[Castor-users] attenuation correction and normalization

[Hadi Rezaei]

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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> --
> 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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