<html><head><meta http-equiv="content-type" content="text/html; charset=utf-8"></head><body dir="auto"><div>New Gate version Thank you and best regards.---------------------------------------ELGHRIBI MOHAMED ZINEDDINEPrincipal Radiation Medical PhysicistCentre Pierre et Marie Curie (CPMC @ Algiers)Tel : <a href="tel:%2B%28213%29555588659" value="+213555588659" target="_blank" style="font-size: 13pt;">+(213)555588659</a>E-mail : <a href="mailto:z.elghrbi@gmail.com" target="_blank">z.elghribi@gmail.com</a>/ <a href="mailto:z.elghrbi@gmail.com" target="_blank">z.elghribi@</a><a href="http://ymail.com/" target="_blank">ymail.com</a></div><div> Le 29 janv. 2014 à 20:50, <a href="mailto:gate-users-request@lists.opengatecollaboration.org">gate-users-request@lists.opengatecollaboration.org</a> a écrit : </div><blockquote type="cite"><div>Send Gate-users mailing list submissions to <a href="mailto:gate-users@lists.opengatecollaboration.org">gate-users@lists.opengatecollaboration.org</a> To subscribe or unsubscribe via the World Wide Web, visit <a href="http://lists.opengatecollaboration.org/mailman/listinfo/gate-users">http://lists.opengatecollaboration.org/mailman/listinfo/gate-users</a> or, via email, send a message with subject or body 'help' to <a href="mailto:gate-users-request@lists.opengatecollaboration.org">gate-users-request@lists.opengatecollaboration.org</a> You can reach the person managing the list at <a href="mailto:gate-users-owner@lists.opengatecollaboration.org">gate-users-owner@lists.opengatecollaboration.org</a> When replying, please edit your Subject line so it is more specific than "Re: Contents of Gate-users digest..." Today's Topics: 1. Re: Wavelength-shifting (WLS) fibres coupled to scintillators (Filipe Castro) 2. Re: Proton Therapy Simulation (David Sarrut) 3. Re: Wavelength-shifting (WLS) fibres coupled to scintillators (Vesna Cuplov) ---------------------------------------------------------------------- Message: 1 Date: Wed, 29 Jan 2014 17:53:35 +0000 From: Filipe Castro <<a href="mailto:ifcastro@ua.pt">ifcastro@ua.pt</a>> To: Vesna Cuplov <<a href="mailto:vesna.cuplov@gmail.com">vesna.cuplov@gmail.com</a>> Cc: "<a href="mailto:gate-users@lists.opengatecollaboration.org">gate-users@lists.opengatecollaboration.org</a>" <<a href="mailto:gate-users@lists.opengatecollaboration.org">gate-users@lists.opengatecollaboration.org</a>> Subject: Re: [Gate-users] Wavelength-shifting (WLS) fibres coupled to scintillators Message-ID: <<a href="mailto:CBA98BEA593F354AA31A7E260FD3FFE2A43855EB@SEQUOIA.ua.pt">CBA98BEA593F354AA31A7E260FD3FFE2A43855EB@SEQUOIA.ua.pt</a>> Content-Type: text/plain; charset="us-ascii" Hello Filipe, Hi Vesna, thanks for the reply. I want to simulate scintillation photons produced by 511 keV gammas and their optical path through a LYSO scintillator with mirror polished ends and reflective side surfaces. One end of the crystal is coupled to a wavelength-shifting fibre (double-cladded BCF-91A fibre), such that crystal and fibre make a 90 degree angle. As I am not experienced with Gate (using vGate 2.1), I have many doubts regarding the proper physics and geometry necessary for the simulation, namely of the optical photons path, optical boundaries and fibre geometry. Is there anyone who has simulated similar experiments with this kind of fibres, for example in the AxPET project, who can help me out? I've already recompiled Gate with optical ON. In order to define the reflective surfaces of the crystal, do I need to first define the volumes with the reflective material or is it possible to define the surfaces only with the crystal volume? If your crystal is the LYSO material, you just need to define your crystal volume with the LYSO material properties in Materials.xml. For the polished ends and reflective surfaces, you define the surfaces with the finish, reflectivity, .... parameters in Surface.xml. Don't I need to have 2 volumes of different materials to define a surface? For now I have only defined the LYSO volume. My question is if I need to define the volume with white reflective material (0.1 mm BaSO4) and then the surface, e.g. /gate/LYSO/surfaces/name Surface-From-LYSO-To-Reflector /gate/LYSO/surfaces/insert