[Castor-users] attenuation correction and normalization
Hadi Rezaei
hrezaei.m.ph at gmail.com
Mon May 3 12:20:29 CEST 2021
Thank you very much.
On Mon, May 3, 2021 at 2:47 PM tmerlin <Thibaut.Merlin at univ-brest.fr> wrote:
> Hi Hadi,
>
> Here is a umap example.
>
> Best,
> Thibaut
>
>
> On 03/05/2021 11:01, Hadi Rezaei wrote:
>
> 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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>>>> at:
>>>> 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
>>
>> --
> 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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