David Sarrut | 1 Dec 07:56 2015
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test please ignore



--
David Sarrut, Phd
Directeur de recherche CNRS
CREATIS, UMR CNRS 5220, Inserm U 1044
Centre de lutte contre le cancer Léon Bérard
28 rue Laënnec, 69373 Lyon cedex 08
Tel : 04 78 78 51 51 / 06 74 72 05 42
http://www.creatis.insa-lyon.fr/~dsarrut
_________________________________
 "2 + 2 = 5,  for extremely large values of 2"
_________________________________
<div><div dir="ltr">
<br clear="all"><div><br></div>-- <br><div class="gmail_signature"><div dir="ltr">David Sarrut, Phd<br>Directeur de recherche CNRS<br>CREATIS, UMR CNRS 5220, Inserm U 1044<div>Centre de lutte contre le cancer L&eacute;on B&eacute;rard<br>28 rue La&euml;nnec, 69373 Lyon cedex 08<br>Tel : 04 78 78 51 51 / 06 74 72 05 42<br><a href="http://www.creatis.insa-lyon.fr/~dsarrut" target="_blank">http://www.creatis.insa-lyon.fr/~dsarrut</a><br>_________________________________</div>
<div>&nbsp;"2 + 2 = 5,&nbsp; for extremely large values of 2"<br>_________________________________</div>
</div></div>
</div></div>
Andre Kyme | 1 Dec 00:25 2015
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Setting Rmax for the CylindricalPET system

Hi,


I've found that the when defining the maximum radius of the CylindricalPET world geometry using the /gate/cylindricalPET/geometry/setRmax command, the value of Rmax can be smaller than what you would expect analytically from the actual scanner geometry, and yet no 'overlapping volumes' error is generated. This is not just machine precision error, since I've seen the radius be up to 0.3 mm less than expected without any error.


Does anyone know why this occurs? Perhaps I'm missing something in how Rmax is defined wrt the scanner geometry. I would have thought that once you've defined the rsector of your PET geometry which you want to repeat around a ring, you can simply calculate the maximum distance from the center of the world coord system to the extremity of this sector, and use this as the Rmax setting. So why can Rmax be less than this?


Thanks,


Andre Kyme


<div>
<div>
<p>Hi,</p>
<p><br></p>
<p>I've found that the when defining the maximum radius of the CylindricalPET world geometry using the /gate/cylindricalPET/geometry/setRmax command, the value of Rmax can be smaller than what you would expect analytically from the actual scanner geometry,
 and yet no 'overlapping volumes' error is generated. This is not just machine precision error, since I've seen the radius be up to 0.3 mm less than expected without any error.</p>
<p><br></p>
<p>Does anyone know why this occurs? Perhaps I'm missing something in how Rmax is defined wrt the scanner geometry. I would have thought that once you've defined the rsector of your PET geometry which you want to repeat around a ring, you can simply calculate
 the maximum distance from the center of the world coord system to the extremity of this sector, and use this as the Rmax setting. So why can Rmax be less than this?</p>
<p><br></p>
<p>Thanks,</p>
<p><br></p>
<p>Andre Kyme<br></p>
<div>
<div name="divtagdefaultwrapper">
<br>
</div>
</div>
</div>
</div>
David Sarrut | 19 Nov 07:30 2015
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Working group: Gate LET Actor

Hello,

it appears that several groups may be interested to add a "LET actor" (Linear Energy Transfer) to Gate.

We propose to set up a small working group of interested people that want to contribute to this new feature. The idea is to define together a set of requirements for this 'actor', then to implement it in Gate, with examples macros and documentation, so that they can be available to everyone in a future Gate release.

Here is a very short initial description of the LET actor:
- score a spatial distribution of LET (Linear Energy Transfert)
- based on the same principle as the DoseActor, or as an option to the current DoseActor
- output in kev/mum
- several definition of LET exists, so we need to select (at least) one or provide option.

I already know the following people/group, that should be interested:
- ludovic.demarzi-9yWgQyi4Ipc@public.gmane.org fanny.marsolat-9yWgQyi4Ipc@public.gmane.org
- loic.grevillot <at> medaustron.at alessio.elia <at> medaustron.at  hermann.fuchs-1Exk/Z/VcF+XamxT8X54fw@public.gmane.org
- david.boersma-JAjqph6Yjy84M/bo5TPICw@public.gmane.org
- maigne-DUSsAKd12Ioj9lkVWJyhCFAUjnlXr6A1@public.gmane.org and François Smekens

Could you please confirm ? If you are not in this list and interested to participate, please send me an email.

As proposed recently by David Boersma: we could also test a new tool that could help us in the discussion. Please create a (free) account on www.slack.com and connect to the forum dedicated to Gate, in the channel dedicated to the let-actor: https://opengateforum.slack.com/messages/let-actor

let me know,

Sincerely,
David


-- 
David Sarrut, Phd
Directeur de recherche CNRS
CREATIS, UMR CNRS 5220, Inserm U 1044
Centre de lutte contre le cancer Léon Bérard
28 rue Laënnec, 69373 Lyon cedex 08
Tel : 04 78 78 51 51 / 06 74 72 05 42
http://www.creatis.insa-lyon.fr/~dsarrut
_________________________________
 "2 + 2 = 5,  for extremely large values of 2"
_________________________________
<div>
<div class="pre">Hello,<br><br> it appears that several groups may be interested to add a "LET actor" (Linear Energy Transfer) to Gate. <br><br> We propose to set up a small working group of interested people that want to contribute to this new feature. The idea is to define together a set of requirements for this 'actor', then to implement it in Gate, with examples macros and documentation, so that they can be available to everyone in a future Gate release.<br><br> Here is a very short initial description of the LET actor:<br> - score a spatial distribution of LET (Linear Energy Transfert)<br> - based on the same principle as the DoseActor, or as an option to the current DoseActor<br> - output in kev/mum<br> - several definition of LET exists, so we need to select (at least) one or provide option.<br><br> I already know the following people/group, that should be interested:<br> - <a href="mailto:ludovic.demarzi@...">ludovic.demarzi@...</a> <a href="mailto:fanny.marsolat@...">fanny.marsolat@...</a><br> - <a href="mailto:loic.grevillot@...">loic.grevillot <at> medaustron.at</a> <a href="mailto:alessio.elia@...">alessio.elia <at> medaustron.at</a> &nbsp;<a href="mailto:hermann.fuchs@...">hermann.fuchs@...</a><br> - <a href="mailto:david.boersma <at> physics.uu.se">david.boersma@...</a> <br> - <a href="mailto:maigne@...">maigne@...</a> and Fran&ccedil;ois Smekens<br><br> Could you please confirm ? If you are not in this list and interested to participate, please send me an email. <br><br> As proposed recently by David Boersma: we could also test a new tool that could help us in the discussion. Please create a (free) account on <a href="http://www.slack.com" target="_blank" rel="noreferrer">www.slack.com</a> and connect to the forum dedicated to Gate, in the channel dedicated to the let-actor: <a href="https://opengateforum.slack.com/messages/let-actor" target="_blank" rel="noreferrer">https://opengateforum.slack.com/messages/let-actor</a><br><br> let me know, <br><br> Sincerely,<br> David<br><br><br><span class="sig">--&nbsp;<br> David Sarrut, Phd<br> Directeur de recherche CNRS<br> CREATIS, UMR CNRS 5220, Inserm U 1044<br> Centre de lutte contre le cancer L&eacute;on B&eacute;rard<br> 28 rue La&euml;nnec, 69373 Lyon cedex 08<br> Tel : 04 78 78 51 51 / 06 74 72 05 42<br><a href="http://www.creatis.insa-lyon.fr/~dsarrut" target="_blank" rel="noreferrer">http://www.creatis.insa-lyon.fr/~dsarrut</a><br> _________________________________<br> &nbsp;"2 + 2 = 5, &nbsp;for extremely large values of 2"<br> _________________________________</span>
</div>
</div>
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Predicting GATE performance with SPECfp?

Hello All,
  I am producing a specification for a new cluster to run GATE, with the aim to have four times the compute
performance of our existing cluster, and to use more modern CPUs.  I am assuming that there will not be a
multi-threaded version of GATE before we purchase the hardware, so I am looking at buying multiple CPUs
and running one instance of GATE per CPU core.  Therefore, I need to find a measure of the performance of
current CPUs relative to those in our existing cluster, so that I can then choose the best CPU based on
price/performance.  I have not been able to find any benchmark information for GATE/GEANT on different
CPUs, so instead I am using SPECfp_rate2006 results downloaded from spec.org, as my hunch is that this is
the most appropriate metric to use.
  I am not familiar with the kind of operations performed by GATE/GEANT, so I don't know if my hunch is correct. 
Is anybody able to say whether SPECfp_rate is a good indicator of GATE/GEANT performance in this
scenario?  Our calculations typically take around an hour to complete, and I am assuming that disk
read/writes are a negligible part of the overall compute time.  Any guidance would be gratefully received.

Many Thanks,
  -- Ian.
--------------------------------------------
Ian Porter, Dept. Medical Physics,
Christie Hospital NHS Foundation Trust,
Wilmslow Road, Manchester, M20 4BX.  England. 
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Zhao, Wei | 18 Nov 16:03 2015

Re: how can I apply TOF information on images

Dear  Hanieh,

To my knowledge, TOF can only be applied to list-mode OSEM 
reconstruction framework. After you extract the tof information using a 
root script, you have to incorporate the information into the 
reconstruction framework. Specifically, suppose  a_ij is the probability 
that an event generated in pixel j is detected by the i_th measurement. 
Then the TOF reconstruction framework have to replace a_ij with

a_ij * (1/(sqrt(2*pi)*sigma))*exp(-(x-x_i)^2/(2*sigma^2))

Here x is the annihilation point calculated using the time information. 
The physical meaning of the above equation is to constraint the location 
of backprojection and forward projection during reconstruction.

