<html>
<head>
<meta http-equiv="Content-Type" content="text/html; charset=Windows-1252">
</head>
<body>
<div dir="auto" style="direction: ltr; margin: 0; padding: 0; font-family: sans-serif; font-size: 11pt; color: black; ">
Hi Rukiah, <br>
<br>
</div>
<div dir="auto" style="direction: ltr; margin: 0; padding: 0; font-family: sans-serif; font-size: 11pt; 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. <br>
<br>
</div>
<div dir="auto" style="direction: ltr; margin: 0; padding: 0; font-family: sans-serif; font-size: 11pt; color: black; ">
Best Regards, <br>
<br>
</div>
<div dir="auto" style="direction: ltr; margin: 0; padding: 0; font-family: sans-serif; font-size: 11pt; color: black; ">
Elise Emond <br>
<br>
</div>
<div dir="auto" style="direction: ltr; margin: 0; padding: 0; font-family: sans-serif; font-size: 11pt; color: black; ">
De : Rukiah<br>
</div>
<div dir="auto" style="direction: ltr; margin: 0; padding: 0; font-family: sans-serif; font-size: 11pt; color: black; ">
Envoyé : vendredi 14 septembre à 22:45<br>
</div>
<div dir="auto" style="direction: ltr; margin: 0; padding: 0; font-family: sans-serif; font-size: 11pt; color: black; ">
Objet : Re: [Gate-users] How to determine positron emission points<br>
</div>
<div dir="auto" style="direction: ltr; margin: 0; padding: 0; font-family: sans-serif; font-size: 11pt; color: black; ">
À : Paulo Caribé<br>
</div>
<div dir="auto" style="direction: ltr; margin: 0; padding: 0; font-family: sans-serif; font-size: 11pt; color: black; ">
Cc : Gate-users<br>
<br>
<br>
</div>
<div dir="auto" style="direction: ltr; margin: 0; padding: 0; font-family: sans-serif; font-size: 11pt; color: black; ">
Hi Pablo, <br>
</div>
<div dir="auto" style="direction: ltr; margin: 0; padding: 0; font-family: sans-serif; font-size: 11pt; color: black; ">
Thank you for your suggestion.<br>
</div>
<div dir="auto" style="direction: ltr; margin: 0; padding: 0; font-family: sans-serif; font-size: 11pt; 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.<br>
</div>
<div dir="auto" style="direction: ltr; margin: 0; padding: 0; font-family: sans-serif; font-size: 11pt; color: black; ">
Thank you.<br>
<br>
<br>
</div>
<div dir="auto" style="direction: ltr; margin: 0; padding: 0; font-family: sans-serif; font-size: 11pt; color: black; ">
<a href="https://overview.mail.yahoo.com/?.src=iOS">Sent from Yahoo Mail for iPhone</a><br>
<br>
</div>
<div dir="auto" style="direction: ltr; margin: 0; padding: 0; font-family: sans-serif; font-size: 11pt; color: black; ">
On Friday, September 14, 2018, 8:40 pm, Paulo Caribé <Paulo.Caribe@UGent.be> wrote:<br>
</div>
<blockquote type="cite">
<div dir="auto" style="direction: ltr; margin: 0; padding: 0; font-family: sans-serif; font-size: 11pt; color: black; ">
Hi Rukiah, <br>
<br>
</div>
<div dir="auto" style="direction: ltr; margin: 0; padding: 0; font-family: sans-serif; font-size: 11pt; 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. <br>
</div>
<div dir="auto" style="direction: ltr; margin: 0; padding: 0; font-family: sans-serif; font-size: 11pt; color: black; ">
To find out more:<br>
<br>
</div>
<div dir="auto" style="direction: ltr; margin: 0; padding: 0; font-family: sans-serif; font-size: 11pt; color: black; ">
<a 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>
<br>
</div>
<div dir="auto" style="direction: ltr; margin: 0; padding: 0; font-family: sans-serif; font-size: 11pt; color: black; ">
Cheers<br>
</div>
<div dir="auto" style="direction: ltr; margin: 0; padding: 0; font-family: sans-serif; font-size: 11pt; color: black; ">
Paulo<br>
</div>
<div dir="auto" style="direction: ltr; margin: 0; padding: 0; font-family: sans-serif; font-size: 11pt; color: black; ">
___________________________________________<br>
<br>
</div>
<div dir="auto" style="direction: ltr; margin: 0; padding: 0; font-family: sans-serif; font-size: 11pt; color: black; ">
Doctoral researcher<br>
