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<p class="MsoNormal"><span style="mso-fareast-language:EN-US">Hi Rukiah,<o:p></o:p></span></p>
<p class="MsoNormal"><span style="mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="mso-fareast-language:EN-US">I had a look at my Gate output this morning and it is similar to yours.
<o:p></o:p></span></p>
<p class="MsoNormal"><span style="mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="mso-fareast-language:EN-US">If you check it carefully you can see the following pattern:<br>
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<o:p></o:p></span></p>
<p class="MsoNormal"><span style="mso-fareast-language:EN-US">1<sup>st</sup> block: positron emission until its annihilation, following by a “list of secondaries” that show you that 2 gamma photons are created by the annihilation event<o:p></o:p></span></p>
<p class="MsoNormal"><span style="mso-fareast-language:EN-US">2<sup>nd</sup> and 3<sup>rd</sup> blocks: tracking of the trajectories of the gamma photons created by the annihilation – you can see at the initStep of those two blocks that the kinetic energies
and the locations are the same as in the “list of secondaries”. Also at the start of those blocks you can see that the “Parent ID” is equal to 1, whereas the Parent ID of the first block is equal to 0, which shows that these 2 blocks concern secondary particles.
<o:p></o:p></span></p>
<p class="MsoNormal"><span style="mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="mso-fareast-language:EN-US">As you have removed all physical interactions for the photons, the gamma photons will be “transported” out of the FOV, until the limits of your world referential. Disabling the photon interactions
does not mean that the photons will not be created by the annihilation.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="mso-fareast-language:EN-US">In my case, I have used the physics list from Gate instead of selecting different physical interactions, as I believe it should be more accurate.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="mso-fareast-language:EN-US">You should check the wiki about actors in Gate:<o:p></o:p></span></p>
<p class="MsoNormal"><span style="mso-fareast-language:EN-US"><a href="http://wiki.opengatecollaboration.org/index.php/Users_Guide:Tools_to_Interact_with_the_Simulation_:_Actors">http://wiki.opengatecollaboration.org/index.php/Users_Guide:Tools_to_Interact_with_the_Simulation_:_Actors</a>
<o:p></o:p></span></p>
<p class="MsoNormal"><span style="mso-fareast-language:EN-US">Using a particle filter you could for example, “kill” all secondary particles or all photons.
<o:p></o:p></span></p>
<p class="MsoNormal"><span style="mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="mso-fareast-language:EN-US">If you want more information, you can contact me personally and I could help you a bit more in details with all of that, especially if you are using something else than a point source.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="mso-fareast-language:EN-US">Regards,<o:p></o:p></span></p>
<p class="MsoNormal"><span style="mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="mso-fareast-language:EN-US">Elise<o:p></o:p></span></p>
<p class="MsoNormal"><span style="mso-fareast-language:EN-US"><o:p> </o:p></span></p>
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<p class="MsoNormal"><b>De :</b> Rukiah <katoshka_7880@yahoo.com> <br>
<b>Envoyé :</b> lundi 17 septembre 2018 05:49<br>
<b>À :</b> Emond, Elise <elise.emond.16@ucl.ac.uk><br>
<b>Cc :</b> Gate-users <gate-users@lists.opengatecollaboration.org><br>
<b>Objet :</b> Re: [Gate-users] How to determine positron emission points<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal"><span style="font-size:12.0pt;font-family:"Times New Roman",serif">Hi Elise,<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:12.0pt;font-family:"Times New Roman",serif"><o:p> </o:p></span></p>
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<p class="MsoNormal"><span style="font-size:12.0pt;font-family:"Times New Roman",serif">Thank you for the information and detail explanation. However, I need clarification about this issue.<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:12.0pt;font-family:"Times New Roman",serif">As I only interested in positron interactions including electron ionisation, Bremsstrahlung, annihilations and multiple scattering, so the photon physics process was turned
off.<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:12.0pt;font-family:"Times New Roman",serif">Attached is the example of Gate output obtained. I understand the 'initStep' in the first block is the emission of positrons. How about the 'initStep' in the second block?
