

[adityaapte]

https://github.com/cerr/CERR/wiki/example-to-obtain-scan-values-within-an-roi-for-the-patient-cohort provides the sample code to obtain scan intensity for the patient/image cohort. The scan values obtained from this can be used to get an idea of intensity/histogram distribution for the patient population. The number of bins or bin width should be such that it picks up characteristics of the intensity distribution. For standard image units it is better to specify bin width. For example, 5 for HU, 0.05 for PET SUV etc.

…

On Mon, Sep 12, 2022 at 2:37 PM laurar2022 ***@***.***> wrote: In order to obtain the GLCM I need to quantize the scan matrix and specify a number of gray levels or bins. However I don't know how to obtain them or if I have to use the number of gray levels specified in the github wiki ( https://github.com/cerr/CERR/wiki/Quantize-scan-matrix). — Reply to this email directly, view it on GitHub <#763>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AAGNJB6WH7MEGDF3SCJTCSTV55Z6DANCNFSM6AAAAAAQKXK47Y> . You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>

[laurar2022]

Thank you. Is the bin width 5 HU for CT scans?

[adityaapte]

That's right. For example, a range of 500HU within the region of interest would be 100 bins with 5HU bin width. The intensity range and distribution can be obtained for the patient population.

…

On Mon, Sep 12, 2022 at 4:48 PM laurar2022 ***@***.***> wrote: Thank you. Is the bin width 5 HU for CT scans? — Reply to this email directly, view it on GitHub <#763 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AAGNJB365ATULZWSPVUZ6IDV56JILANCNFSM6AAAAAAQKXK47Y> . You are receiving this because you commented.Message ID: ***@***.***>

[laurar2022]

I've used the sample code you posted above and I've obtained the scan values from the ROI. How do I figure out the numbers of bins i need so it picks up characteristics of the intensity distribution?

[EvandroMolinari1998]

In order to obtain the GLCM I need to quantize the scan matrix and specify a number of gray levels or bins. However I don't know how to obtain them or if I have to use the number of gray levels specified in the github wiki (https://github.com/cerr/CERR/wiki/Quantize-scan-matrix).

Did you have to match de dimensions of the mask array with the dose array? Or dindn't you segment the image?

[laurar2022]

I didn't have to match the dimensions of the arrays. The thing is I want to obtain the Gray Level Co-ocurrence Matrix from a specific region of interest, namely a structure. However I don't know how to get the numbers of bins or gray levels from the region of interest so the data I get is right.