I believe there are a lot of paper about the TOF reconstruction 
framework and you can get more from these papers.

Best
Wei

On 11/18/2015 7:00 PM, 
gate-users-request@... wrote:
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>     1. Re: how can I apply TOF information on images (Hanieh)
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> ----------------------------------------------------------------------
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> Message: 1
> Date: Wed, 18 Nov 2015 15:08:52 +0330
> From: Hanieh <Hanieh_jozi69@...>
> To: STRYDHORST Jared <Jared.STRYDHORST@...>
> Cc: "gate-users@..."
> 	<gate-users@...>
> Subject: Re: [Gate-users] how can I apply TOF information on images
> Message-ID: <A207DF27-9428-4213-A481-7F31B46ECDDD@...>
> Content-Type: text/plain; charset="utf-8"
>
> So is it true to say: " This timing information (TOF) is then taken into account during the fully 3D
reconstruction of the data. And for example:I will convert the list mode to a ROOT format to produce
sinograms. "
>
> Je vous  remercie.
>
> Hanieh jozi
> Ms.student in Medical Radiation Engineering
>
> Amiti?s
> Envoy? de mon iPhone
>
>> Le 17 nov. 2015 ? 14:46, STRYDHORST Jared <Jared.STRYDHORST@...> a ?crit :
>>
>> I don't think any of the built-in methods for exporting sinograms or list mode data include TOF
information. The time of each single is stored for the coincidences in the root output, so the TOF list mode
or sinogram data can be extracted, but it requires writing a root script to convert the root data to the
output format you want.
>>
>> Jared STRYDHORST
>>
>> Laboratoire Imagerie Mol?culaire In Vivo (IMIV)
>> UMR 1023 Inserm/CEA/Universit? Paris Sud - ERL 9218 CNRS
>> CEA/I2BM/Service Hospitalier Fr?d?ric Joliot
>> 4, place du G?n?ral Leclerc
>> 91401 ORSAY Cedex
>>
>> http://i2bm.cea.fr/dsv/i2bm/shfj/imiv
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Pietrzyk, Uwe | 17 Nov 15:14 2015
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Re: Best physics list for positron annihilation.


Dear Andrea,

maybe, it is related to the fact that you are using cGATE
and that the visualisation somehow has a problem.
Did you try any other form of visualisation based on
X11. Since the vGATE-base is a unix operating system you
should be able to type xclock and a small window with a clock
should show up. It might also depend on the viewer, which 
you have to specify. I briefly checked the eMails concerning
vGATE3.0 at it seems, that this is an issue. However, I have
no own experience with vGATE3.0.

Kind regards,

Uwe
/----------------------------------------------------------------------
Prof. Dr. Uwe Pietrzyk
Diplom-Physiker
Institut für Neurowissenschaften und Medizin / INM-4
Forschungszentrum Jülich GmbH
52425 Jülich
Tel: +49-2461-61 4763
Fax: +49-2461-61 2820
Mobil: +49-162-103-4871
eMail: U.Pietrzyk <at> fz-juelich.de
http://www.fz-juelich.de/inm/inm-4/DE/Home/home_node.html
&
Bergische Universität Wuppertal
Fakultät für Mathematik und Naturwissenschaften
Büro:  D.08.01
Gaußstr. 20
42097 Wuppertal
Tel: +49-(0)202-439-3523
Fax: +49-(0)202-439-2811
eMail: Uwe.Pietrzyk-QoZ5z9YNi+XRHuS+YikPfA@public.gmane.org
http://www.medizinphysik.uni-wuppertal.de
----------------------------------------------------------------------/

On 17 Nov 2015, at 14:58, Andrea González <andreita_5_92-PkbjNfxxIARBDgjK7y7TUQ@public.gmane.org> wrote:

<!-- .hmmessage P { margin:0px; padding:0px } body.hmmessage { font-size: 12pt; font-family:Calibri } -->
But when I run the simulation in my PC, I don't see the lines...
I will try with the EduGATE example.

Thank you very much, I really appreciate your help.
Very useful comments.

Andrea.


From: u.pietrzyk-97/bSmCnXvjoK6nBLMlh1Q@public.gmane.org
To: andreita_5_92-PkbjNfxxIARBDgjK7y7TUQ@public.gmane.org
CC: gate-users <at> lists.opengatecollaboration.org
Subject: Re: [Gate-users] Best physics list for positron annihilation.
Date: Tue, 17 Nov 2015 13:39:05 +0000


Dear Andrea,

there is nothing wrong with your macros and the findings can be
explained by basic physics:

you have placed a Na-22 source in the middle of a small cylinder
with Rmax= 12mm and height of 6mm and PMMA as material.
The cylinder is defined as detector.

Starting the visualisation I can see:
- blue lines, i.e. positively charged particles, obviously positrons whose
energy was too high to be stopped in the PMMA.

- green lines are the annihilation photons since only some of them are
stopped in the very small cylinder but most of them can escape.

Using ROOT to read the root-file, there is a simple means to check
for all processes that happened (processName).

To study the effect of the positron range and SEE the distribution of the
emitted positrons before annihilation, we have prepared a special
Module for EduGATE (all for free and found on the GATE homepage),
called MR_PET, which besides showing the effect of charged particles
in the magnetic field, can also be used (with the B-field being set to 0.0T)
to study their spatial distribution. We have built in an option to switch off
the annihilation to ease the visualisation without the green lines from
the annihilation photons.

I hope this is helpful for you!

Kind regards and best wishes,

Uwe Pietrzyk

/----------------------------------------------------------------------
Prof. Dr. Uwe Pietrzyk
Diplom-Physiker
Institut für Neurowissenschaften und Medizin / INM-4
Forschungszentrum Jülich GmbH
52425 Jülich
Tel: +49-2461-61 4763
Fax: +49-2461-61 2820
Mobil: +49-162-103-4871
eMail: U.Pietrzyk <at> fz-juelich.de
http://www.fz-juelich.de/inm/inm-4/DE/Home/home_node.html
&
Bergische Universität Wuppertal
Fakultät für Mathematik und Naturwissenschaften
Büro:  D.08.01
Gaußstr. 20
42097 Wuppertal
Tel: +49-(0)202-439-3523
Fax: +49-(0)202-439-2811
eMail: Uwe.Pietrzyk-QoZ5z9YNi+XRHuS+YikPfA@public.gmane.org
http://www.medizinphysik.uni-wuppertal.de
----------------------------------------------------------------------/

On 17 Nov 2015, at 12:22, Andrea González <andreita_5_92-PkbjNfxxIARBDgjK7y7TUQ@public.gmane.org> wrote:

<!-- .ExternalClass .ecxhmmessage P { padding:0px; } .ExternalClass body.ecxhmmessage { font-size:12pt; font-family:Calibri; } -->

My version is vGATE 3.0
Ok, I attached my macros, if you can try I will be very pleased.

Thank you again!



<!-- .ExternalClass .ecxhmmessage P { padding:0px; } .ExternalClass body.ecxhmmessage { font-size:12pt; font-family:Calibri; } --><!-- .ExternalClass .ecxx_hmmessage { padding:0px; } .ExternalClass body.ecxx_hmmessage { font-size:12pt; font-family:Calibri; } --><!-- .ExternalClass .ecxx_ExternalClass .ecxx_ecxhmmessage { padding:0px; } .ExternalClass .ecxx_ExternalClass body.ecxx_ecxhmmessage { font-size:12pt; font-family:Calibri; } -->


------------------------------------------------------------------------------------------------
------------------------------------------------------------------------------------------------
Forschungszentrum Juelich GmbH
52425 Juelich
Sitz der Gesellschaft: Juelich
Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498
Vorsitzender des Aufsichtsrats: MinDir Dr. Karl Eugen Huthmacher
Geschaeftsfuehrung: Prof. Dr.-Ing. Wolfgang Marquardt (Vorsitzender),
Karsten Beneke (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt,
Prof. Dr. Sebastian M. Schmidt
------------------------------------------------------------------------------------------------
------------------------------------------------------------------------------------------------


