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

Tue Mar 9 06:53:41 CET 2021

great !
Note that the default energy is set to 1 MeV in Geant4 (which may make
sense in another context). Since PR#366 it is now set to 0 in Gate.

David

On Tue, Mar 9, 2021 at 12:23 AM Albert Grace Lieu <albertnew2018 at gmail.com>
wrote:

> 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"
>> _________________________________
>>
> _______________________________________________
> 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/20210309/25f9a008/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/20210309/25f9a008/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/20210309/25f9a008/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/20210309/25f9a008/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/20210309/25f9a008/attachment-0001.png>