[Gate-users] Gate dose to water problem

Fri Feb 3 08:02:58 CET 2017

Hello,

as a first workaround, Luc's suggestion is done here :
https://github.com/OpenGATE/Gate/commit/90327e12eb4559dd838d02d2c1d97e5751251fda

Please test and report.

Sincerely,
David

On Thu, Feb 2, 2017 at 6:01 PM, Grevillot Loic <loic.grevillot at medaustron.at
> wrote:

> Hello,
>
>
>
> Currently the DoseToWater part is incomplete and should contain other
> particles, e.g. carbon ions, helium, etc.
>
> The else part only means at the moment that if the system encounter
> another type of particle, it will calculate the dose to water assuming this
> particle is equivalent to a proton with an energy of 100 MeV.
>
> If we would remove the if (which could also be an option), then the dose
> to water would be equal to the dose, as it would not be rescaled by the
> stopping power ratio.
>
>
>
> So currently the DoseToWater works for electrons, photons and proton beams
> as far as I know.
>
> I have in my to do list to upgrade it for particles up to carbon ions, but
> did not have time yet, that being said it should not be very difficult,
> just require a bit of time and also to find out the correct naming
> convention used in Geant4 for the different particles that can be generated.
>
>
>
> Hope this help!
>
>
>
> Best,
>
> Loïc
>
>
>
>
>
>
>
> *From:* Manuel Bardiès [mailto:manuel.bardies at inserm.fr]
> *Sent:* Thursday, February 02, 2017 5:27 PM
> *To:* Luc SIMON
> *Cc:* Grevillot Loic; gate-users at lists.opengatecollaboration.org
> *Subject:* Re: [Gate-users] Gate dose to water problem
>
>
>
> And thanks to Andreas as well (Luc missed his mail ;-)
>
>
>
> Le 2 févr. 2017 à 17:23, Luc SIMON <uhqd75 at gmail.com> a écrit :
>
>
>
> Dear all and in particular:
>
>
>
> *david.sarrut at creatis.insa-lyon.fr <david.sarrut at creatis.insa-lyon.fr>
> gergely.patay at gmail.com <gergely.patay at gmail.com> alexvergaragil at gmail.com
> <alexvergaragil at gmail.com> thomas at deschler.fr <thomas at deschler.fr>*
>
> *and all the authors of DoseActor.cc <http://doseactor.cc> ...*
>
>
>
> *Following the mail of Tony Younes we investigated this bug.*
>
>
> *We found that the NaN values seem to come from DoseToActor.cc
> <http://dosetoactor.cc> at this level (l 360) *
>
>
>
>     // Other particles should be taken into account (Helium etc), but bug
> ? FIXME
>     if (PartName== "proton" || PartName== "e-" || PartName== "e+" ||
> PartName== "deuteron") {
>
>       DEDX = emcalc->ComputeTotalDEDX(Energy, PartName, material, cut);
>       DEDX_Water = emcalc->ComputeTotalDEDX(Energy, PartName, "G4_WATER",
> cut);
>       doseToWater=edep/density/Volume/gray*(DEDX_Water/1.)/(
> DEDX/(density*e_SI));
>     }
>     else {
>       DEDX = emcalc->ComputeTotalDEDX(100, "proton", material, cut);
>       DEDX_Water = emcalc->ComputeTotalDEDX(100, "proton", "G4_WATER",
> cut);
>       doseToWater=edep/density/Volume/gray*(DEDX_Water/1.)/(
> DEDX/(density*e_SI));
>     }
>
> *In this "if" section sometimes DEDX and DEDX_Water are 0.0 and the
> division 0 / 0 is NaN (please note that 3 / 0 is infinite, which is not a
> NaN value...)*
>
> This problem is fixed. But now another question : why in the "else" part
> DEDX_water is computed for proton ????? (while proton should be considered
> in the first part... )
>
> Moreover, photons should not contribute to "dose". So why do we need this
> "else" part ????
>
> Thank you for your help.
>
> Luc & Tony
>
>
>
>
>
>
>
>
>
>
>
>
>
> 2017-01-31 16:22 GMT+01:00 Grevillot Loic <loic.grevillot at medaustron.at>:
>
> Hi,
>
> Could you send macros and output files?
>
> Best,
>
> Loïc
>
>
>
>
>
>
>
> *From:* tony youness [mailto:tony_youness at live.com]
> *Sent:* Tuesday, January 31, 2017 3:14 PM
> *To:* Grevillot Loic; gate-users at lists.opengatecollaboration.org
> *Subject:* Re: Gate dose to water problem
>
>
>
> Hi,
>
> I am simulating high energy photon beams (6 and 10 MeV) for external
> radiotherapy applications.
>
> I tried both ("Water" and "G4_WATER") and I am still getting NAN values
> (only when the absorbed dose is reported as absorbed dose to water). The
> voxel values between both absorbed dose report (Dose to medium and Dose to
> water) are also different even though that the medium is WATER.
>
> Regards,
>
> Tony
>
>
>
> On 31/01/17 8:37 am, Grevillot Loic wrote:
>
> Hello,
>
>
>
> Which beam are you simulating? (photons, electrons, light ions, etc.)
>
> Which water did you define in your simulation? “Water” is different from
> “GEANT4_WATER” -> could you try using GEANT4_WATER?
>
>
>
> Best,
>
> Loïc
>
>
>
>
>
>
>
> *From:* Gate-users [mailto:gate-users-bounces at lists.opengatecollaboration.
> org <gate-users-bounces at lists.opengatecollaboration.org>] *On Behalf Of *tony
> youness
> *Sent:* Monday, January 30, 2017 1:04 PM
> *To:* gate-users at lists.opengatecollaboration.org
> *Subject:* [Gate-users] Gate dose to water problem
>
>
>
> Dear All,
>
> I am facing a problem with gate dose actor. When enabling dose to water i
> get Nan values in some of the voxels in the water region of my phantom. I
> also get different values in the water voxels between both dose reports
> (dose to medium and dose to water). It seems like there's a bug when gate
> tries to converts dose to medium into the dose to water *when in the
> water region*. Has anyone already faced this problem? Any help would be
> much appreciated.
>
> Kind Regards,
>
> Tony Younes
>
>
>
>
>
>
>
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>
> --
>
> ___________________
>
> SIMON Luc, Physicien Médical, PhD
> Département d'Ingénierie et de Physique Médicale - IUCT-Oncopole -
> Toulouse, FRANCE
>
> INSERM UMR 1037 (CRCT) - Equipe 15 - Toulouse, FRANCE
>
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-- 
David Sarrut, Phd
Directeur de recherche CNRS
CREATIS, UMR CNRS 5220, Inserm U1206
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
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 "2 + 2 = 5,  for extremely large values of 2"
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