<div dir="ltr">Hello, <div> </div><div>as a first workaround, Luc's suggestion is done here : </div><div><a href="https://github.com/OpenGATE/Gate/commit/90327e12eb4559dd838d02d2c1d97e5751251fda">https://github.com/OpenGATE/Gate/commit/90327e12eb4559dd838d02d2c1d97e5751251fda</a> <div> </div><div>Please test and report. </div><div> </div><div>Sincerely, </div><div>David</div><div> </div><div> </div></div></div><div class="gmail_extra"> <div class="gmail_quote">On Thu, Feb 2, 2017 at 6:01 PM, Grevillot Loic <<a href="mailto:loic.grevillot@medaustron.at" target="_blank">loic.grevillot@medaustron.at</a>> wrote: <blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"> <div lang="EN-US" link="blue" vlink="purple"> <div class="m_-956619090171563397WordSection1"> 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 <div> <div style="border:none;border-top:solid #b5c4df 1.0pt;padding:3.0pt 0in 0in 0in"> From: Manuel Bardiès [mailto:<a href="mailto:manuel.bardies@inserm.fr" target="_blank">manuel.bardies@inserm.fr</a>] Sent: Thursday, February 02, 2017 5:27 PM To: Luc SIMON Cc: Grevillot Loic; <a href="mailto:gate-users@lists.opengatecollaboration.org" target="_blank">gate-users@lists.opengatecollaboration.org</a> Subject: Re: [Gate-users] Gate dose to water problem </div> </div><div><div class="h5"> And thanks to Andreas as well (Luc missed his mail ;-) <div> <div> <blockquote style="margin-top:5.0pt;margin-bottom:5.0pt"> <div> Le 2 févr. 2017 à 17:23, Luc SIMON <<a href="mailto:uhqd75@gmail.com" target="_blank">uhqd75@gmail.com</a>> a écrit : </div> <div> <div> <div> Dear all and in particular: <a href="mailto:david.sarrut@creatis.insa-lyon.fr" target="_blank">david.sarrut@creatis.insa-lyon.fr</a> <a href="mailto:gergely.patay@gmail.com" target="_blank">gergely.patay@gmail.com</a> <a href="mailto:alexvergaragil@gmail.com" target="_blank">alexvergaragil@gmail.com</a> <a href="mailto:thomas@deschler.fr" target="_blank">thomas@deschler.fr</a> </div> and all the authors of <a href="http://doseactor.cc" target="_blank">DoseActor.cc</a> ... <div> </div> <div> Following the mail of Tony Younes we investigated this bug. </div> <div> We found that the NaN values seem to come from <a href="http://dosetoactor.cc" target="_blank">DoseToActor.cc</a> 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)); } </div> <div> 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...) </div> <div> 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... ) </div> <div> Moreover, photons should not contribute to "dose". So why do we need this "else" part ???? </div> <div> Thank you for your help. </div> <div> Luc & Tony </div> <div> </div> <div> </div> <div> </div> <div> </div> <div> </div> </div> <div> <div> 2017-01-31 16:22 GMT+01:00 Grevillot Loic <<a href="mailto:loic.grevillot@medaustron.at" target="_blank">loic.grevillot@medaustron.at</a>>: <div> <div> Hi, Could you send macros and output files? Best, Loïc <div> <div style="border:none;border-top:solid #b5c4df 1.0pt;padding:3.0pt 0in 0in 0in"> From: tony youness [mailto:<a href="mailto:tony_youness@live.com" target="_blank">tony_youness@live.com</a>] Sent: Tuesday, January 31, 2017 3:14 PM To: Grevillot Loic; <a href="mailto:gate-users@lists.opengatecollaboration.org" target="_blank"> gate-users@lists.opengatecollaboration.org</a> Subject: Re: Gate dose to water problem </div> </div> 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 <div> On 31/01/17 8:37 am, Grevillot Loic wrote: </div> <blockquote style="margin-top:5.0pt;margin-bottom:5.0pt"> 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 <div> <div style="border:none;border-top:solid #b5c4df 1.0pt;padding:3.0pt 0in 0in 0in"> From: Gate-users [<a href="mailto:gate-users-bounces@lists.opengatecollaboration.org" target="_blank">mailto:gate-users-bounces@lists.opengatecollaboration.org</a>] On Behalf Of tony youness Sent: Monday, January 30, 2017 1:04 PM To: <a href="mailto:gate-users@lists.opengatecollaboration.org" target="_blank"> gate-users@lists.opengatecollaboration.org</a> Subject: [Gate-users] Gate dose to water problem </div> </div> 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 Disclaimer: Please notice our E-Mail Disclaimer <a href="http://www.medaustron.at/email-disclaimer/" target="_blank">http://www.medaustron.at/email-disclaimer/</a> </blockquote> </div> <div> Disclaimer: Please notice our E-Mail Disclaimer <a href="http://www.medaustron.at/email-disclaimer/" target="_blank">http://www.medaustron.at/email-disclaimer/</a> </div> </div> _______________________________________________ Gate-users mailing list <a href="mailto:Gate-users@lists.opengatecollaboration.org" target="_blank">Gate-users@lists.opengatecollaboration.org</a> <a href="http://lists.opengatecollaboration.org/mailman/listinfo/gate-users" target="_blank">http://lists.opengatecollaboration.org/mailman/listinfo/gate-users</a> </div> -- <div> <div> <div> <div> <div> ___________________ SIMON Luc, Physicien Médical, PhD Département d'Ingénierie et de Physique Médicale - IUCT-Oncopole - Toulouse, FRANCE </div> <div> INSERM UMR 1037 (CRCT) - Equipe 15 - Toulouse, FRANCE </div> </div> </div> </div> </div> </div> _______________________________________________ Gate-users mailing list <a href="mailto:Gate-users@lists.opengatecollaboration.org" target="_blank">Gate-users@lists.opengatecollaboration.org</a> <a href="http://lists.opengatecollaboration.org/mailman/listinfo/gate-users" target="_blank">http://lists.opengatecollaboration.org/mailman/listinfo/gate-users</a> </div> </blockquote> </div> </div> </div></div></div><div><div class="h5"> <div class="m_-956619090171563397WordSection1"> Disclaimer: Please notice our E-Mail Disclaimer <a href="http://www.medaustron.at/email-disclaimer/" target="_blank">http://www.medaustron.at/email-disclaimer/</a> </div> </div></div></div> _______________________________________________ Gate-users mailing list <a href="mailto:Gate-users@lists.opengatecollaboration.org">Gate-users@lists.opengatecollaboration.org</a> <a href="http://lists.opengatecollaboration.org/mailman/listinfo/gate-users" rel="noreferrer" target="_blank">http://lists.opengatecollaboration.org/mailman/listinfo/gate-users</a> </blockquote></div> <div> </div>-- <div class="gmail_signature" data-smartmail="gmail_signature"><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr">David Sarrut, Phd Directeur de recherche CNRS CREATIS, UMR CNRS 5220, Inserm U1206<div>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 <a href="http://www.creatis.insa-lyon.fr/~dsarrut" target="_blank">http://www.creatis.insa-lyon.fr/~dsarrut</a> _________________________________</div><div> "2 + 2 = 5, for extremely large values of 2" _________________________________</div></div></div></div></div></div></div> </div>