[Castor-users] How to apply attenuation correction for PET reconstruction using GATE root data

[STUTE Simon]

Dear Suguru,


Simply use the "-atn" option in castor-recon to give it the attenuation image you created.


In a very general manner, to get help for all options, just launch castor-recon without arguments.

Then it provides all specific options to get specific help about many themes.

For you, "castor-recon -help-in" provides helps for all options about input files.


Best

Simon


________________________________
De : Castor-users <castor-users-bounces at lists.castor-project.org> de la part de Suguru Katsube <sug.katsu at gmail.com>
Envoyé : mercredi 15 juillet 2020 12:29
À : tmerlin
Cc : castor-users at lists.castor-project.org
Objet : Re: [Castor-users] How to apply attenuation correction for PET reconstruction using GATE root data

Dear Thibaut Merlin,

Thank you for your quick response.
Successfully, I made the attenuation image. Then, I made **.cdh and **.cdf with attenuaton correrction using castor-GATERootToCastor (This is list-mode format for reconstructing with scatter and random correction).

When I run castor-recon, the message below was displayed.

***** oSensitivityGenerator::InitializeAttenuationFiles() -> Attenuation correction is included in the data file while it is not in the sensitivity computation !
***** oSensitivityGenerator::Initialize() -> A problem occurred while initializing the attenuation files !
***** castor-recon() -> A problem occurred while initializing the sensitivity generator !

I know that the attenuation image MUST be providen to the castor-recon exe as well, in order to perform sensitivity image computation for PET list-mode. How should I provide attenuation image to reconstruct the data?

Thank you in advance.
Best regards,

Suguru

2020年6月30日(火) 0:00 tmerlin <Thibaut.Merlin at univ-brest.fr<mailto:Thibaut.Merlin at univ-brest.fr>>:

Hi Suguru,

Attenuation image must be in interfile format, and must be in cm-1. The dimensions/voxel sizes will be interpolated to the reconstruction image dimensions, so you don't need to provide an image with the exact same dimensions than for the reconstruction. Additionally, you should make sure that the reconstruction image dimensions are large enough to include all attenuated materials of the attenuation image, otherwise the attenuation correction will be incorrect.

Regarding the image itself, you should generate it from the geometry of the phantom you use in the GATE simulation, or derive it directly from the phantom image if you used a voxelized phantom.

Hope this helps,

Thibaut


On 29/06/2020 09:57, Suguru Katsube wrote:
Hi all,

I am trying to reconstruct a GATE root file (PET).
I want to apply attenuation correction and reconstruct it. The manual states I need an attenuation image, how do I create it ? The phantom was designed on a GATE and no CT images were acquired. There are many unclear points such as image format, number of pixels, number of slices, alignment, etc. Can I create the attenuation image using a root file or mac file?

Any advice is appreciated.

Best regards,

--
○●----------------------------------------------------------●○
　勝部　俊（Suguru Katsube）

　九州大学大学院医学系学府保健学専攻

　医用量子線科学分野　修士課程2年


　Medical Quantum Radiation Science Course,

　Department of Health Sciences,

　Graduate School of Medical Sciences,

　Kyushu University, Fukuoka, Japan

　E-mail: sug.katsu at gmail.com<mailto:E-mail%3Aymmk88kmmy at gmail.com>

○●----------------------------------------------------------●○



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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
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--
○●----------------------------------------------------------●○
　勝部　俊（Suguru Katsube）

　九州大学大学院医学系学府保健学専攻

　医用量子線科学分野　修士課程2年


　Medical Quantum Radiation Science Course,

　Department of Health Sciences,

　Graduate School of Medical Sciences,

　Kyushu University, Fukuoka, Japan

　E-mail: sug.katsu at gmail.com<mailto:E-mail%3Aymmk88kmmy at gmail.com>

○●----------------------------------------------------------●○
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