Is it the photon emission or positron emission since the photon physics interaction was turned off?<o:p></o:p></span></p>
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<p class="MsoNormal" style="margin-bottom:12.0pt"><span style="font-size:12.0pt;font-family:"Times New Roman",serif">Thank you.<br>
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<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:12.0pt;font-family:"Times New Roman",serif"><o:p> </o:p></span></p>
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<p class="MsoNormal"><em><span style="font-size:12.0pt;font-family:"Calibri",sans-serif">Rukiah A Latiff</span></em><span style="font-size:12.0pt;font-family:"Times New Roman",serif"><o:p></o:p></span></p>
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<p class="MsoNormal"><em><span style="font-size:12.0pt;font-family:"Calibri",sans-serif">PhD student</span></em><span style="font-size:12.0pt;font-family:"Times New Roman",serif"><o:p></o:p></span></p>
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<p class="MsoNormal"><em><span style="font-size:12.0pt;font-family:"Calibri",sans-serif">Faculty of Health Sciences</span></em><span style="font-size:12.0pt;font-family:"Times New Roman",serif"><o:p></o:p></span></p>
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<p class="MsoNormal"><em><span style="font-size:12.0pt;font-family:"Calibri",sans-serif">The University of Sydney</span></em><span style="font-size:12.0pt;font-family:"Times New Roman",serif"><o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:12.0pt;font-family:"Times New Roman",serif"><o:p> </o:p></span></p>
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<p class="MsoNormal"><span style="font-size:12.0pt;font-family:"Times New Roman",serif"><o:p> </o:p></span></p>
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<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Helvetica",sans-serif;color:#26282A">On Saturday, September 15, 2018, 4:55:33 PM GMT+10, Emond, Elise <</span><a href="mailto:elise.emond.16@ucl.ac.uk"><span style="font-size:10.0pt;font-family:"Helvetica",sans-serif">elise.emond.16@ucl.ac.uk</span></a><span style="font-size:10.0pt;font-family:"Helvetica",sans-serif;color:#26282A">>
wrote: <o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Helvetica",sans-serif;color:#26282A"><o:p> </o:p></span></p>
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<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Helvetica",sans-serif;color:#26282A"><o:p> </o:p></span></p>
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<p class="MsoNormal" style="margin-bottom:12.0pt"><span style="font-family:"Arial",sans-serif;color:black">Hi Rukiah,
<o:p></o:p></span></p>
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<p class="MsoNormal" style="margin-bottom:12.0pt"><span style="font-family:"Arial",sans-serif;color:black">The locations of the emission points can be indeed extracted using the 'initStep' line, just before the "annihil" line. However, be careful not to take
into account other interactions that are also marked with 'initStep', such as the emission of photons. When you run Gate code.mac you should see that all interactions of the positron, from its emission to its annihilation, are given in one "block". After the
"phantom_phys annihil" line, the block ends, and another block corresponding to the emission of the photons follows, with two 'initStep' lines in it. There are also secondary interactions... Therefore if you use "grep 'phantom_phys initStep\|phantom_phys annihil'
" you will afterwards have to process the output file to discard all initStep which do not correspond to the emission of the positrons.
<o:p></o:p></span></p>
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<p class="MsoNormal" style="margin-bottom:12.0pt"><span lang="FR" style="font-family:"Arial",sans-serif;color:black">Best Regards,
<o:p></o:p></span></p>
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<p class="MsoNormal" style="margin-bottom:12.0pt"><span lang="FR" style="font-family:"Arial",sans-serif;color:black">Elise Emond
<o:p></o:p></span></p>
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<p class="MsoNormal"><span lang="FR" style="font-family:"Arial",sans-serif;color:black">De : Rukiah<o:p></o:p></span></p>
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<p class="MsoNormal"><span lang="FR" style="font-family:"Arial",sans-serif;color:black">Envoyé : vendredi 14 septembre à 22:45<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-family:"Arial",sans-serif;color:black">Objet : Re: [Gate-users] How to determine positron emission points<o:p></o:p></span></p>
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<p class="MsoNormal"><span lang="FR" style="font-family:"Arial",sans-serif;color:black">À : Paulo Caribé<o:p></o:p></span></p>
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<p class="MsoNormal" style="margin-bottom:12.0pt"><span lang="FR" style="font-family:"Arial",sans-serif;color:black">Cc : Gate-users<br>
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<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-family:"Arial",sans-serif;color:black">Hi Pablo,
<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-family:"Arial",sans-serif;color:black">Thank you for your suggestion.<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-family:"Arial",sans-serif;color:black">I am using Gate7.2 and managed to obtain the annihilations point. However,I cannot get the emissions point and that is where I am stucked.Is it possible to get the emissions point
data? I wonder if the process called ‘initStep’ represents the emissions point.<o:p></o:p></span></p>
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<p class="MsoNormal" style="margin-bottom:12.0pt"><span style="font-family:"Arial",sans-serif;color:black">Thank you.<br>
<br>
<o:p></o:p></span></p>
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<p class="MsoNormal" style="margin-bottom:12.0pt"><a href="https://overview.mail.yahoo.com/?.src=iOS" target="_blank"><span style="font-family:"Arial",sans-serif">Sent from Yahoo Mail for iPhone</span></a><span style="font-family:"Arial",sans-serif;color:black"><o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-family:"Arial",sans-serif;color:black">On Friday, September 14, 2018, 8:40 pm, Paulo Caribé <</span><a href="mailto:Paulo.Caribe@UGent.be"><span style="font-family:"Arial",sans-serif">Paulo.Caribe@UGent.be</span></a><span style="font-family:"Arial",sans-serif;color:black">>
