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

Fri Jul 17 05:25:37 CEST 2020

Hi Xinjie,

Thank you for your advice for converting format.

> does this process 'Process > Math > Add: Add the attenuation coefficient'
need any outer info or it did calculation based on the image you input?

Attenuation coefficients were outer information. I looked it up on XCOM. I
am simulating a simple structure phantom like the NEMA phantom and consist
of two materials, water and air. Thus, it was not difficult to add the
values manually. For complex phantoms, adding the attenuation coefficient
may be a bit complicated.

Best,
Suguru

2020年7月16日(木) 23:51 Xinjie Cao <xinjie.cao at stonybrook.edu>:

> Hi Suguru,
>
> Thanks for your reply, really appreciate it!
>
> From my understanding, the attenuation map/correction image helps improve
> the real reconstructed image quality because it is based on the
> different tissues or parts of the phantom. So how does ImageJ generate the
> attenuation correction image by adding coefficients without any other
> look-up-table or atlas? I mean, does this process 'Process > Math > Add:
> Add the attenuation coefficient' need any outer info or it did
> calculation based on the image you input?
>
> PS: For image format conversion, I recommend you use Medcon instead of
> AMIDE because it looks like there are some little bugs in AMIDE conversion.
>
> Best,
> Xinjie
>
> On Wed, Jul 15, 2020 at 4:33 PM Suguru Katsube <sug.katsu at gmail.com>
> wrote:
>
>>   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 <https://www.google.com/maps/search/12+Avenue+Foch,+29200+Brest,+FRANCE?entry=gmail&source=g>
>>>>>> 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>
>> ○●----------------------------------------------------------●○
>> _______________________________________________
>> 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>
○●----------------------------------------------------------●○
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