Reflector (previously defined?) /gate/LYSO/surfaces/Surface-From-LYSO-To-Reflector/SetSurface surface_name (defined in Surface.xml) Or if these 3 lines are enough and I only need to define the surface properties in Surface.xml ? Is it necessary to define separate volumes with the different materials of the fibre (core, first clad and 2nd clad)? In this case, it is a square fibre, so what would be the best way to do it? For the WLS fiber, you can describe it as one volume or more detailed volumes. I think one volume would be enough as long as you have its properties which are the absorption/emission wls spectra, mixture (in case you use one volume that is a mix of sub components) refractive index, ... The thing is that the core of the fibre is polystyrene (n = 1.60), the 1st clad is acrylic (n = 1.49) and the 2nd clad fluor-acrylic (n = 1.42). These refractive index differences are designed to obtain a higher photon trapping efficiency. In the case of a square 1 mm fiber, the core has approx. 0.94 mm thickness, the 1st clad 0.04 mm and the 2nd clad 0.02 mm. I'd like to have the simulation as realistic as possible, so I wonder what is the best solution to achieve this. I can assume the whole volume of the fibre to have the same absorption/emission wls spectra. Are these physics processes enough: Scintillation, PhotoElectric, Compton, GammaConversion, OpticalAbsorption, OpticalWLS, OpticalBoundary ? You might also need OpticalRayleigh and OpticalMie which are the physics processes related to the optical photon scattering. In that case you would need the Mie and/or Rayleigh scattering lenghts, material anisotropy for Mie scattering. This depends on your crystal and fiber materials. Thanks, I will look that up. I hope this helps, Vesna Thanks again! It sure helps. I hope you or someone can help with the remaining doubts. Best, Filipe -------------- next part -------------- An HTML attachment was scrubbed... URL: <<a href="http://lists.opengatecollaboration.org/mailman/private/gate-users/attachments/20140129/74ccce49/attachment-0001.html">http://lists.opengatecollaboration.org/mailman/private/gate-users/attachments/20140129/74ccce49/attachment-0001.html</a>> ------------------------------ Message: 2 Date: Wed, 29 Jan 2014 20:20:06 +0100 From: David Sarrut <<a href="mailto:David.Sarrut@creatis.insa-lyon.fr">David.Sarrut@creatis.insa-lyon.fr</a>> To: Loic Grevillot <<a href="mailto:loic.grevillot@gmail.com">loic.grevillot@gmail.com</a>> Cc: gate-users <<a href="mailto:gate-users@lists.opengatecollaboration.org">gate-users@lists.opengatecollaboration.org</a>>, Edward Smith <<a href="mailto:edwardaksmith@gmail.com">edwardaksmith@gmail.com</a>> Subject: Re: [Gate-users] Proton Therapy Simulation Message-ID: <<a href="mailto:CAKTJC4Bs5id_QtZa+yc1by3Hy6eFSr_B0+y6w8SfVhP8Qbt8tg@mail.gmail.com">CAKTJC4Bs5id_QtZa+yc1by3Hy6eFSr_B0+y6w8SfVhP8Qbt8tg@mail.gmail.com</a>> Content-Type: text/plain; charset="iso-8859-1" and there is an example of proton simulation in the source code : example/example_Radiotherapy/ look the listofexample.txt file David On Wed, Jan 29, 2014 at 4:03 PM, Loic Grevillot <<a href="mailto:loic.grevillot@gmail.com">loic.grevillot@gmail.com</a>>wrote: <blockquote type="cite">Dear Edward, </blockquote><blockquote type="cite"> </blockquote><blockquote type="cite">I think you should look into the documentation section Radiotherapy </blockquote><blockquote type="cite">applications from </blockquote><blockquote type="cite"><a href="http://wiki.opengatecollaboration.org/index.php/Users_Guide_V6.2">http://wiki.opengatecollaboration.org/index.php/Users_Guide_V6.2</a>.