wrote:<o:p></o:p></span></p>
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<p class="MsoNormal" style="margin-bottom:12.0pt"><span style="font-family:"Arial",sans-serif;color:black">Hi Rukiah,
<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-family:"Arial",sans-serif;color:black">I would highly recommend double check your Physics list and make sure that the annihilation process was “enabled” (/gate/physics/addProcess PositronAnnihilation). In addition,
take into account the the physic list mechanism has been changing since the GATEv 7.0 and now there is a big change as compared to GATEv 8.1. <o:p></o:p></span></p>
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<p class="MsoNormal" style="margin-bottom:12.0pt"><span style="font-family:"Arial",sans-serif;color:black">To find out more:<o:p></o:p></span></p>
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<p class="MsoNormal" style="margin-bottom:12.0pt"><a href="http://wiki.opengatecollaboration.org/index.php/Users_Guide:Setting_up_the_physics" target="_blank"><span style="font-family:"Arial",sans-serif">http://wiki.opengatecollaboration.org/index.php/Users_Guide:Setting_up_the_physics</span></a><span style="font-family:"Arial",sans-serif;color:black"><o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-family:"Arial",sans-serif;color:black">Cheers<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-family:"Arial",sans-serif;color:black">Paulo<o:p></o:p></span></p>
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<p class="MsoNormal" style="margin-bottom:12.0pt"><span style="font-family:"Arial",sans-serif;color:black">___________________________________________<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-family:"Arial",sans-serif;color:black">Doctoral researcher<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-family:"Arial",sans-serif;color:black">Ghent University & KU Leuven - CNPq<o:p></o:p></span></p>
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<p class="MsoNormal" style="margin-bottom:12.0pt"><span style="font-family:"Arial",sans-serif;color:black">Medical Imaging and Signal Processing (MEDISIP)<br>
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<p class="MsoNormal" style="margin-bottom:12.0pt"><span style="font-family:"Arial",sans-serif;color:black">On 13 Sep 2018, at 08:12, Rukiah <</span><a href="mailto:katoshka_7880@yahoo.com" target="_blank"><span style="font-family:"Arial",sans-serif">katoshka_7880@yahoo.com</span></a><span style="font-family:"Arial",sans-serif;color:black">>
wrote:<o:p></o:p></span></p>
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<p class="MsoNormal" style="margin-bottom:12.0pt"><span style="font-family:"Arial",sans-serif;color:black">Hi Gate users,<o:p></o:p></span></p>
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<p class="MsoNormal" style="margin-bottom:12.0pt"><span style="font-family:"Arial",sans-serif;color:black">To measure a positron range, I had to collect the positron annihilation points coordinates and emission points coordinates. As I am an intermediate user
of GATE and Linux, I used this method to collect the coordinates:<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-family:"Arial",sans-serif;color:black">#to print all simulation output on screen<o:p></o:p></span></p>
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<p class="MsoNormal" style="margin-bottom:12.0pt"><span style="font-family:"Arial",sans-serif;color:black">/tracking/verbose 2
<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-family:"Arial",sans-serif;color:black">#extract the annihilation point coordinates<o:p></o:p></span></p>
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<p class="MsoNormal" style="margin-bottom:12.0pt"><span style="font-family:"Arial",sans-serif;color:black">Gate code.mac | grep "phantom_phys annihil" >output.txt
<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-family:"Arial",sans-serif;color:black">However, I have difficulties to find the emission points as there is no physics process output that related to it, except the process called
<o:p></o:p></span></p>
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<p class="MsoNormal" style="margin-bottom:12.0pt"><span style="font-family:"Arial",sans-serif;color:black">' initStep ' for example as attached. Can anyone confirm if the InitStep is actually represents the emission points?<o:p></o:p></span></p>
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<p class="MsoNormal" style="margin-bottom:12.0pt"><span style="font-family:"Arial",sans-serif;color:black">Thank you.<br>
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<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-family:"Arial",sans-serif;color:black"> <o:p></o:p></span></p>
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<p class="MsoNormal"><i><span style="font-family:"Arial",sans-serif;color:black">Rukiah A Latiff</span></i><span style="font-family:"Arial",sans-serif;color:black"><o:p></o:p></span></p>
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<p class="MsoNormal"><i><span style="font-family:"Arial",sans-serif;color:black">PhD student</span></i><span style="font-family:"Arial",sans-serif;color:black"><o:p></o:p></span></p>
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<p class="MsoNormal"><i><span style="font-family:"Arial",sans-serif;color:black">The University of Sydney</span></i><span style="font-family:"Arial",sans-serif;color:black"><o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-family:"Arial",sans-serif;color:black"><Gate_InitStep.png>_______________________________________________<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-family:"Arial",sans-serif;color:black">Gate-users mailing list<o:p></o:p></span></p>
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<p class="MsoNormal"><a href="mailto:Gate-users@lists.opengatecollaboration.org" target="_blank"><span style="font-family:"Arial",sans-serif">Gate-users@lists.opengatecollaboration.org</span></a><span style="font-family:"Arial",sans-serif;color:black"><o:p></o:p></span></p>
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<p class="MsoNormal"><a href="http://lists.opengatecollaboration.org/mailman/listinfo/gate-users"><span style="font-family:"Arial",sans-serif">http://lists.opengatecollaboration.org/mailman/listinfo/gate-users</span></a><span style="font-family:"Arial",sans-serif;color:black"><o:p></o:p></span></p>
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