[Castor-users] attenuation correction and normalization

[Hadi Rezaei]

Hi Thibaut
I am sorry for the delay.
Could you share a sample of the header (.hdr) file ??
Thank you so much.
Hadi

On Thu, Apr 29, 2021 at 6:27 PM tmerlin <Thibaut.Merlin at univ-brest.fr>
wrote:

> Hi Hadi,
>
> Could you check if there is an issue with the file ? I couldn't open it
> using regular text editors.
>
> Best,
> Thibaut
> On 28/04/2021 20:57, Hadi Rezaei wrote:
>
> 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
>>>
>>> _______________________________________________
>>> Castor-users mailing list
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>>> https://lists.castor-project.org/mailman/listinfo/castor-users
>>>
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>>> https://castor-project.org/mailing-list
>>
>> --
>> 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
>>
>> --
> 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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