[Gate-users] How to determine positron emission points

Emond, Elise elise.emond.16 at ucl.ac.uk
Mon Sep 17 15:46:42 CEST 2018

Hi Rukiah,

I had a look at my Gate output this morning and it is similar to yours.

If you check it carefully you can see the following pattern:

1st 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
2nd and 3rd 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.

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.

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.

You should check the wiki about actors in Gate:
Using a particle filter you could for example, “kill” all secondary particles or all photons.

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.



De : Rukiah <katoshka_7880 at yahoo.com>
Envoyé : lundi 17 septembre 2018 05:49
À : Emond, Elise <elise.emond.16 at ucl.ac.uk>
Cc : Gate-users <gate-users at lists.opengatecollaboration.org>
Objet : Re: [Gate-users] How to determine positron emission points

Hi Elise,

Thank you for the information and detail explanation. However, I need clarification about this issue.
As I only interested in positron interactions including electron ionisation, Bremsstrahlung, annihilations and multiple scattering, so the photon physics process was turned off.
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?
Thank you.

Rukiah A Latiff
PhD student
Faculty of Health Sciences
The University of Sydney

On Saturday, September 15, 2018, 4:55:33 PM GMT+10, Emond, Elise <elise.emond.16 at ucl.ac.uk<mailto:elise.emond.16 at ucl.ac.uk>> wrote:

Hi Rukiah,
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.
Best Regards,
Elise Emond
De : Rukiah
Envoyé : vendredi 14 septembre à 22:45
Objet : Re: [Gate-users] How to determine positron emission points
À : Paulo Caribé
Cc : Gate-users

Hi Pablo,
Thank you for your suggestion.
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.
Thank you.

Sent from Yahoo Mail for iPhone<https://overview.mail.yahoo.com/?.src=iOS>
On Friday, September 14, 2018, 8:40 pm, Paulo Caribé <Paulo.Caribe at UGent.be<mailto:Paulo.Caribe at UGent.be>> wrote:
Hi Rukiah,
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.
To find out more:
Doctoral researcher
Ghent University & KU Leuven - CNPq
Medical Imaging and Signal Processing (MEDISIP)

On 13 Sep 2018, at 08:12, Rukiah <katoshka_7880 at yahoo.com<mailto:katoshka_7880 at yahoo.com>> wrote:
Hi Gate users,
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:
#to print all simulation output on screen
/tracking/verbose 2
#extract the annihilation point coordinates
Gate code.mac | grep "phantom_phys annihil" >output.txt
However, I have difficulties to find the emission points as there is no physics process output that related to it, except the process called
' initStep ' for example as attached. Can anyone confirm if the InitStep is actually represents the emission points?
Thank you.

Rukiah A Latiff
PhD student
The University of Sydney
Gate-users mailing list
Gate-users at lists.opengatecollaboration.org<mailto:Gate-users at lists.opengatecollaboration.org>

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