Average Activity Concentration (Bq/ml) and SUV

[Dean AlTazi]

Hello CERR community, 

I am analyzing PET scans for the purpose of Texture feature extraction. 

I have a GE Discovery STE. 

I built a  C-code program to extract the data needed from the DICOM file. Unfortunately, the output is not correct due to miscalculation and/or mislocation of Pixel intensity values hence by, SUV.

However, CERR contour volume and SUVmax,min,mean almost exactly matches the ones from Mirada Imaging Processing system. 

As per NEMA and GE manual : 

SUVbw (g/ml) = [ Activity Concentration (bq/ml)/ Actual Activity (Bq) ] * weight (g)

my questions : 

How does CERR calculate SUV and most importantly Activity Concentration ? 

How do you locate Pixel or Voxel intensity Value in GE DICOM file ? 

NEMA referring for DICOM tags that is missed in my GE DICOM files : total dose, tracer activity (0018,1075) 

Your response is highly appreciated ,

Dean

Physics Grad student 

[ap...@mskcc.org]

Dean,

Take a look at the calc_suv.m file.

Regards,
Aditya

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[ap...@mskcc.org]

I also wanted to point out that CERR has tools to calculate texture, shape and statistics-based features. For example:

 

getHaralicParams.m: Used to calculate grayscale co-occurrence based texture features like Entrppy, contrast etc.

 

getShapeParams.m: Used to calculate shape based features like Eccentricity.

 

radiomics_first_order_stats.m: Used to calculate statistics based features like min, mean, kurtosis, etc.

 

All these functions accept structure number as an input (which can be ROI or 42% SUVmax for PET scans).

 

Regards,

Aditya

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[Dean AlTazi]

Aditya, 

Thank you very much for your response. I followed you on github and downloaded your CERR matlab files library. the files are not executing properly but I am sure it is just an issue of calling variables into functions.  It seems like I need to refresh my matlab skills after working on C for a long time. I am sure I will get it. 

can I please get your email to directly ask for your guide, if you dont mind ? 

Thanks, 

Deen 

To post to this group, send email to cerr...@googlegroups.com.

[Dean AlTazi]

Aditya, 

How can I run these m files ? 

it is not built in my the CERR.exe 

should I run it separately using matlab ? 

or should I try to add it in the bin folder of CERR software ? 

[ap...@mskcc.org]

You need to have Matlab in order to run the source code. Add all folders/subfolders to Matlab path and type CERR in Matlab command window to get going.

 

Regards,

Aditya

[Dean AlTazi]

Yes, I do have matlab 2010a with MCR compiler version 7.14 and the path is added to the environment settings. 

Now,  on CERR website there are : 

• Compiled CERR download ( the May29 version). The zip file is not opening after downloading. I tried to download it using google chrome and explorer. However, I got the February20 version, which has the .exe file of CERR. It is limited to importing, exporting and viewing. the only beneficial tool for me is IVH generation but it also has it own bugs. 
  

• https://github.com/adityaapte/CERR File doesnt contain .exe file and I get the following error when I type CERR after specifing "CERR_core" folder in matlab path

• ??? Undefined function or variable 'getCERRPath'.

            Error in ==> CERR at 50

             pathStr = getCERRPath;

your guidance is highly appreciated,

Deen

[Dean AlTazi]

Hello Aditya, 

please look at the attached picture and please provide me with answers to my questions if you dont mind.

Regards,

Deen

[ap...@mskcc.org]

Deen,

 

Since you already have Matlab, you do not need the MCR and the compiled version. Just checkout cerr form gitHub, add all folders/sub-folders to Matlab path and type CERR in Matlab command window.