<div>
<div><br></div>
Dear Andrea,
<div><br></div>
<div>maybe, it is related to the fact that you are using cGATE</div>
<div>and that the visualisation somehow has a problem.</div>
<div>Did you try any other form of visualisation based on</div>
<div>X11. Since the vGATE-base is a unix operating system you</div>
<div>should be able to type xclock and a small window with a clock</div>
<div>should show up. It might also depend on the viewer, which&nbsp;</div>
<div>you have to specify. I briefly checked the eMails concerning</div>
<div>vGATE3.0 at it seems, that this is an issue. However, I have</div>
<div>no own experience with vGATE3.0.</div>
<div><br></div>
<div>Kind regards,</div>
<div><br></div>
<div>Uwe<br><div>
<div>
<div><span>/----------------------------------------------------------------------</span></div>
<div>Prof. Dr. Uwe Pietrzyk<br>
Diplom-Physiker<br>
Institut f&uuml;r Neurowissenschaften und Medizin / INM-4<br>
Forschungszentrum J&uuml;lich GmbH<br>
52425 J&uuml;lich<br>
Tel: +49-2461-61 4763<br>
Fax: +49-2461-61 2820<br>
Mobil: +49-162-103-4871<br>
eMail:&nbsp;<a href="mailto:U.Pietrzyk@...">U.Pietrzyk <at> fz-juelich.de</a><br><a href="http://www.fz-juelich.de/inm/inm-4/DE/Home/home_node.html">http://www.fz-juelich.de/inm/inm-4/DE/Home/home_node.html</a><br>
&amp;<br>
Bergische Universit&auml;t Wuppertal<br>
Fakult&auml;t f&uuml;r Mathematik und Naturwissenschaften</div>
<div>B&uuml;ro: &nbsp;D.08.01<br>
Gau&szlig;str. 20<br>
42097 Wuppertal<br>
Tel: +49-(0)202-439-3523<br>
Fax: +49-(0)202-439-2811<br>
eMail:&nbsp;<a href="mailto:Uwe.Pietrzyk@...">Uwe.Pietrzyk@...</a><br><a href="http://www.medizinphysik.uni-wuppertal.de/">http://www.medizinphysik.uni-wuppertal.de</a><br>
----------------------------------------------------------------------/</div>
</div>
</div>
<br><div>
<div>On 17 Nov 2015, at 14:58, Andrea Gonz&aacute;lez &lt;<a href="mailto:andreita_5_92@...">andreita_5_92@...</a>&gt; wrote:</div>
<br class="Apple-interchange-newline"><blockquote type="cite">&lt;!--
.hmmessage P
{
margin:0px;
padding:0px
}
body.hmmessage
{
font-size: 12pt;
font-family:Calibri
}
--&gt;<div class="hmmessage">
<div dir="ltr">But when I run the simulation in my PC, I don't see the lines...
<div>I will try with the EduGATE example.</div>
<div><br></div>
<div>Thank you very much, I really appreciate your help.</div>
<div>Very useful comments.</div>
<div><br></div>
<div>Andrea.</div>
<div>
<br><br><div>

From: <a href="mailto:u.pietrzyk@...">u.pietrzyk@...</a><br>
To: <a href="mailto:andreita_5_92@...">andreita_5_92@...</a><br>
CC: <a href="mailto:gate-users@...">gate-users <at> lists.opengatecollaboration.org</a><br>
Subject: Re: [Gate-users] Best physics list for positron annihilation.<br>
Date: Tue, 17 Nov 2015 13:39:05 +0000<br><br><div><br></div>
Dear Andrea,
<div><br></div>
<div>there is nothing wrong with your macros and the findings can be</div>
<div>explained by basic physics:</div>
<div><br></div>
<div>you have placed a Na-22 source in the middle of a small cylinder</div>
<div>with Rmax= 12mm and height of 6mm and PMMA as material.</div>
<div>The cylinder is defined as detector.</div>
<div><br></div>
<div>Starting the visualisation I can see:</div>
<div>- blue lines, i.e. positively charged particles, obviously positrons whose</div>
<div>energy was too high to be stopped in the PMMA.</div>
<div><br></div>
<div>- green lines are the annihilation photons since only some of them are</div>
<div>stopped in the very small cylinder but most of them can escape.</div>
<div><br></div>
<div>Using ROOT to read the root-file, there is a simple means to check</div>
<div>for all processes that happened (processName).</div>
<div><br></div>
<div>To study the effect of the positron range and SEE the distribution of the</div>
<div>emitted positrons before annihilation, we have prepared a special</div>
<div>Module for EduGATE (all for free and found on the GATE homepage),</div>
<div>called MR_PET, which besides showing the effect of charged particles</div>
<div>in the magnetic field, can also be used (with the B-field being set to 0.0T)</div>
<div>to study their spatial distribution. We have built in an option to switch off</div>
<div>the annihilation to ease the visualisation without the green lines from</div>
<div>the annihilation photons.</div>
<div><br></div>
<div>I hope this is helpful for you!</div>
<div><br></div>
<div>Kind regards and best wishes,</div>
<div><br></div>
<div>Uwe Pietrzyk</div>
<div><br></div>
<div>
<div>
<div>
<div><span>/----------------------------------------------------------------------</span></div>
<div>Prof. Dr. Uwe Pietrzyk<br>
Diplom-Physiker<br>
Institut f&uuml;r Neurowissenschaften und Medizin / INM-4<br>
Forschungszentrum J&uuml;lich GmbH<br>
52425 J&uuml;lich<br>
Tel: +49-2461-61 4763<br>
Fax: +49-2461-61 2820<br>
Mobil: +49-162-103-4871<br>
eMail:&nbsp;<a href="mailto:U.Pietrzyk@...">U.Pietrzyk <at> fz-juelich.de</a><br><a href="http://www.fz-juelich.de/inm/inm-4/DE/Home/home_node.html" target="_blank">http://www.fz-juelich.de/inm/inm-4/DE/Home/home_node.html</a><br>
&amp;<br>
Bergische Universit&auml;t Wuppertal<br>
Fakult&auml;t f&uuml;r Mathematik und Naturwissenschaften</div>
<div>B&uuml;ro: &nbsp;D.08.01<br>
Gau&szlig;str. 20<br>
42097 Wuppertal<br>
Tel: +49-(0)202-439-3523<br>
Fax: +49-(0)202-439-2811<br>
eMail:&nbsp;<a href="mailto:Uwe.Pietrzyk@...">Uwe.Pietrzyk@...</a><br><a href="http://www.medizinphysik.uni-wuppertal.de/" target="_blank">http://www.medizinphysik.uni-wuppertal.de</a><br>
----------------------------------------------------------------------/</div>
</div>
</div>
<br><div>
<div>On 17 Nov 2015, at 12:22, Andrea Gonz&aacute;lez &lt;<a href="mailto:andreita_5_92@...">andreita_5_92@...</a>&gt; wrote:</div>
<br class="ecxApple-interchange-newline"><blockquote>&lt;!--
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<div dir="ltr">
<br>
My version is vGATE 3.0
<div>Ok, I attached my macros, if you can try I will be very pleased.</div>
<div><br></div>
<div>Thank you again!<br><div>
<br><div>
<br><div>
</div>
</div>
</div>
</div>
</div>
</div>
</blockquote>
</div>
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<br><br>
------------------------------------------------------------------------------------------------<br>
------------------------------------------------------------------------------------------------<br>
Forschungszentrum Juelich GmbH<br>
52425 Juelich<br>
Sitz der Gesellschaft: Juelich<br>
Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498<br>
Vorsitzender des Aufsichtsrats: MinDir Dr. Karl Eugen Huthmacher<br>
Geschaeftsfuehrung: Prof. Dr.-Ing. Wolfgang Marquardt (Vorsitzender),<br>
Karsten Beneke (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt,<br>
Prof. Dr. Sebastian M. Schmidt<br>
------------------------------------------------------------------------------------------------<br>
------------------------------------------------------------------------------------------------<br><br>
</div>
</div>
</div>
</div>
</blockquote>
</div>
<br>
</div>
</div>
Pietrzyk, Uwe | 17 Nov 14:39 2015
Picon
Picon

Re: Best physics list for positron annihilation.


Dear Andrea,

there is nothing wrong with your macros and the findings can be
explained by basic physics:

you have placed a Na-22 source in the middle of a small cylinder
with Rmax= 12mm and height of 6mm and PMMA as material.
The cylinder is defined as detector.

Starting the visualisation I can see:
- blue lines, i.e. positively charged particles, obviously positrons whose
energy was too high to be stopped in the PMMA.

- green lines are the annihilation photons since only some of them are
stopped in the very small cylinder but most of them can escape.

Using ROOT to read the root-file, there is a simple means to check
for all processes that happened (processName).

To study the effect of the positron range and SEE the distribution of the
emitted positrons before annihilation, we have prepared a special
Module for EduGATE (all for free and found on the GATE homepage),
called MR_PET, which besides showing the effect of charged particles
in the magnetic field, can also be used (with the B-field being set to 0.0T)
to study their spatial distribution. We have built in an option to switch off
the annihilation to ease the visualisation without the green lines from
the annihilation photons.

I hope this is helpful for you!

Kind regards and best wishes,

Uwe Pietrzyk

/----------------------------------------------------------------------
Prof. Dr. Uwe Pietrzyk
Diplom-Physiker
Institut für Neurowissenschaften und Medizin / INM-4
Forschungszentrum Jülich GmbH
52425 Jülich
Tel: +49-2461-61 4763
Fax: +49-2461-61 2820
Mobil: +49-162-103-4871
eMail: U.Pietrzyk <at> fz-juelich.de
http://www.fz-juelich.de/inm/inm-4/DE/Home/home_node.html
&
Bergische Universität Wuppertal
Fakultät für Mathematik und Naturwissenschaften
Büro:  D.08.01
Gaußstr. 20
42097 Wuppertal
Tel: +49-(0)202-439-3523
Fax: +49-(0)202-439-2811
eMail: Uwe.Pietrzyk-QoZ5z9YNi+XRHuS+YikPfA@public.gmane.org
http://www.medizinphysik.uni-wuppertal.de
----------------------------------------------------------------------/

On 17 Nov 2015, at 12:22, Andrea González <andreita_5_92-PkbjNfxxIARBDgjK7y7TUQ@public.gmane.org> wrote:

<!-- .hmmessage P { margin:0px; padding:0px } body.hmmessage { font-size: 12pt; font-family:Calibri } -->

My version is vGATE 3.0
Ok, I attached my macros, if you can try I will be very pleased.

Thank you again!



