<html><head></head><body><div style="font-family:times new roman, new york, times, serif;font-size:16px;"><div style="font-family:times new roman, new york, times, serif;font-size:16px;"><div style="font-family:times new roman, new york, times, serif;font-size:16px;"><div style="font-family:times new roman, new york, times, serif;font-size:16px;"><div style="font-family:times new roman, new york, times, serif;font-size:16px;"><div style="font-family:times new roman, new york, times, serif;font-size:16px;"><div style="font-family:times new roman, new york, times, serif;font-size:16px;"><div><div>Hi Elise,</div><div><br></div><div>Thank you for the information and detail explanation. However, I need clarification about this issue.<br></div><div>As I only interested <span>in positron interactions including electron ionisation, Bremsstrahlung, annihilations and multiple scattering, so <span>the photon physics process was turned off.</span></span><br></div><div>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?</div><div>Thank you.<br><br><br></div><div class="ydp5664c677signature"><div><br></div><div><em><font size="3">Rukiah A Latiff</font></em></div><div><div><em><font size="3">PhD student</font></em></div><div><em><font size="3">Faculty of Health Sciences</font></em></div><div><em><font size="3">The University of Sydney<br></font></em></div><em></em><font size="3"><em><var id="ydp5664c677yui-ie-cursor"></var></em></font></div><div style="margin: 5px 0px; padding: 0px; border-color: rgb(204, 204, 204); border-style: solid; border-width: 1px; min-height: 0px; line-height: 0; font-size: 0px;" class="ydp5664c677hr"></div></div></div>
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On Saturday, September 15, 2018, 4:55:33 PM GMT+10, Emond, Elise <elise.emond.16@ucl.ac.uk> wrote:
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Hi Rukiah, <br clear="none">
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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. <br clear="none">
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Best Regards, <br clear="none">
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Elise Emond <br clear="none">
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De : Rukiah<br clear="none">
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Envoyé : vendredi 14 septembre à 22:45<br clear="none">
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Objet : Re: [Gate-users] How to determine positron emission points<br clear="none">
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À : Paulo Caribé<br clear="none">
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Cc : Gate-users<br clear="none">
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Hi Pablo, <br clear="none">
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Thank you for your suggestion.<br clear="none">
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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.<br clear="none">
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Thank you.<br clear="none">
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<a rel="nofollow" shape="rect" target="_blank" href="https://overview.mail.yahoo.com/?.src=iOS">Sent from Yahoo Mail for iPhone</a><br clear="none">
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On Friday, September 14, 2018, 8:40 pm, Paulo Caribé <Paulo.Caribe@UGent.be> wrote:<br clear="none">
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Hi Rukiah, <br clear="none">
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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. <br clear="none">
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To find out more:<br clear="none">
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<a rel="nofollow" shape="rect" target="_blank" href="http://wiki.opengatecollaboration.org/index.php/Users_Guide:Setting_up_the_physics">http://wiki.opengatecollaboration.org/index.php/Users_Guide:Setting_up_the_physics</a><br clear="none">
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Cheers<br clear="none">
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Paulo<br clear="none">
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Doctoral researcher<br clear="none">
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Ghent University & KU Leuven - CNPq<br clear="none">
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Medical Imaging and Signal Processing (MEDISIP)<br clear="none">
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On 13 Sep 2018, at 08:12, Rukiah <<a rel="nofollow" shape="rect" ymailto="mailto:katoshka_7880@yahoo.com" target="_blank" href="mailto:katoshka_7880@yahoo.com">katoshka_7880@yahoo.com</a>> wrote:<br clear="none">
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Hi Gate users,<br clear="none">
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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:<br clear="none">
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#to print all simulation output on screen<br clear="none">
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/tracking/verbose 2 <br clear="none">
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#extract the annihilation point coordinates<br clear="none">
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Gate code.mac | grep "phantom_phys annihil" >output.txt <br clear="none">
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However, I have difficulties to find the emission points as there is no physics process output that related to it, except the process called
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' initStep ' for example as attached. Can anyone confirm if the InitStep is actually represents the emission points?<br clear="none">
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Thank you.<br clear="none">
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<i>Rukiah A Latiff</i><br clear="none">
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<i>PhD student</i><br clear="none">
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<i>The University of Sydney</i><br clear="none">
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<Gate_InitStep.png>_______________________________________________<br clear="none">
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