[Castor-users] attenuation correction and normalization
tmerlin
Thibaut.Merlin at univ-brest.fr
Thu Apr 29 15:58:53 CEST 2021
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>
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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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> --
> 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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