<!-- .ExternalClass .ecxhmmessage P { padding:0px; } .ExternalClass body.ecxhmmessage { font-size:12pt; font-family:Calibri; } --><!-- .ExternalClass .ecxx_hmmessage { padding:0px; } .ExternalClass body.ecxx_hmmessage { font-size:12pt; font-family:Calibri; } --><!-- .ExternalClass .ecxx_ExternalClass .ecxx_ecxhmmessage { padding:0px; } .ExternalClass .ecxx_ExternalClass body.ecxx_ecxhmmessage { font-size:12pt; font-family:Calibri; } -->


------------------------------------------------------------------------------------------------
------------------------------------------------------------------------------------------------
Forschungszentrum Juelich GmbH
52425 Juelich
Sitz der Gesellschaft: Juelich
Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498
Vorsitzender des Aufsichtsrats: MinDir Dr. Karl Eugen Huthmacher
Geschaeftsfuehrung: Prof. Dr.-Ing. Wolfgang Marquardt (Vorsitzender),
Karsten Beneke (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt,
Prof. Dr. Sebastian M. Schmidt
------------------------------------------------------------------------------------------------
------------------------------------------------------------------------------------------------

<div>
<div><br></div>
Dear Andrea,
<div><br></div>
<div>there is nothing wrong with your macros and the findings can be</div>
<div>explained by basic physics:</div>
<div><br></div>
<div>you have placed a Na-22 source in the middle of a small cylinder</div>
<div>with Rmax= 12mm and height of 6mm and PMMA as material.</div>
<div>The cylinder is defined as detector.</div>
<div><br></div>
<div>Starting the visualisation I can see:</div>
<div>- blue lines, i.e. positively charged particles, obviously positrons whose</div>
<div>energy was too high to be stopped in the PMMA.</div>
<div><br></div>
<div>- green lines are the annihilation photons since only some of them are</div>
<div>stopped in the very small cylinder but most of them can escape.</div>
<div><br></div>
<div>Using ROOT to read the root-file, there is a simple means to check</div>
<div>for all processes that happened (processName).</div>
<div><br></div>
<div>To study the effect of the positron range and SEE the distribution of the</div>
<div>emitted positrons before annihilation, we have prepared a special</div>
<div>Module for EduGATE (all for free and found on the GATE homepage),</div>
<div>called MR_PET, which besides showing the effect of charged particles</div>
<div>in the magnetic field, can also be used (with the B-field being set to 0.0T)</div>
<div>to study their spatial distribution. We have built in an option to switch off</div>
<div>the annihilation to ease the visualisation without the green lines from</div>
<div>the annihilation photons.</div>
<div><br></div>
<div>I hope this is helpful for you!</div>
<div><br></div>
<div>Kind regards and best wishes,</div>
<div><br></div>
<div>Uwe Pietrzyk</div>
<div><br></div>
<div>
<div>
<div>
<div><span>/----------------------------------------------------------------------</span></div>
<div>Prof. Dr. Uwe Pietrzyk<br>
Diplom-Physiker<br>
Institut f&uuml;r Neurowissenschaften und Medizin / INM-4<br>
Forschungszentrum J&uuml;lich GmbH<br>
52425 J&uuml;lich<br>
Tel: +49-2461-61 4763<br>
Fax: +49-2461-61 2820<br>
Mobil: +49-162-103-4871<br>
eMail:&nbsp;<a href="mailto:U.Pietrzyk@...">U.Pietrzyk <at> fz-juelich.de</a><br><a href="http://www.fz-juelich.de/inm/inm-4/DE/Home/home_node.html">http://www.fz-juelich.de/inm/inm-4/DE/Home/home_node.html</a><br>
&amp;<br>
Bergische Universit&auml;t Wuppertal<br>
Fakult&auml;t f&uuml;r Mathematik und Naturwissenschaften</div>
<div>B&uuml;ro: &nbsp;D.08.01<br>
Gau&szlig;str. 20<br>
42097 Wuppertal<br>
Tel: +49-(0)202-439-3523<br>
Fax: +49-(0)202-439-2811<br>
eMail:&nbsp;<a href="mailto:Uwe.Pietrzyk@...">Uwe.Pietrzyk@...</a><br><a href="http://www.medizinphysik.uni-wuppertal.de/">http://www.medizinphysik.uni-wuppertal.de</a><br>
----------------------------------------------------------------------/</div>
</div>
</div>
<br><div>
<div>On 17 Nov 2015, at 12:22, Andrea Gonz&aacute;lez &lt;<a href="mailto:andreita_5_92@...">andreita_5_92@...</a>&gt; wrote:</div>
<br class="Apple-interchange-newline"><blockquote type="cite">&lt;!--
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<div dir="ltr">
<br>
My version is vGATE 3.0
<div>Ok, I attached my macros, if you can try I will be very pleased.</div>
<div><br></div>
<div>Thank you again!<br><div>
<br><div>
<br><div>
</div>
</div>
</div>
</div>
</div>
</div>
</blockquote>
</div>
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--&gt;</div>
<br><br>
------------------------------------------------------------------------------------------------<br>
------------------------------------------------------------------------------------------------<br>
Forschungszentrum Juelich GmbH<br>
52425 Juelich<br>
Sitz der Gesellschaft: Juelich<br>
Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498<br>
Vorsitzender des Aufsichtsrats: MinDir Dr. Karl Eugen Huthmacher<br>
Geschaeftsfuehrung: Prof. Dr.-Ing. Wolfgang Marquardt (Vorsitzender),<br>
Karsten Beneke (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt,<br>
Prof. Dr. Sebastian M. Schmidt<br>
------------------------------------------------------------------------------------------------<br>
------------------------------------------------------------------------------------------------<br><br>
</div>
Picon

Collimator geometry Z-rotation with repeaters

Dear Gaters,

 

I’m trying to construct a hexagonal parallel hole collimator with the hexagone shape. But I want to rotate the hexagon about its radius, which makes repeating the geometry more complicated.

 

I have only managed to successfully repeat the geometry using a generic repeater – I tried linear, cubic array and quadrant, but no luck.

Also, I cannot find a way to repeat partial volumes at the collimator’s edges. This results in holes over-extending beyond my desired collimator geometry.

 

Can anyone advise on a more efficient repeater method?

Is there a simple way to create partial holes at the collimator edge?

(see attached image for the generic repeater arrangement, green line is desired edge of collimator).

 

And here’s the hexagone specification:

 

/gate/collimator/daughters/name hole

/gate/collimator/daughters/insert hexagone

/gate/hole/geometry/setHeight 10. mm

/gate/hole/geometry/setRadius 2. mm

/gate/hole/placement/setRotationAxis 0 0 1

/gate/hole/placement/setRotationAngle 45 deg

/gate/hole/setMaterial Air

 

Thanks for your help,

 

 

Alex Grimwood

 

--------------------------------------

a.grimwood <at> nhs.net

Trainee Clinical Scientist

Royal Surrey County Hospital,

Guildford,

Surrey

GU2 7XX

 


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Please do not disclose, copy or distribute information in this e-mail or take any action in reliance on its contents:
to do so is strictly prohibited and may be unlawful.

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<div>
<div class="WordSection1">
<p class="MsoNormal">Dear Gaters,<p></p></p>
<p class="MsoNormal"><p>&nbsp;</p></p>
<p class="MsoNormal">I&rsquo;m trying to construct a hexagonal parallel hole collimator with the hexagone shape. But I want to rotate the hexagon about its radius, which makes repeating the geometry more complicated.<p></p></p>
<p class="MsoNormal"><p>&nbsp;</p></p>
<p class="MsoNormal">I have only managed to successfully repeat the geometry using a generic repeater &ndash; I tried linear, cubic array and quadrant, but no luck.<p></p></p>
<p class="MsoNormal">Also, I cannot find a way to repeat partial volumes at the collimator&rsquo;s edges. This results in holes over-extending beyond my desired collimator geometry.<p></p></p>
<p class="MsoNormal"><p>&nbsp;</p></p>
<p class="MsoNormal">Can anyone advise on a more efficient repeater method?<p></p></p>
<p class="MsoNormal">Is there a simple way to create partial holes at the collimator edge?<p></p></p>
<p class="MsoNormal">(see attached image for the generic repeater arrangement, green line is desired edge of collimator).<p></p></p>
<p class="MsoNormal"><p>&nbsp;</p></p>
<p class="MsoNormal">And here&rsquo;s the hexagone specification:<p></p></p>
<p class="MsoNormal"><p>&nbsp;</p></p>
<p class="MsoNormal"><span>/gate/collimator/daughters/name hole<p></p></span></p>
<p class="MsoNormal"><span>/gate/collimator/daughters/insert hexagone<p></p></span></p>
<p class="MsoNormal"><span>/gate/hole/geometry/setHeight 10. mm<p></p></span></p>
<p class="MsoNormal"><span>/gate/hole/geometry/setRadius 2. mm<p></p></span></p>
<p class="MsoNormal"><span>/gate/hole/placement/setRotationAxis 0 0 1<p></p></span></p>
<p class="MsoNormal"><span>/gate/hole/placement/setRotationAngle 45 deg<p></p></span></p>
<p class="MsoNormal"><span>/gate/hole/setMaterial Air<p></p></span></p>
<p class="MsoNormal"><p>&nbsp;</p></p>
<p class="MsoNormal">Thanks for your help,<p></p></p>
<p class="MsoNormal"><p>&nbsp;</p></p>
<p class="MsoNormal"><p>&nbsp;</p></p>
<p class="MsoPlainText"><span>Alex Grimwood<p></p></span></p>
<p class="MsoPlainText"><span><p>&nbsp;</p></span></p>
<p class="MsoPlainText"><span>--------------------------------------<p></p></span></p>
<p class="MsoPlainText"><span><a href="mailto:a.grimwood@...">a.grimwood <at> nhs.net</a><p></p></span></p>
<p class="MsoPlainText"><span>Trainee Clinical Scientist<p></p></span></p>
<p class="MsoPlainText"><span>Royal Surrey County Hospital,<p></p></span></p>
<p class="MsoPlainText"><span>Guildford,<p></p></span></p>
<p class="MsoPlainText"><span>Surrey<p></p></span></p>
<p class="MsoPlainText"><span>GU2 7XX<p></p></span></p>
<p class="MsoNormal"><p>&nbsp;</p></p>
</div>
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This message may contain confidential information. If you are not the intended recipient please inform the<br>
sender that you have received the message in error before deleting it.<br>
Please do not disclose, copy or distribute information in this e-mail or take any action in reliance on its contents:<br>
to do so is strictly prohibited and may be unlawful.<br><br>
Thank you for your co-operation.<br><br>
NHSmail is the secure email and directory service available for all NHS staff in England and Scotland<br>
NHSmail is approved for exchanging patient data and other sensitive information with NHSmail and GSi recipients<br>
NHSmail provides an email address for your career in the NHS and can be accessed anywhere<br><br>
********************************************************************************************************************≤br>
</div>
STRYDHORST Jared | 17 Nov 12:16 2015
Picon

