[Castor-users] attenuation correction and normalization
tmerlin
Thibaut.Merlin at univ-brest.fr
Mon May 3 12:19:38 CEST 2021
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
> <mailto: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
>> <mailto: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
>>> <mailto: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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>>>> Castor-users at lists.castor-project.org <mailto:Castor-users at lists.castor-project.org>
>>>> https://lists.castor-project.org/mailman/listinfo/castor-users
>>>>
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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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>>> <mailto:Castor-users at lists.castor-project.org>
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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
>>
> --
> 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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