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

[Suguru Katsube]

  Hi, Xinjie


1) Which kind of phantom are you using? Normal phantom or voxelized phantom?
I made normal phantom.

2) What tool did you use for generating the attenuation image? GATE or
CASToR?
Attenuation image was generated outside the CASToR. I made attenuation
image using ImageJ.
In ImageJ,
File > New > Image: A fresh stack image is opened.
Image > properties: Set the pixel size
Edit > Selection > Specify: Set regions
Process > Math > Add: Add the attenuation coefficient
File > save As > Raw Data

ImageJ didn't seem to support interfile format without a plugin. So I used
AMIDE to convert the file format.
In AMIDE,
File > Import File(Specify) > Raw Data
File > Export Data Set

It may not be a very wise approach. I hope this helps you.

Best regards,
Suguru

2020年7月16日(木) 5:30 Suguru Katsube <sug.katsu at gmail.com>:

> Hi, Xinjie
>
>
> 1) Which kind of phantom are you using? Normal phantom or voxelized
> phantom?
> I made normal phantom.
>
> 2) What tool did you use for generating the attenuation image? GATE or
> CASToR?
> Attenuation image was generated outside the CASToR. I made attenuation
> image using ImageJ.
> In ImageJ,
> File > New > Image: A fresh stack image is opened.
> Image > properties: Set the pixel size
> Edit > Selection > Specify: Set regions
> Process > Math > Add: Add the attenuation coefficient
> File > save As > Raw Data
>
> ImageJ didn't seem to support interfileformat without a plugin. So I used
> AMIDE to convert the file format.
> In AMIDE,
> File > Import File(Specify) > Raw Data
> File > Export Data Set
>
> It may not be a very wise approach. I hope this helps you.
>
> I hope we can continue to share information with each other as we are all
> interested in the same field.
>
> Best regards,
> Suguru
>
>
>
> 2020年7月15日(水) 23:43 Xinjie Cao <xinjie.cao at stonybrook.edu>:
>
>> Hi Suguru,
>>
>> I am also curious about how to generate the attenuation correction image
>> and have a few questions, could you share some experience about that?
>>
>> 1) Which kind of phantom are you using? Normal phantom or voxelized
>> phantom?
>> 2) What tool did you use for generating the attenuation image? GATE or
>> CASToR?
>>
>> Any reply will be highly appreciated! Thank you!
>>
>> Best,
>>
>> On Wed, Jul 15, 2020 at 6:29 AM Suguru Katsube <sug.katsu at gmail.com>
>> wrote:
>>
>>> 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>:
>>>
>>>> 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 <E-mail%3Aymmk88kmmy at gmail.com>
>>>> ○●----------------------------------------------------------●○
>>>>
>>>> _______________________________________________
>>>> Castor-users mailing listCastor-users at lists.castor-project.orghttp://lists.castor-project.org/listinfo/castor-users
>>>>
>>>> --
>>>> 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
>>>> http://lists.castor-project.org/listinfo/castor-users
>>>>
>>>
>>>
>>> --
>>> ○●----------------------------------------------------------●○
>>> 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 <E-mail%3Aymmk88kmmy at gmail.com>
>>> ○●----------------------------------------------------------●○
>>> _______________________________________________
>>> Castor-users mailing list
>>> Castor-users at lists.castor-project.org
>>> http://lists.castor-project.org/listinfo/castor-users
>>>
>>
>>
>> --
>> *....................................................*
>> *Xinjie Cao*
>> *M.E. / Ph.D. student*
>> *Research Project Assistant*
>> *Department of Electrical and Computer Engineering & Radiology *
>> *Novel Medical Imaging Technologies Lab*
>> *Health Science Center Level 8*
>> *Stony Brook, NY 11794-8460 *
>> *Tel: +1 (631)202-9445*
>> you.stonybrook.edu/goldan/people/
>> *email: **xinjie.cao at stonybroo*k.edu <xinjie.cao at stonybrook.edu>
>>
>>
>> *....................................................*
>> It is prohibited to distribute or publish the files attached to any other
>> people unless you get permission from the writer himself. All rights
>> reserved.
>>
>
>
> --
> ○●----------------------------------------------------------●○
> 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 <E-mail%3Aymmk88kmmy at gmail.com>
> ○●----------------------------------------------------------●○
>


-- 
○●----------------------------------------------------------●○
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 <E-mail%3Aymmk88kmmy at gmail.com>
○●----------------------------------------------------------●○
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.castor-project.org/pipermail/castor-users/attachments/20200716/839ad78c/attachment-0001.html>