Re: how can I apply TOF information on images

I don't think any of the built-in methods for exporting sinograms or list mode data include TOF information. The time of each single is stored for the coincidences in the root output, so the TOF list mode or sinogram data can be extracted, but it requires writing a root script to convert the root data to the output format you want.

Jared STRYDHORST

Laboratoire Imagerie Moléculaire In Vivo (IMIV)
UMR 1023 Inserm/CEA/Université Paris Sud - ERL 9218 CNRS
CEA/I2BM/Service Hospitalier Frédéric Joliot
4, place du Général Leclerc
91401 ORSAY Cedex


<div>
<div>I don't think any of the built-in methods for exporting sinograms or list mode data include TOF information. The time of each single is stored for the coincidences in the root output,
 so the TOF list mode or sinogram data can be extracted, but it requires writing a root script to convert the root data to the output format you want.<br><div>
<br><div>
<div>
<div class="BodyFragment"><span>
<div class="PlainText">Jared STRYDHORST<br><br><span lang="fr">
<div><span><span>Laboratoire Imagerie Mol&eacute;culaire In Vivo (IMIV)</span><span><br>
UMR 1023 Inserm/CEA/Universit&eacute; Paris Sud - ERL&nbsp;9218 CNRS</span></span></div>
<div><span><span>CEA/I2BM/Service Hospitalier Fr&eacute;d&eacute;ric Joliot</span></span></div>
<div><span><span>4, place du G&eacute;n&eacute;ral Leclerc</span><span><br>
91401 ORSAY Cedex</span><span><br></span><span></span><span><br></span><a href="mailto:karima.ait-aissa@..." target="_blank"><span></span></a></span></div>
<div><span><a href="http://i2bm.cea.fr/dsv/i2bm/shfj/imiv" target="_blank"><span>http://i2bm.cea.fr/dsv/i2bm/shfj/imiv</span></a></span></div>
</span>
</div>
</span></div>
</div>
</div>
</div>
</div>
</div>
Pietrzyk, Uwe | 17 Nov 12:12 2015
Picon
Picon

Re: Best physics list for positron annihilation.



Hi Andrea,

to give further help, there are some more infos needed:
Which version of Gate are you using and which OS?
Also, I you wish, I can run your program in my environment
as I did for many other GATE users in the past.
Feel free to send the macros fickly to me and I can test them
on my system. It is difficult to help just from a simple output
not knowing the basic setup.

Kind regards,

Uwe Pietrzyk
/----------------------------------------------------------------------
Prof. Dr. Uwe Pietrzyk
Diplom-Physiker
Institut für Neurowissenschaften und Medizin / INM-4
Forschungszentrum Jülich GmbH
52425 Jülich
Tel: +49-2461-61 4763
Fax: +49-2461-61 2820
Mobil: +49-162-103-4871
eMail: U.Pietrzyk <at> fz-juelich.de
http://www.fz-juelich.de/inm/inm-4/DE/Home/home_node.html
&
Bergische Universität Wuppertal
Fakultät für Mathematik und Naturwissenschaften
Büro:  D.08.01
Gaußstr. 20
42097 Wuppertal
Tel: +49-(0)202-439-3523
Fax: +49-(0)202-439-2811
eMail: Uwe.Pietrzyk-QoZ5z9YNi+XRHuS+YikPfA@public.gmane.org
http://www.medizinphysik.uni-wuppertal.de
----------------------------------------------------------------------/

On 17 Nov 2015, at 11:55, Andrea González <andreita_5_92-PkbjNfxxIARBDgjK7y7TUQ@public.gmane.org> wrote:

<!-- .hmmessage P { margin:0px; padding:0px } body.hmmessage { font-size: 12pt; font-family:Calibri } -->
Thank you very much!

But If I do like the example, my source doens't decay... I have the RadioactiveDecay included in my physics list... 
Maybe something is wrong with my version of GATE.

I have attached the spectrum with this simulations, obviously positrons are not being annihilated. Now I'm using the PENELOPE physics list...
Now I have implemented the source as follows:

#
# S O U R C E S
#

# source: ion
/gate/source/addSource         IonSource

/gate/source/IonSource/setActivity  1000 Bq


/gate/source/IonSource/gps/type Plane
/gate/source/IonSource/gps/shape Circle

/gate/source/IonSource/gps/radius 0.5 mm
/gate/source/IonSource/gps/centre  0.0 0.0 0.0 cm

/gate/source/IonSource/gps/particle ion
/gate/source/IonSource/gps/ion  11 22 0 0
/gate/source/IonSource/setForcedUnstableFlag  true
/gate/source/IonSource/setForcedHalfLife  81993600.0 s
/gate/source/IonSource/gps/energytype  Mono
/gate/source/IonSource/gps/monoenergy  0. MeV
/gate/source/IonSource/gps/number  1

/gate/source/IonSource/gps/angtype iso


/gate/source/list

From: u.pietrzyk-97/bSmCnXvjoK6nBLMlh1Q@public.gmane.org
To: andreita_5_92-PkbjNfxxIARBDgjK7y7TUQ@public.gmane.org
CC: gate-users <at> lists.opengatecollaboration.org
Subject: Re: [Gate-users] Best physics list for positron annihilation.
Date: Tue, 17 Nov 2015 10:20:39 +0000


Hi Andrea,

in your macro you are specifying a source which emits positrons
with a fixed energy! To simulate the range of positrons from
Na-22 decay you better use an ion-source! 
Here is the code we use in the EduGATE example “Spectro”
& see macro file attached to this eMail.

In the case of Na-22 the aliases in { } are replaced by

Ion_Z_val -> 11
Ion_A_val -> 22

NOTE: this is done automatically in the Spectro example
according to the users’ choice for the Isotope. We simply read
the file: RadioactiveDecay3.3 used in GEANT4.

This finally should give you  more realistic data about the positron
range, since it takes into account the energy distribution of the
emitted positron.

I hope this helps!

Kind regards,

Uwe Pietrzyk

-----------------------------------------
#
# S O U R C E S
#

# source: ion
/gate/source/addSource        IonSource

/gate/source/IonSource/setActivity        {SourceActivity}


/gate/source/IonSource/gps/type Volume
/gate/source/IonSource/gps/shape Sphere
#/gate/source/IonSource/gps/radius 0.1 mm
/gate/source/IonSource/gps/radius {SourceRad}
/gate/source/IonSource/gps/centre 0.0 0.0 0.0 cm

##
## universal ion source
## with arbitrary halflife
##
/gate/source/IonSource/gps/particle ion
/gate/source/IonSource/gps/ion {Ion_Z_val} {Ion_A_val} 0 0
/gate/source/IonSource/setForcedUnstableFlag true
/gate/source/IonSource/setForcedHalfLife 99999999.0 s
/gate/source/IonSource/gps/energytype Mono
/gate/source/IonSource/gps/monoenergy 0. MeV
/gate/source/IonSource/gps/number 1

/gate/source/IonSource/gps/angtype iso
/gate/source/IonSource/gps/mintheta 0. deg
/gate/source/IonSource/gps/maxtheta 180. deg
/gate/source/IonSource/gps/minphi 0. deg
/gate/source/IonSource/gps/maxphi 360. deg

/gate/source/list

#/gate/source/IonSource/gps/confine source_vol


/----------------------------------------------------------------------
Prof. Dr. Uwe Pietrzyk
Diplom-Physiker
Institut für Neurowissenschaften und Medizin / INM-4
Forschungszentrum Jülich GmbH
52425 Jülich
Tel: +49-2461-61 4763
Fax: +49-2461-61 2820
Mobil: +49-162-103-4871
eMail: U.Pietrzyk <at> fz-juelich.de
http://www.fz-juelich.de/inm/inm-4/DE/Home/home_node.html
&
Bergische Universität Wuppertal
Fakultät für Mathematik und Naturwissenschaften
Büro:  D.08.01
Gaußstr. 20
42097 Wuppertal
Tel: +49-(0)202-439-3523
Fax: +49-(0)202-439-2811
eMail: Uwe.Pietrzyk-QoZ5z9YNi+XRHuS+YikPfA@public.gmane.org
http://www.medizinphysik.uni-wuppertal.de
----------------------------------------------------------------------/





On 17 Nov 2015, at 10:47, Andrea González <andreita_5_92-PkbjNfxxIARBDgjK7y7TUQ@public.gmane.org> wrote:

<!-- .ExternalClass .ecxx_hmmessage { padding:0px; } .ExternalClass body.ecxx_hmmessage { font-size:12pt; font-family:Calibri; } -->
Sorry, you are right!
I'm using 22-Na as follows:


/gate/source/addSource na22
/gate/source/na22/setActivity 10000 Bq

/gate/source/na22/gps/particle e+
/gate/source/na22/setForcedUnstableFlag true
/gate/source/na22/setForcedHalfLife 81993600 s
#/gate/source/na22/gps/energytype Mono
#/gate/source/na22/gps/monoenergy 545 keV 
/gate/source/na22/gps/monoenergy 195 keV 


/gate/source/na22/gps/type Plane
/gate/source/na22/gps/shape Circle
/gate/source/na22/gps/radius 0.5 mm

/gate/source/na22/gps/angtype iso
/gate/source/na22/gps/centre 0. 0. 0. cm

/gate/source/list

Do you thing is correct?

