[Gate-users] Potential bug report of Edep in DoseActor (Edep always == 1 Mev for any Ion)

Albert Grace Lieu albertnew2018 at gmail.com
Tue Mar 9 00:23:03 CET 2021 

Hi David and Loïc,

Thank you two very much help for helping me.

* /gate/source/voxel_body/gps/energy 0 MeV* solved my problem.  It seems by
default the energy of any ion is set to 1 Mev, which does not make sense.
After forcing the ion's kinetic energy to 0 mev, the output matches my hand
calculated value.

Thank you again very much.
Stay safe and healthy,

Albert


On Mon, Mar 8, 2021 at 6:03 AM David Sarrut <
David.Sarrut at creatis.insa-lyon.fr> wrote:

> Hi,
>
> could you try to force the ion Energy to be 0 MeV ?
> (something like /gate/source/voxel_body/energy 0 MeV)
> see https://github.com/OpenGATE/Gate/issues/358
>
> thanks
> David
>
>
>
> On Mon, Mar 8, 2021 at 2:08 PM Grevillot Loic <
> loic.grevillot at medaustron.at> wrote:
>
>> Hi !
>>
>>
>>
>> Sorry, I did not have time to go through your macros, but you also said “I
>> did not find the example where DoseActor is used to record energy deposited
>> by ions for dosimetry”
>>
>> è You can find it under the gitcontrib
>> <https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2FOpenGATE%2FGateContrib%2Ftree%2Fmaster%2FGATE-RTion&data=04%7C01%7Cloic.grevillot%40medaustron.at%7C991a8c8daae94bce6fbc08d8e03752cf%7Cadb749e06dfd4f6fbea8cd9f8e0c9b89%7C0%7C0%7C637505876735190754%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=ggXJ1p8887dT%2FsE8jSOOZVsHivOVWG91KQ1M%2FTCNiGw%3D&reserved=0>
>> repository, in DoseActor (scrren-shots below)
>>
>> è You can find an example of energy to dose conversion validation for
>> ions – further testing include mass-weighting, volume-weighting algorithms,
>> etc. are also available.
>>
>>
>>
>>
>>
>>
>>
>> Best,
>>
>> Loïc
>>
>>
>>
>>
>>
>>
>>
>> *From:* Albert Grace Lieu [mailto:albertnew2018 at gmail.com]
>> *Sent:* Saturday, March 6, 2021 1:27 AM
>> *To:* Grevillot Loic <loic.grevillot at medaustron.at>; gate-users <
>> gate-users at lists.opengatecollaboration.org>
>> *Cc:* Peter Olcott <polcott at reflexion.com>
>> *Subject:* Re: Potential bug report of Edep in DoseActor (Edep always ==
>> 1 Mev for any Ion)
>>
>>
>>
>> Hi Loïc,
>>
>>
>>
>> Thank you very much for actively answering DoseActor related questions in
>> the past ten years. I saw your answers in the GATE archive quite often. I
>> did read through almost all example codes in GATE-RTiON, but I did not find
>> the example where DoseActor is used to record energy deposited by ions for
>> dosimetry.
>>
>>
>>
>> Here is the problem I have found with Edep in DoseActor, a similar
>> question
>> <https://eur03.safelinks.protection.outlook.com/?url=http%3A%2F%2Flists.opengatecollaboration.org%2Fpipermail%2Fgate-users%2F2009-July%2F003406.html&data=04%7C01%7Cloic.grevillot%40medaustron.at%7C991a8c8daae94bce6fbc08d8e03752cf%7Cadb749e06dfd4f6fbea8cd9f8e0c9b89%7C0%7C0%7C637505876735180759%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=GVfn7d0HY3KvSz1EbfNrBCt9r6FcT%2FbbHW%2FRN1BUIrw%3D&reserved=0>
>> was also asked many years ago. No matter what source I use, like I-131,
>> Lu-177, Edep in DoseActor always returns *1 (Mev) per disintegration*.
>> Dose in DoseActor also utilizes the value returned Edep, which leads to a
>> wrong result. I would rather believe that I made a mistake somewhere
>> than think GATE's DoseActor failed in my case.
>>
>>
>>
