[Castor-users] attenuation correction and normalization

[tmerlin]

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
>>
>>
>>     _______________________________________________
>>     Castor-users mailing list
>>     Castor-users at lists.castor-project.org  <mailto:Castor-users at lists.castor-project.org>
>>     https://lists.castor-project.org/mailman/listinfo/castor-users
>>
>>     To look for something in the mailing-list archives, use the search box 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
>
>     _______________________________________________
>     Castor-users mailing list
>     Castor-users at lists.castor-project.org
>     <mailto:Castor-users at lists.castor-project.org>
>     https://lists.castor-project.org/mailman/listinfo/castor-users
>
>     To look for something in the mailing-list archives, use the search
>     box 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

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.castor-project.org/pipermail/castor-users/attachments/20210428/28154647/attachment.html>