My physics list:

#=====================================
#    Electromagnetic  processes
#=====================================



/gate/physics/addProcess RadioactiveDecay

/gate/physics/addProcess PhotoElectric
/gate/physics/processes/PhotoElectric/setModel StandardModel

/gate/physics/addProcess Compton
/gate/physics/processes/Compton/setModel StandardModel

/gate/physics/addProcess GammaConversion
/gate/physics/processes/GammaConversion/setModel StandardModel

/gate/physics/addProcess ElectronIonisation
/gate/physics/processes/ElectronIonisation/setModel StandardModel e-
/gate/physics/processes/ElectronIonisation/setModel StandardModel e+
/gate/physics/processes/ElectronIonisation/setStepFunction e+ 0.2 0.1 mm
/gate/physics/processes/ElectronIonisation/setStepFunction e- 0.2 0.1 mm
/gate/physics/processes/ElectronIonisation/setLinearLossLimit electron 0.01

/gate/physics/addProcess Bremsstrahlung
/gate/physics/processes/Bremsstrahlung/setModel StandardModel e-
/gate/physics/processes/Bremsstrahlung/setModel StandardModel e+

/gate/physics/addProcess PositronAnnihilation

/gate/physics/addProcess eMultipleScattering e-
/gate/physics/addProcess eMultipleScattering e+
/gate/physics/addProcess/eMultipleScattering/setModel Urban95Model

/gate/physics/processes/eMultipleScattering/setGeometricalStepLimiterType e- distanceToBoundary
/gate/physics/processes/eMultipleScattering/setGeometricalStepLimiterType e+ distanceToBoundary

#=========
# Options
#=========

/gate/physics/setEMin 0.1 keV
/gate/physics/setEMax 10 GeV


The problem is about the annihilation range of the positrons in PMMA, because it shows a distrubution much broader than it should be...

I really appreciate your help and comments.

Best regards, Andrea.






From: u.pietrzyk-97/bSmCnXvjoK6nBLMlh1Q@public.gmane.org
To: andreita_5_92-PkbjNfxxIARBDgjK7y7TUQ@public.gmane.org
CC: gate-users <at> lists.opengatecollaboration.org
Subject: Re: [Gate-users] Best physics list for positron annihilation.
Date: Mon, 16 Nov 2015 15:40:00 +0000


Dear Andrea,

you didn’t mention the type of problem, but when
you use 22-Na as an ion source you need to specify
the radioactive decay explicitly. In our test and examples,
we use the following:

/gate/physics/addPhysicsList emstandard
/gate/physics/addProcess RadioactiveDecay

and this seems to work fine.
In case you mean something else, please let us know.

Kind regards,

Uwe Pietrzyk

/----------------------------------------------------------------------
Prof. Dr. Uwe Pietrzyk
Diplom-Physiker
Institut für Neurowissenschaften und Medizin / INM-4
Forschungszentrum Jülich GmbH
52425 Jülich
Tel: +49-2461-61 4763
Fax: +49-2461-61 2820
Mobil: +49-162-103-4871
eMail: U.Pietrzyk <at> fz-juelich.de
http://www.fz-juelich.de/inm/inm-4/DE/Home/home_node.html
&
Bergische Universität Wuppertal
Fakultät für Mathematik und Naturwissenschaften
Büro:  D.08.01
Gaußstr. 20
42097 Wuppertal
Tel: +49-(0)202-439-3523
Fax: +49-(0)202-439-2811
eMail: Uwe.Pietrzyk-QoZ5z9YNi+XRHuS+YikPfA@public.gmane.org
http://www.medizinphysik.uni-wuppertal.de
----------------------------------------------------------------------/

On 16 Nov 2015, at 15:58, Andrea González <andreita_5_92-PkbjNfxxIARBDgjK7y7TUQ@public.gmane.org> wrote:

<!-- .ExternalClass .ecxx_ExternalClass .ecxx_ecxhmmessage { padding:0px; } .ExternalClass .ecxx_ExternalClass body.ecxx_ecxhmmessage { font-size:12pt; font-family:Calibri; } -->
Hello, I'm trying to simulate positron annihilitaion for 22-Na in PMMA.

I would like to know wich is the best physics list in this case, because I have problems with my list (standard EM).

Thank you very much.

Andrea.


_______________________________________________
Gate-users mailing list
Gate-users <at> lists.opengatecollaboration.org
http://lists.opengatecollaboration.org/mailman/listinfo/gate-users



------------------------------------------------------------------------------------------------
------------------------------------------------------------------------------------------------
Forschungszentrum Juelich GmbH
52425 Juelich
Sitz der Gesellschaft: Juelich
Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498
Vorsitzender des Aufsichtsrats: MinDir Dr. Karl Eugen Huthmacher
Geschaeftsfuehrung: Prof. Dr.-Ing. Wolfgang Marquardt (Vorsitzender),
Karsten Beneke (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt,
Prof. Dr. Sebastian M. Schmidt
------------------------------------------------------------------------------------------------
------------------------------------------------------------------------------------------------


<Captura.JPG>

<div>
<div><br></div>
<div><br></div>
Hi Andrea,
<div><br></div>
<div>to give further help, there are some more infos needed:</div>
<div>Which version of Gate are you using and which OS?</div>
<div>Also, I you wish, I can run your program in my environment</div>
<div>as I did for many other GATE users in the past.</div>
<div>Feel free to send the macros fickly to me and I can test them</div>
<div>on my system. It is difficult to help just from a simple output</div>
<div>not knowing the basic setup.</div>
<div><br></div>
<div>Kind regards,</div>
<div><br></div>
<div>Uwe Pietrzyk<br><div>
<div>
<div><span>/----------------------------------------------------------------------</span></div>
<div>Prof. Dr. Uwe Pietrzyk<br>
Diplom-Physiker<br>
Institut f&uuml;r Neurowissenschaften und Medizin / INM-4<br>
Forschungszentrum J&uuml;lich GmbH<br>
52425 J&uuml;lich<br>
Tel: +49-2461-61 4763<br>
Fax: +49-2461-61 2820<br>
Mobil: +49-162-103-4871<br>
eMail:&nbsp;<a href="mailto:U.Pietrzyk@...">U.Pietrzyk <at> fz-juelich.de</a><br><a href="http://www.fz-juelich.de/inm/inm-4/DE/Home/home_node.html">http://www.fz-juelich.de/inm/inm-4/DE/Home/home_node.html</a><br>
&amp;<br>
Bergische Universit&auml;t Wuppertal<br>
Fakult&auml;t f&uuml;r Mathematik und Naturwissenschaften</div>
<div>B&uuml;ro: &nbsp;D.08.01<br>
Gau&szlig;str. 20<br>
42097 Wuppertal<br>
Tel: +49-(0)202-439-3523<br>
Fax: +49-(0)202-439-2811<br>
eMail:&nbsp;<a href="mailto:Uwe.Pietrzyk@...">Uwe.Pietrzyk@...</a><br><a href="http://www.medizinphysik.uni-wuppertal.de/">http://www.medizinphysik.uni-wuppertal.de</a><br>
----------------------------------------------------------------------/</div>
</div>
</div>
<br><div>
<div>On 17 Nov 2015, at 11:55, Andrea Gonz&aacute;lez &lt;<a href="mailto:andreita_5_92@...">andreita_5_92@...</a>&gt; wrote:</div>
<br class="Apple-interchange-newline"><blockquote type="cite">&lt;!--
.hmmessage P
{
margin:0px;
padding:0px
}
body.hmmessage
{
font-size: 12pt;
font-family:Calibri
}
--&gt;<div class="hmmessage">
<div dir="ltr">Thank you very much!
<div><br></div>
<div>But If I do like the example, my source doens't decay... I have the RadioactiveDecay included in my physics list...&nbsp;</div>
<div>Maybe something is wrong with my version of GATE.</div>
<div><br></div>
<div>I have attached the spectrum with this simulations, obviously positrons are not being annihilated. Now I'm using the PENELOPE physics list...</div>
<div>Now I have implemented the source as follows:</div>
<div><br></div>
<div>
<div>#</div>
<div>#<span class="ecxx_Apple-tab-span">
</span>S O U R C E S</div>
<div>#</div>
<div><br></div>
<div># source: ion</div>
<div>/gate/source/addSource&nbsp;<span class="ecxx_Apple-tab-span">
</span>&nbsp; &nbsp; &nbsp; &nbsp;IonSource</div>
<div><br></div>
<div>/gate/source/IonSource/setActivity&nbsp;<span class="ecxx_Apple-tab-span">
</span>1000 Bq</div>
<div><br></div>
<div><br></div>
<div>/gate/source/IonSource/gps/type<span class="ecxx_Apple-tab-span">
</span>Plane</div>
<div>/gate/source/IonSource/gps/shape<span class="ecxx_Apple-tab-span">
</span>Circle</div>
<div><br></div>
<div>/gate/source/IonSource/gps/radius<span class="ecxx_Apple-tab-span">
</span>0.5 mm</div>
<div>/gate/source/IonSource/gps/centre&nbsp;<span class="ecxx_Apple-tab-span">
</span>0.0 0.0 0.0 cm</div>
<div><br></div>
<div>/gate/source/IonSource/gps/particle<span class="ecxx_Apple-tab-span">
</span>ion</div>
<div>/gate/source/IonSource/gps/ion&nbsp;<span class="ecxx_Apple-tab-span">
</span>11 22 0 0</div>
<div>/gate/source/IonSource/setForcedUnstableFlag&nbsp;<span class="ecxx_Apple-tab-span">
</span>true</div>
<div>/gate/source/IonSource/setForcedHalfLife&nbsp;<span class="ecxx_Apple-tab-span">
</span>81993600.0 s</div>
<div>/gate/source/IonSource/gps/energytype&nbsp;<span class="ecxx_Apple-tab-span">
</span>Mono</div>
<div>/gate/source/IonSource/gps/monoenergy&nbsp;<span class="ecxx_Apple-tab-span">
</span>0. MeV</div>
<div>/gate/source/IonSource/gps/number&nbsp;<span class="ecxx_Apple-tab-span">
</span>1</div>
<div><br></div>
<div>/gate/source/IonSource/gps/angtype<span class="ecxx_Apple-tab-span">
</span>iso</div>
<div><br></div>
<div><br></div>
<div>/gate/source/list</div>
</div>
<div>
<br><div>