<<a href="http://wiki.opengatecollaboration.org/index.php/Users_Guide_V6.2">http://wiki.opengatecollaboration.org/index.php/Users_Guide_V6.2</a>> </blockquote><blockquote type="cite">Especially Readout parameters for Radiotherapy applications: Actors<<a href="http://wiki.opengatecollaboration.org/index.php/Users_Guide_V6.2:Readout_parameters_for_Radiotherapy_applications:_Actors">http://wiki.opengatecollaboration.org/index.php/Users_Guide_V6.2:Readout_parameters_for_Radiotherapy_applications:_Actors</a>> here </blockquote><blockquote type="cite"> </blockquote><blockquote type="cite"><a href="http://wiki.opengatecollaboration.org/index.php/Users_Guide_V6.2:Readout_parameters_for_Radiotherapy_applications:_Actors">http://wiki.opengatecollaboration.org/index.php/Users_Guide_V6.2:Readout_parameters_for_Radiotherapy_applications:_Actors</a> </blockquote><blockquote type="cite"> </blockquote><blockquote type="cite">Some actors such as </blockquote><blockquote type="cite">* Electromagnetic (EM) properties </blockquote><blockquote type="cite">* Track length </blockquote><blockquote type="cite">* Delta kinetic energy </blockquote><blockquote type="cite">could be helpful for you. </blockquote><blockquote type="cite"> </blockquote><blockquote type="cite">You can also use the "filter" capabilities for a specific particle. </blockquote><blockquote type="cite"> </blockquote><blockquote type="cite">Hope this helps! </blockquote><blockquote type="cite"> </blockquote><blockquote type="cite">LG </blockquote><blockquote type="cite"> </blockquote><blockquote type="cite"> </blockquote><blockquote type="cite"> </blockquote><blockquote type="cite"> </blockquote><blockquote type="cite">Lo?c </blockquote><blockquote type="cite"> </blockquote><blockquote type="cite"> </blockquote><blockquote type="cite">2014-01-29 Edward Smith <<a href="mailto:edwardaksmith@gmail.com">edwardaksmith@gmail.com</a>> </blockquote><blockquote type="cite"> </blockquote><blockquote type="cite"><blockquote type="cite"> Hi, </blockquote></blockquote><blockquote type="cite"><blockquote type="cite"> </blockquote></blockquote><blockquote type="cite"><blockquote type="cite">I'm trying to model a linear energy transfer for a proton beam and for </blockquote></blockquote><blockquote type="cite"><blockquote type="cite">this I need energy deposited for each step and the step's length. I've been </blockquote></blockquote><blockquote type="cite"><blockquote type="cite">reading through the online user manual and I'm not sure if this is </blockquote></blockquote><blockquote type="cite"><blockquote type="cite">possible? From what I've understood to get this data I would need to define </blockquote></blockquote><blockquote type="cite"><blockquote type="cite">everything within a system. I've tried using the scanner system and </blockquote></blockquote><blockquote type="cite"><blockquote type="cite">attaching a crystalSD as a work out but it's failed to work. </blockquote></blockquote><blockquote type="cite"><blockquote type="cite"> </blockquote></blockquote><blockquote type="cite"><blockquote type="cite">Is there any way I can use GATE to do this? </blockquote></blockquote><blockquote type="cite"><blockquote type="cite"> </blockquote></blockquote><blockquote type="cite"><blockquote type="cite">Regards, </blockquote></blockquote><blockquote type="cite"><blockquote type="cite"> </blockquote></blockquote><blockquote type="cite"><blockquote type="cite">Edward </blockquote></blockquote><blockquote type="cite"><blockquote type="cite"> </blockquote></blockquote><blockquote type="cite"><blockquote type="cite">_______________________________________________ </blockquote></blockquote><blockquote type="cite"><blockquote type="cite">Gate-users mailing list </blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><a href="mailto:Gate-users@lists.opengatecollaboration.org">Gate-users@lists.opengatecollaboration.org</a> </blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><a href="http://lists.opengatecollaboration.org/mailman/listinfo/gate-users">http://lists.opengatecollaboration.org/mailman/listinfo/gate-users</a> </blockquote></blockquote><blockquote type="cite"><blockquote type="cite"> </blockquote></blockquote><blockquote type="cite"> </blockquote><blockquote type="cite"> </blockquote><blockquote type="cite">_______________________________________________ </blockquote><blockquote type="cite">Gate-users mailing list </blockquote><blockquote type="cite"><a href="mailto:Gate-users@lists.opengatecollaboration.org">Gate-users@lists.opengatecollaboration.org</a> </blockquote><blockquote type="cite"><a href="http://lists.opengatecollaboration.org/mailman/listinfo/gate-users">http://lists.opengatecollaboration.org/mailman/listinfo/gate-users</a> </blockquote><blockquote