>> Could you or any other GATE user have a look at my code? It is
>> self-containt code. You will finish the entire verification in less than 5
>> minutes. Here is what the GATE code does:
>>
>>    - Phantom: 101*101*101 voxelized tissue ( water equivalent) phantom,
>>    with a side of 2 mm for each voxel
>>    - Source: 10 mm radius sphere voxelized Lu177 source with a side of 2
>>    mm for each voxel, and being placed in the center of the phantom
>>    - DoseActor: record dose, Edep, and export a mass image of the
>>    phantom (all 3D array)
>>    - ProductionAndStoppingActor: record the number of Lu177 generated in
>>    each voxel, indicated by Lu177-Stop (3D array)
>>
>>         According to the user manual, "The unit of edep is MeV and the
>> unit of dose is Gy".
>>
>>
>>
>> You will also find a python script (result-analysis.ipynb) to do the
>> analysis:
>>
>>    - reads dose, edep, mass, and particle-prod
>>    - calculate the average energy deposited by a single disintegration.
>>
>> Thank you very much for any help and verification.
>>
>>
>>
>> Albert
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>> On Fri, Mar 5, 2021 at 12:48 AM Grevillot Loic <
>> loic.grevillot at medaustron.at> wrote:
>>
>> FYI,
>>
>> DoseActor validation tests were provided for the GATE-RTiON
>> <https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgate.uca.fr%2Fdownload%2Fgate-rtion&data=04%7C01%7Cloic.grevillot%40medaustron.at%7C991a8c8daae94bce6fbc08d8e03752cf%7Cadb749e06dfd4f6fbea8cd9f8e0c9b89%7C0%7C0%7C637505876735180759%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=Zn97wCKsFa%2BxCi3%2BYO%2F2hLVeY9%2BUf9jOfKAxU3xP1x4%3D&reserved=0>
>> release, in the context of light ion beam therapy under the gitcontrib
>> <https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2FOpenGATE%2FGateContrib%2Ftree%2Fmaster%2FGATE-RTion&data=04%7C01%7Cloic.grevillot%40medaustron.at%7C991a8c8daae94bce6fbc08d8e03752cf%7Cadb749e06dfd4f6fbea8cd9f8e0c9b89%7C0%7C0%7C637505876735190754%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=ggXJ1p8887dT%2FsE8jSOOZVsHivOVWG91KQ1M%2FTCNiGw%3D&reserved=0>
>> repository.
>>
>> The tests can be applied in principle to any GATE release and may help
>> you as a starting point.
>>
>> It would be nice to increase the collection of tests for other clinical
>> applications such as  yours!
>>
>>
>>
>> Best,
>>
>> Loïc
>>
>>
>>
>>
>>
>>
>>
>> *From:* Gate-users [mailto:
>> gate-users-bounces at lists.opengatecollaboration.org] *On Behalf Of *Albert
>> Grace Lieu
>> *Sent:* Freitag, 5. März 2021 05:59
>> *To:* gate-users <gate-users at lists.opengatecollaboration.org>
>> *Subject:* [Gate-users] Edep returned by DoseActor is about 7 times
>> bigger then hand calculated value
>>
>>
>>
>> Hi Gate users,
>>
>>
>>
>> I am validating the validity of DoseActor in GATE for
>> radionuclide dosimetry application. Surprisingly, I found the Edep returned
>> by DoseActor is about 7 times bigger than my hand calculated value, so does
>> the dose returned by DoseActor. I could be wrong, but I double-checked
>> everything I did and had been as prudent as I can before asking for
>> suggestions here.
>>
>>
>>
>> Here is what I did in GATE:
>>
>>    - Phantom: 101*101*101 voxelized tissue ( water equivalent) phantom,
>>    with a side of 2 mm for each voxel
>>    - Source: 10 mm radius sphere voxelized Lu177 source with a side of 2
>>    mm for each voxel, and being placed in the center of the phantom