From: <a href="mailto:u.pietrzyk@...">u.pietrzyk@...</a><br>
To: <a href="mailto:andreita_5_92@...">andreita_5_92@...</a><br>
CC: <a href="mailto:gate-users@...">gate-users <at> lists.opengatecollaboration.org</a><br>
Subject: Re: [Gate-users] Best physics list for positron annihilation.<br>
Date: Tue, 17 Nov 2015 10:20:39 +0000<br><br><div>
<div><br></div>
<div>Hi Andrea,</div>
<div><br></div>
<div>in your macro you are specifying a source which emits positrons</div>
<div>with a fixed energy! To simulate the range of positrons from</div>
<div>Na-22 decay you better use an ion-source!&nbsp;</div>
<div>Here is the code we use in the EduGATE example &ldquo;Spectro&rdquo;</div>
<div>(see also:&nbsp;<a href="http://www.opengatecollaboration.org/EduGATE" target="_blank">http://www.opengatecollaboration.org/EduGATE</a>)</div>
<div>&amp; see macro file attached to this eMail.</div>
<div><br></div>
<div>In the case of Na-22 the aliases in { } are replaced by</div>
<div><br></div>
<div>Ion_Z_val -&gt; 11</div>
<div>Ion_A_val -&gt; 22</div>
<div><br></div>
<div>NOTE: this is done automatically in the Spectro example</div>
<div>according to the users&rsquo; choice for the Isotope. We simply read</div>
<div>the file:&nbsp;RadioactiveDecay3.3 used in GEANT4.</div>
<div><br></div>
<div>This finally should give you &nbsp;more realistic data about the positron</div>
<div>range, since it takes into account the energy distribution of the</div>
<div>emitted positron.</div>
<div><br></div>
<div>I hope this helps!</div>
<div><br></div>
<div>Kind regards,</div>
<div><br></div>
<div>Uwe Pietrzyk</div>
<div><br></div>
<div>-----------------------------------------</div>
<div>
<div>#</div>
<div>#<span class="ecxx_Apple-tab-span"> </span>S O U R C E S</div>
<div>#</div>
<div><br></div>
<div># source: ion</div>
<div>/gate/source/addSource <span class="ecxx_Apple-tab-span">
</span>&nbsp; &nbsp; &nbsp; &nbsp;IonSource</div>
<div><br></div>
<div>/gate/source/IonSource/setActivity <span class="ecxx_Apple-tab-span">
</span>&nbsp; &nbsp; &nbsp; &nbsp;{SourceActivity}</div>
<div><br></div>
<div><br></div>
<div>/gate/source/IonSource/gps/type<span class="ecxx_Apple-tab-span">
</span>Volume</div>
<div>/gate/source/IonSource/gps/shape<span class="ecxx_Apple-tab-span">
</span>Sphere</div>
<div>#/gate/source/IonSource/gps/radius<span class="ecxx_Apple-tab-span">
</span>0.1 mm</div>
<div>/gate/source/IonSource/gps/radius<span class="ecxx_Apple-tab-span">
</span>{SourceRad}</div>
<div>/gate/source/IonSource/gps/centre <span class="ecxx_Apple-tab-span">
</span>0.0 0.0 0.0 cm</div>
<div><br></div>
<div>##</div>
<div>## universal ion source</div>
<div>## with arbitrary halflife</div>
<div>##</div>
<div>/gate/source/IonSource/gps/particle<span class="ecxx_Apple-tab-span">
</span>ion</div>
<div>/gate/source/IonSource/gps/ion <span class="ecxx_Apple-tab-span">
</span>{Ion_Z_val} {Ion_A_val} 0 0</div>
<div>/gate/source/IonSource/setForcedUnstableFlag <span class="ecxx_Apple-tab-span">
</span>true</div>
<div>/gate/source/IonSource/setForcedHalfLife <span class="ecxx_Apple-tab-span">
</span>99999999.0 s</div>
<div>/gate/source/IonSource/gps/energytype <span class="ecxx_Apple-tab-span">
</span>Mono</div>
<div>/gate/source/IonSource/gps/monoenergy <span class="ecxx_Apple-tab-span">
</span>0. MeV</div>
<div>/gate/source/IonSource/gps/number <span class="ecxx_Apple-tab-span">
</span>1</div>
<div><br></div>
<div>/gate/source/IonSource/gps/angtype<span class="ecxx_Apple-tab-span">
</span>iso</div>
<div>/gate/source/IonSource/gps/mintheta<span class="ecxx_Apple-tab-span">
</span>0. deg</div>
<div>/gate/source/IonSource/gps/maxtheta <span class="ecxx_Apple-tab-span">
</span>180. deg</div>
<div>/gate/source/IonSource/gps/minphi <span class="ecxx_Apple-tab-span">
</span>0. deg</div>
<div>/gate/source/IonSource/gps/maxphi <span class="ecxx_Apple-tab-span">
</span>360. deg</div>
<div><br></div>
<div>/gate/source/list</div>
<div><br></div>
<div>#/gate/source/IonSource/gps/confine <span class="ecxx_Apple-tab-span">
</span>source_vol</div>
<div><br></div>
</div>
<br><div>
<div>
<div><span>/----------------------------------------------------------------------</span></div>
<div>Prof. Dr. Uwe Pietrzyk<br>
Diplom-Physiker<br>
Institut f&uuml;r Neurowissenschaften und Medizin / INM-4<br>
Forschungszentrum J&uuml;lich GmbH<br>
52425 J&uuml;lich<br>
Tel: +49-2461-61 4763<br>
Fax: +49-2461-61 2820<br>
Mobil: +49-162-103-4871<br>
eMail:&nbsp;<a href="mailto:U.Pietrzyk@...">U.Pietrzyk <at> fz-juelich.de</a><br><a href="http://www.fz-juelich.de/inm/inm-4/DE/Home/home_node.html" target="_blank">http://www.fz-juelich.de/inm/inm-4/DE/Home/home_node.html</a><br>
&amp;<br>
Bergische Universit&auml;t Wuppertal<br>
Fakult&auml;t f&uuml;r Mathematik und Naturwissenschaften</div>
<div>B&uuml;ro: &nbsp;D.08.01<br>
Gau&szlig;str. 20<br>
42097 Wuppertal<br>
Tel: +49-(0)202-439-3523<br>
Fax: +49-(0)202-439-2811<br>
eMail:&nbsp;<a href="mailto:Uwe.Pietrzyk@...">Uwe.Pietrzyk@...</a><br><a href="http://www.medizinphysik.uni-wuppertal.de/" target="_blank">http://www.medizinphysik.uni-wuppertal.de</a><br>
----------------------------------------------------------------------/</div>
</div>
</div>
<div><br class="ecxx_webkit-block-placeholder"></div>
<div><br></div>
<div></div>
</div>
<div>
<div></div>
<div><br></div>
<div><br></div>
<br><div>
<div>On 17 Nov 2015, at 10:47, Andrea Gonz&aacute;lez &lt;<a href="mailto:andreita_5_92@...">andreita_5_92@...</a>&gt; wrote:</div>
<br class="ecxx_Apple-interchange-newline"><blockquote>&lt;!--
.ExternalClass .ecxx_hmmessage {
padding:0px;
}

