[Castor-users] attenuation correction and normalization

[Hadi Rezaei]

Hi Thibaut
Thank you for your answer.
I shared it. I got it from GATE directly.
Thank you

On Wed, Apr 28, 2021 at 9:02 PM tmerlin <Thibaut.Merlin at univ-brest.fr>
wrote:

> Hi Hadi,
>
> Could you share the header of your mumap (myMapFileName-MuMap.hdr) ? It
> looks like the problem comes from some interfile keys.
>
> Best,
> Thibaut
> On 27/04/2021 20:32, Hadi Rezaei wrote:
>
> Hi Tmerlin
> Thank you for your answer.
> I provided an attenuation map using mu map actor in GATE using the
> following commands:
> #
> /gate/actor/addActor MuMapActor getMuMap
> /gate/actor/getMuMap/attachTo world
> /gate/actor/getMuMap/save mhdoutput/myMapFileName.hdr
> /gate/actor/getMuMap/setPosition 0 0 0 mm
> /gate/actor/getMuMap/setVoxelSize 2.344 2.344 2.344 mm
> /gate/actor/getMuMap/setResolution 300 300 900
> /gate/actor/getMuMap/setEnergy 511 keV
> /gate/actor/getMuMap/setMuUnit 1  1/cm
> and the hdr/image file was provided. But after I added this hdr file to
> castor-recon (./castor-recon -df myfile_df.Cdh -dout output -opti MLEM -it
> 10:20 -th 40 -dim 256,256,827 -fov 600,600,1940 -atn
> myMapFileName-MuMap.hdr) I found some error as follow:
>
>
>
>
>
>
>
>
>
> *"oOptimizerManager::Initialize() -> Initialize optimizer and penalty
> ***** IntfCheckConsistency()-> Error : some mandatory keys not initialized.
> Cannot read the interfile image !                                Error when
> trying to read path to image data                                Error when
> trying to read matrix size (image dimensions) : x= 0, y= 0, z= 1 *****
> oInterfileIO::IntfReadImage() -> A error occurred while checking
> consistencies between reconstruction parameters and interfile keys in the
> header
> '../../GATE_9/gate/Gate/benchmarks/benchPET/Hadi/mhdoutput/myMapFileName-SourceMap.hdr'
> ! ***** oImageSpace::InitAttenuationImage() -> An error occurred while
> reading from file
> '../../GATE_9/gate/Gate/benchmarks/benchPET/Hadi/mhdoutput/myMapFileName-SourceMap.hdr'
> ! ***** oSensitivityGenerator::Initialize() -> A problem occurred while
> initializing the attenuation image into the image space ! *****
> oSensitivityGenerator::Initialize() -> A problem occurred while
> initializing the attenuation files ! ***** castor-recon() -> A problem
> occurred while initializing the sensitivity generator ! ***** Exit function
> called. Abort with code 1."*
> any suggestion to fix it would be appreciated.
> Best,
> Hadi
>
> On Mon, Apr 26, 2021 at 2:58 PM tmerlin <Thibaut.Merlin at univ-brest.fr>
> wrote:
>
>> Hi Hadi,
>>
>> You can provide an attenuation map to castor-recon if you use list-mode
>> format with the -atn option (or directly to castor-GATERootToCastor if you
>> want to get an histogram) .
>>
>> castor-GATERootToCastor doesn't perform normalization correction, so
>> normalization correction coefficients would have to be computed manually
>> and inserted directly in the datafiles, as indicated in the documentation
>> section 6.1.
>>
>> Looking at your image, it is not easy to know what is wrong without
>> details about the simulation and the image values, but it seems it was
>> reconstructed from a simulation with very low statistics.
>>
>> Hope this helps,
>> Thibaut
>> On 24/04/2021 12:23, Hadi Rezaei wrote:
>>
>> Dear CASToR users
>> I simulated an IEC NEMA phantom on a PET using GATE and reconstructed it
>> using CASTOR without any correction (random, scatter, attenuation and
>> normalization). The reconstructed image was undesirable. I found that for
>> random and scatter correction I can write "-t" on
>> the castor-GATERootToCastor to convert only trues (is it right?). But, how
>> can I perform the attenuation correction (and also normalization)?
>> I used bellow commands for convert to CASTOR and reconstructed it.
>>  ./castor-GATERootToCastor -i output.root -m mymacfile.mac -o IEC -s IEC
>> -geo -k
>> ./castor-recon -df IEC_df.Cdh -dout IEC -opti MLEM -it 10:20 -th 40 -dim
>> 512,512,1655 -fov 600,600,1940
>> I attached the reconstructed image here.  I would therefore
>> appreciate it if anyone could help me to apply any correction on it.
>> Best regards
>> Hadi
>>
>>
>> _______________________________________________
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>>
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>>
>> --
>> Thibaut MERLIN -- PhD
>>
>> Docteur en Imagerie Médicale au Laboratoire de Traitement de l'Information Medicale (LaTIM - INSERM UMR 1101)
>> Institut Brestois de recherche en Bio-Santé (IBRBS)
>> 12 Avenue Foch, 29200 Brest, FRANCE
>> Tel: 06.75.12.24.90
>>
>> _______________________________________________
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>>
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>
> --
> Thibaut MERLIN -- PhD
>
> Docteur en Imagerie Médicale au Laboratoire de Traitement de l'Information Medicale (LaTIM - INSERM UMR 1101)
> Institut Brestois de recherche en Bio-Santé (IBRBS)
> 12 Avenue Foch, 29200 Brest, FRANCE
> Tel: 06.75.12.24.90
>
>
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