type="cite"> </blockquote> -- David Sarrut, Phd Directeur de recherche CNRS CREATIS, UMR CNRS 5220, Inserm U 1044 Centre de lutte contre le cancer L?on B?rard 28 rue La?nnec, 69373 Lyon cedex 08 Tel : 04 78 78 51 51 / 06 74 72 05 42 <a href="http://www.creatis.insa-lyon.fr/~dsarrut">http://www.creatis.insa-lyon.fr/~dsarrut</a> _________________________________ "2 + 2 = 5, for extremely large values of 2" _________________________________ -------------- next part -------------- An HTML attachment was scrubbed... URL: <<a href="http://lists.opengatecollaboration.org/mailman/private/gate-users/attachments/20140129/c488ea2c/attachment-0001.html">http://lists.opengatecollaboration.org/mailman/private/gate-users/attachments/20140129/c488ea2c/attachment-0001.html</a>> ------------------------------ Message: 3 Date: Wed, 29 Jan 2014 21:25:37 +0100 From: Vesna Cuplov <<a href="mailto:vesna.cuplov@gmail.com">vesna.cuplov@gmail.com</a>> To: Filipe Castro <<a href="mailto:ifcastro@ua.pt">ifcastro@ua.pt</a>> Cc: "<a href="mailto:gate-users@lists.opengatecollaboration.org">gate-users@lists.opengatecollaboration.org</a>" <<a href="mailto:gate-users@lists.opengatecollaboration.org">gate-users@lists.opengatecollaboration.org</a>> Subject: Re: [Gate-users] Wavelength-shifting (WLS) fibres coupled to scintillators Message-ID: <<a href="mailto:CAOibXMEkqL7QZ+rrXRFUnVPcbGjYQ+S2ir0kUSoJNb5pq+rKQg@mail.gmail.com">CAOibXMEkqL7QZ+rrXRFUnVPcbGjYQ+S2ir0kUSoJNb5pq+rKQg@mail.gmail.com</a>> Content-Type: text/plain; charset="iso-8859-1" Hello, <blockquote type="cite"> </blockquote><blockquote type="cite"> I want to simulate scintillation photons produced by 511 keV gammas and </blockquote><blockquote type="cite">their optical path through a LYSO scintillator with mirror polished ends </blockquote><blockquote type="cite">and reflective side surfaces. One end of the crystal is coupled to a </blockquote><blockquote type="cite">wavelength-shifting fibre (double-cladded BCF-91A fibre), such that crystal </blockquote><blockquote type="cite">and fibre make a 90 degree angle. </blockquote><blockquote type="cite"> </blockquote><blockquote type="cite">As I am not experienced with Gate (using vGate 2.1), I have many doubts </blockquote><blockquote type="cite">regarding the proper physics and geometry necessary for the simulation, </blockquote><blockquote type="cite">namely of the optical photons path, optical boundaries and fibre geometry. </blockquote><blockquote type="cite">Is there anyone who has simulated similar experiments with this kind of </blockquote><blockquote type="cite">fibres, for example in the AxPET project, who can help me out? </blockquote><blockquote type="cite"> </blockquote><blockquote type="cite">I've already recompiled Gate with optical ON. </blockquote><blockquote type="cite"> </blockquote><blockquote type="cite">In order to define the reflective surfaces of the crystal, do I need to </blockquote><blockquote type="cite">first define the volumes with the reflective material or is it possible to </blockquote><blockquote type="cite">define the surfaces only with the crystal volume? </blockquote><blockquote type="cite"> </blockquote><blockquote type="cite"> </blockquote><blockquote type="cite"> </blockquote><blockquote type="cite">If your crystal is the LYSO material, you just need to define your crystal </blockquote><blockquote type="cite">volume with the LYSO material properties in Materials.xml. For the polished </blockquote><blockquote type="cite">ends and reflective surfaces, you define the surfaces with the finish, </blockquote><blockquote type="cite">reflectivity, .... parameters in Surface.xml. </blockquote><blockquote type="cite"> </blockquote><blockquote type="cite"> </blockquote><blockquote type="cite"> </blockquote><blockquote type="cite"> Don't I need to have 2 volumes of different materials to </blockquote><blockquote type="cite">define a surface? For now I have only defined the LYSO volume. My question </blockquote><blockquote type="cite">is if I need to define the volume with white reflective material (0.1 mm </blockquote><blockquote type="cite">BaSO4) and then the surface, e.g. </blockquote><blockquote