</div>
<div dir="auto" style="direction: ltr; margin: 0; padding: 0; font-family: sans-serif; font-size: 11pt; color: black; ">
Ghent University & KU Leuven - CNPq<br>
</div>
<div dir="auto" style="direction: ltr; margin: 0; padding: 0; font-family: sans-serif; font-size: 11pt; color: black; ">
Medical Imaging and Signal Processing (MEDISIP)<br>
<br>
<br>
<br>
<br>
<br>
<br>
<br>
<br>
<br>
<br>
<br>
<br>
</div>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">
<div dir="auto" style="direction: ltr; margin: 0; padding: 0; font-family: sans-serif; font-size: 11pt; color: black; ">
On 13 Sep 2018, at 08:12, Rukiah <<a href="mailto:katoshka_7880@yahoo.com">katoshka_7880@yahoo.com</a>> wrote:<br>
<br>
</div>
<div dir="auto" style="direction: ltr; margin: 0; padding: 0; font-family: sans-serif; font-size: 11pt; color: black; ">
Hi Gate users,<br>
<br>
</div>
<div dir="auto" style="direction: ltr; margin: 0; padding: 0; font-family: sans-serif; font-size: 11pt; 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:<br>
<br>
</div>
<div dir="auto" style="direction: ltr; margin: 0; padding: 0; font-family: sans-serif; font-size: 11pt; color: black; ">
#to print all simulation output on screen<br>
</div>
<div dir="auto" style="direction: ltr; margin: 0; padding: 0; font-family: sans-serif; font-size: 11pt; color: black; ">
/tracking/verbose 2 <br>
<br>
</div>
<div dir="auto" style="direction: ltr; margin: 0; padding: 0; font-family: sans-serif; font-size: 11pt; color: black; ">
#extract the annihilation point coordinates<br>
</div>
<div dir="auto" style="direction: ltr; margin: 0; padding: 0; font-family: sans-serif; font-size: 11pt; color: black; ">
Gate code.mac | grep "phantom_phys annihil" >output.txt <br>
<br>
</div>
<div dir="auto" style="direction: ltr; margin: 0; padding: 0; font-family: sans-serif; font-size: 11pt; 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
<br>
</div>
<div dir="auto" style="direction: ltr; margin: 0; padding: 0; font-family: sans-serif; font-size: 11pt; color: black; ">
' initStep ' for example as attached. Can anyone confirm if the InitStep is actually represents the emission points?<br>
<br>
</div>
<div dir="auto" style="direction: ltr; margin: 0; padding: 0; font-family: sans-serif; font-size: 11pt; color: black; ">
Thank you.<br>
<br>
<br>
</div>
<div dir="auto" style="direction: ltr; margin: 0; padding: 0; font-family: sans-serif; font-size: 11pt; color: black; ">
<br>
</div>
<div dir="auto" style="direction: ltr; margin: 0; padding: 0; font-family: sans-serif; font-size: 11pt; color: black; ">
<i>Rukiah A Latiff</i><br>
</div>
<div dir="auto" style="direction: ltr; margin: 0; padding: 0; font-family: sans-serif; font-size: 11pt; color: black; ">
<i>PhD student</i><br>
</div>
<div dir="auto" style="direction: ltr; margin: 0; padding: 0; font-family: sans-serif; font-size: 11pt; color: black; ">
<i>The University of Sydney</i><br>
</div>
<div dir="auto" style="direction: ltr; margin: 0; padding: 0; font-family: sans-serif; font-size: 11pt; color: black; ">
<Gate_InitStep.png>_______________________________________________<br>
</div>
<div dir="auto" style="direction: ltr; margin: 0; padding: 0; font-family: sans-serif; font-size: 11pt; color: black; ">
Gate-users mailing list<br>
</div>
<div dir="auto" style="direction: ltr; margin: 0; padding: 0; font-family: sans-serif; font-size: 11pt; color: black; ">
<a href="mailto:Gate-users@lists.opengatecollaboration.org">Gate-users@lists.opengatecollaboration.org</a><br>
</div>
<div dir="auto" style="direction: ltr; margin: 0; padding: 0; font-family: sans-serif; font-size: 11pt; color: black; ">
http://lists.opengatecollaboration.org/mailman/listinfo/gate-users<br>
</div>
</blockquote>
</blockquote>
<div dir="auto" style="direction: ltr; margin: 0; padding: 0; font-family: sans-serif; font-size: 11pt; color: black; ">
<br>
<br>
<br>
</div>
</body>
</html>