>>    - DoseActor: record dose, Edep, and export a mass image of the
>>    phantom (all 3D array)
>>    - ProductionAndStoppingActor: record the number of Lu177 generated in
>>    each voxel, indicated by Lu177-Stop (3D array)
>>
>>         According to the user manual, "The unit of edep is MeV and the
>> unit of dose is Gy".
>>
>>
>>
>> Here is how I calculate the average of the energy of Lu177 in water,
>> Lu177 is a beta emitter, the range of electron in water is way smaller than
>> 2mm, thus it is stopped where is created. Given the branching ratio of
>> Lu177, on average a single Lu177 disintegration would deposit 134.16 Kev
>> (electrons only) or 162.95 Kev (electrons and gammas).
>>
>>
>>
>> [image: RTEmagicC_Lu-177_decays.png.png]
>>
>>
>>
>> However, when I divide Edep by Lu177-Stop, the energy per Lu177
>> disintegration returned by DoseActor is ~1.0 Mev, which 7 times bigger
>> than my hand calculated value. Is this an internal issue? I attach my Gate
>> code for your review.
>>
>>
>>
>>
>>
>> Thanks a lot for your help.
>>
>> Sincere wishes,
>>
>> Stay safe and healthy
>>
>> Albert
>>
>>
>>
>>
>>
>> *Disclaimer:*
>> Please notice our E-Mail Disclaimer
>> http://www.medaustron.at/email-disclaimer/
>> <https://eur03.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.medaustron.at%2Femail-disclaimer%2F&data=04%7C01%7Cloic.grevillot%40medaustron.at%7C991a8c8daae94bce6fbc08d8e03752cf%7Cadb749e06dfd4f6fbea8cd9f8e0c9b89%7C0%7C0%7C637505876735190754%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=TJ6%2FLuGasDDIW3Udh8VS9QnmUyzQV3didHXGHiUhyh4%3D&reserved=0>
>>
>>
>>
>>
>> *Disclaimer:*
>> Please notice our E-Mail Disclaimer
>> http://www.medaustron.at/email-disclaimer/
>>
>> _______________________________________________
>> Gate-users mailing list
>> Gate-users at lists.opengatecollaboration.org
>> http://lists.opengatecollaboration.org/mailman/listinfo/gate-users
>
>
>
> --
> David Sarrut, Phd
> Directeur de recherche CNRS
> CREATIS, UMR CNRS 5220, Inserm U1294
> Centre de lutte contre le cancer Léon Bérard
> 28 rue Laënnec, 69373 Lyon cedex 08
> Tel : 04 78 78 51 51 / 06 74 72 05 42
> http://dsarrut.github.io <http://www.creatis.insa-lyon.fr/~dsarrut>
> _________________________________
>  "2 + 2 = 5,  for extremely large values of 2"
> _________________________________
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.opengatecollaboration.org/pipermail/gate-users/attachments/20210308/320dca73/attachment-0001.html>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: image001.jpg
Type: image/jpeg
Size: 21015 bytes
Desc: not available
URL: <http://lists.opengatecollaboration.org/pipermail/gate-users/attachments/20210308/320dca73/attachment-0003.jpg>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: image002.jpg
Type: image/jpeg
Size: 32161 bytes
Desc: not available
URL: <http://lists.opengatecollaboration.org/pipermail/gate-users/attachments/20210308/320dca73/attachment-0004.jpg>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: image003.jpg
Type: image/jpeg
Size: 144936 bytes
Desc: not available
URL: <http://lists.opengatecollaboration.org/pipermail/gate-users/attachments/20210308/320dca73/attachment-0005.jpg>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: image004.png
Type: image/png
Size: 20731 bytes
Desc: not available
URL: <http://lists.opengatecollaboration.org/pipermail/gate-users/attachments/20210308/320dca73/attachment-0001.png>

More information about the Gate-users mailing list