type="cite"> </blockquote><blockquote type="cite"> </blockquote><blockquote type="cite"> </blockquote><blockquote type="cite">/gate/LYSO/surfaces/name Surface-From-LYSO-To-Reflector </blockquote><blockquote type="cite"> </blockquote><blockquote type="cite">/gate/LYSO/surfaces/insert Reflector (previously defined?) </blockquote><blockquote type="cite"> </blockquote><blockquote type="cite">/gate/LYSO/surfaces/Surface-From-LYSO-To-Reflector/SetSurface surface_name </blockquote><blockquote type="cite">(defined in Surface.xml) </blockquote><blockquote type="cite"> </blockquote><blockquote type="cite"> Or if these 3 lines are enough and I only need to define </blockquote><blockquote type="cite">the surface properties in Surface.xml ? </blockquote><blockquote type="cite"> </blockquote> Yes, to define a surface you need to define both volumes: crystal and the 0.1mm reflector. In your definition of the surface, you only specified the behavior of the surface for photons going from the reflector towards the Lyso crystal. You need to define the surface behavior for photons going from the Lyso towards the reflector. These are 2 different surfaces. See the user's guide, there is a drawing. <blockquote type="cite"> Is it necessary to define separate volumes with the different </blockquote><blockquote type="cite">materials of the fibre (core, first clad and 2nd clad)? In this case, it </blockquote><blockquote type="cite">is a square fibre, so what would be the best way to do it? </blockquote><blockquote type="cite"> </blockquote><blockquote type="cite"> For the WLS fiber, you can describe it as one volume or more detailed </blockquote><blockquote type="cite">volumes. I think one volume would be enough as long as you have its </blockquote><blockquote type="cite">properties which are the absorption/emission wls spectra, mixture (in case </blockquote><blockquote type="cite">you use one volume that is a mix of sub components) refractive index, ... </blockquote><blockquote type="cite"> </blockquote><blockquote type="cite"> </blockquote><blockquote type="cite"> </blockquote><blockquote type="cite">The thing is that the core of the fibre is polystyrene (n = 1.60), the 1stclad is acrylic (n = 1.49) and the 2 </blockquote><blockquote type="cite">nd clad fluor-acrylic (n = 1.42). These refractive index differences are </blockquote><blockquote type="cite">designed to obtain a higher photon trapping efficiency. In the case of a </blockquote><blockquote type="cite">square 1 mm fiber, the core has approx. 0.94 mm thickness, the 1st clad </blockquote><blockquote type="cite">0.04 mm and the 2nd clad 0.02 mm. I'd like to have the simulation as </blockquote><blockquote type="cite">realistic as possible, so I wonder what is the best solution to achieve </blockquote><blockquote type="cite">this. I can assume the whole volume of the fibre to have the same </blockquote><blockquote type="cite">absorption/emission wls spectra. </blockquote><blockquote type="cite"> </blockquote> If you have all the specifications of your fiber as you seem to have, you can simulate it with all these details. I don't know about the best solution. Regarding the trapping efficiency (which you know as it is derived from the 3 refractive index), I think this is actually related to the WLS absorption length (you have the spectrum?). The WLS absorption/emission will tell where inside the fiber the optical photon absorption/emission took place. Maybe the safe way to make sure you get the right trapping efficiency is actually to simulate the core, 1st and 2nd clads. vesna -------------- next part -------------- An HTML attachment was scrubbed... URL: <<a href="http://lists.opengatecollaboration.org/mailman/private/gate-users/attachments/20140129/9014d04d/attachment.html">http://lists.opengatecollaboration.org/mailman/private/gate-users/attachments/20140129/9014d04d/attachment.html</a>> ------------------------------ _______________________________________________ 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">http://lists.opengatecollaboration.org/mailman/listinfo/gate-users</a> End of Gate-users Digest, Vol 92, Issue 39 ****************************************** </div></blockquote></body></html>