.ExternalClass body.ecxx_hmmessage {
font-size:12pt;
font-family:Calibri;
}

--&gt;<div class="ecxx_hmmessage">
<div dir="ltr">Sorry, you are right!
<div>I'm using 22-Na as follows:</div>
<div>
<div><br></div>
<div><br></div>
<div><span>/gate/source/addSource na22</span></div>
<div>/gate/source/na22/setActivity 10000 Bq</div>
<div><br></div>
<div>/gate/source/na22/gps/particle e+</div>
<div>/gate/source/na22/setForcedUnstableFlag true</div>
<div>/gate/source/na22/setForcedHalfLife 81993600 s</div>
<div>#/gate/source/na22/gps/energytype Mono</div>
<div>#/gate/source/na22/gps/monoenergy 545 keV&nbsp;</div>
<div>/gate/source/na22/gps/monoenergy 195 keV&nbsp;</div>
<div><br></div>
<div><br></div>
<div>/gate/source/na22/gps/type Plane</div>
<div>/gate/source/na22/gps/shape Circle</div>
<div>/gate/source/na22/gps/radius 0.5 mm</div>
<div><br></div>
<div>/gate/source/na22/gps/angtype iso</div>
<div>/gate/source/na22/gps/centre 0. 0. 0. cm</div>
<div><br></div>
<div>/gate/source/list</div>
</div>
<div><br></div>
<div>Do you thing is correct?</div>
<div><br></div>
<div>My physics list:</div>
<div><br></div>
<div>
<div>#=====================================</div>
<div># &nbsp; &nbsp;Electromagnetic &nbsp;processes</div>
<div>#=====================================</div>
<div><br></div>
<div><br></div>
<div><br></div>
<div>/gate/physics/addProcess RadioactiveDecay</div>
<div><br></div>
<div>/gate/physics/addProcess PhotoElectric</div>
<div>/gate/physics/processes/PhotoElectric/setModel StandardModel</div>
<div><br></div>
<div>/gate/physics/addProcess Compton</div>
<div>/gate/physics/processes/Compton/setModel StandardModel</div>
<div><br></div>
<div>/gate/physics/addProcess GammaConversion</div>
<div>/gate/physics/processes/GammaConversion/setModel StandardModel</div>
<div><br></div>
<div>/gate/physics/addProcess ElectronIonisation</div>
<div>/gate/physics/processes/ElectronIonisation/setModel StandardModel e-</div>
<div>/gate/physics/processes/ElectronIonisation/setModel StandardModel e+</div>
<div>/gate/physics/processes/ElectronIonisation/setStepFunction e+ 0.2 0.1 mm</div>
<div>/gate/physics/processes/ElectronIonisation/setStepFunction e- 0.2 0.1 mm</div>
<div>/gate/physics/processes/ElectronIonisation/setLinearLossLimit electron 0.01</div>
<div><br></div>
<div>/gate/physics/addProcess Bremsstrahlung</div>
<div>/gate/physics/processes/Bremsstrahlung/setModel StandardModel e-</div>
<div>/gate/physics/processes/Bremsstrahlung/setModel StandardModel e+</div>
<div><br></div>
<div>/gate/physics/addProcess PositronAnnihilation</div>
<div><br></div>
<div>/gate/physics/addProcess eMultipleScattering e-</div>
<div>/gate/physics/addProcess eMultipleScattering e+</div>
<div>/gate/physics/addProcess/eMultipleScattering/setModel Urban95Model</div>
<div><br></div>
<div>/gate/physics/processes/eMultipleScattering/setGeometricalStepLimiterType e- distanceToBoundary</div>
<div>/gate/physics/processes/eMultipleScattering/setGeometricalStepLimiterType e+ distanceToBoundary</div>
<div><br></div>
<div>#=========</div>
<div># Options</div>
<div>#=========</div>
<div><br></div>
<div>/gate/physics/setEMin 0.1 keV</div>
<div>/gate/physics/setEMax 10 GeV</div>
<div><br></div>
</div>
<div><br></div>
<div>The problem is about the annihilation range of the positrons in PMMA, because it shows a distrubution much broader than it should be...</div>
<div><br></div>
<div>I really appreciate your help and comments.</div>
<div><br></div>
<div>Best regards, Andrea.</div>
<div><br></div>
<div><br></div>
<div><br></div>
<div><br></div>
<div><br></div>
<div>
<br><div>

From: <a href="mailto:u.pietrzyk@...">u.pietrzyk@...</a><br>
To: <a href="mailto:andreita_5_92@...">andreita_5_92@...</a><br>
CC: <a href="mailto:gate-users@...">gate-users <at> lists.opengatecollaboration.org</a><br>
Subject: Re: [Gate-users] Best physics list for positron annihilation.<br>
Date: Mon, 16 Nov 2015 15:40:00 +0000<br><br><div><br></div>
<div>Dear Andrea,</div>
<div><br></div>
<div>you didn&rsquo;t mention the type of problem, but when</div>
<div>you use 22-Na as an ion source you need to specify</div>
<div>the radioactive decay explicitly. In our test and examples,</div>
<div>we use the following:</div>
<div><br></div>
<div>
<div>/gate/physics/addPhysicsList emstandard</div>
<div>/gate/physics/addProcess RadioactiveDecay</div>
</div>
<div><br></div>
<div>and this seems to work fine.</div>
<div>In case you mean something else, please let us know.</div>
<div><br></div>
<div>Kind regards,</div>
<div><br></div>
<div>Uwe Pietrzyk</div>
<br><div>
<div>
<div><span>/----------------------------------------------------------------------</span></div>
<div>Prof. Dr. Uwe Pietrzyk<br>
Diplom-Physiker<br>
Institut f&uuml;r Neurowissenschaften und Medizin / INM-4<br>
Forschungszentrum J&uuml;lich GmbH<br>
52425 J&uuml;lich<br>
Tel: +49-2461-61 4763<br>
Fax: +49-2461-61 2820<br>
Mobil: +49-162-103-4871<br>
eMail:&nbsp;<a href="mailto:U.Pietrzyk@...">U.Pietrzyk <at> fz-juelich.de</a><br><a href="http://www.fz-juelich.de/inm/inm-4/DE/Home/home_node.html" target="_blank">http://www.fz-juelich.de/inm/inm-4/DE/Home/home_node.html</a><br>
&amp;<br>
Bergische Universit&auml;t Wuppertal<br>
Fakult&auml;t f&uuml;r Mathematik und Naturwissenschaften</div>
<div>B&uuml;ro: &nbsp;D.08.01<br>
Gau&szlig;str. 20<br>
42097 Wuppertal<br>
Tel: +49-(0)202-439-3523<br>
Fax: +49-(0)202-439-2811<br>
eMail:&nbsp;<a href="mailto:Uwe.Pietrzyk@...">Uwe.Pietrzyk@...</a><br><a href="http://www.medizinphysik.uni-wuppertal.de/" target="_blank">http://www.medizinphysik.uni-wuppertal.de</a><br>
----------------------------------------------------------------------/</div>
</div>
</div>
<br><div>
<div>On 16 Nov 2015, at 15:58, Andrea Gonz&aacute;lez &lt;<a href="mailto:andreita_5_92@...">andreita_5_92@...</a>&gt; wrote:</div>
<br class="ecxx_ecxApple-interchange-newline"><blockquote>&lt;!--
.ExternalClass .ecxx_ExternalClass .ecxx_ecxhmmessage {
padding:0px;
}

.ExternalClass .ecxx_ExternalClass body.ecxx_ecxhmmessage {
font-size:12pt;
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--&gt;<div class="ecxx_ecxhmmessage">
<div dir="ltr">Hello, I'm trying to simulate positron annihilitaion for 22-Na in PMMA.
<div>
<br><div>I would like to know wich is the best physics list in this case, because I have problems with my list (standard EM).</div>
<div><br></div>
<div>Thank you very much.</div>
<div><br></div>
<div>Andrea.</div>
<div><br></div>
<div><br></div>
</div>
</div>
</div>
_______________________________________________<br>
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</blockquote>
</div>
<br><br><br>
------------------------------------------------------------------------------------------------<br>
------------------------------------------------------------------------------------------------<br>
Forschungszentrum Juelich GmbH<br>
52425 Juelich<br>
Sitz der Gesellschaft: Juelich<br>
Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498<br>
Vorsitzender des Aufsichtsrats: MinDir Dr. Karl Eugen Huthmacher<br>
Geschaeftsfuehrung: Prof. Dr.-Ing. Wolfgang Marquardt (Vorsitzender),<br>
Karsten Beneke (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt,<br>
Prof. Dr. Sebastian M. Schmidt<br>
------------------------------------------------------------------------------------------------<br>
------------------------------------------------------------------------------------------------<br><br>
</div>
</div>
</div>
</div>
</blockquote>
</div>
<br>
</div>
</div>
</div>
</div>
</div>
<span>&lt;Captura.JPG&gt;</span>
</blockquote>
</div>
<br>
</div>
</div>
Pietrzyk, Uwe | 17 Nov 11:20 2015
Picon
Picon

Re: Best physics list for positron annihilation.


Hi Andrea,

in your macro you are specifying a source which emits positrons
with a fixed energy! To simulate the range of positrons from
Na-22 decay you better use an ion-source! 
Here is the code we use in the EduGATE example “Spectro”
& see macro file attached to this eMail.

In the case of Na-22 the aliases in { } are replaced by

Ion_Z_val -> 11
Ion_A_val -> 22

NOTE: this is done automatically in the Spectro example
according to the users’ choice for the Isotope. We simply read
the file: RadioactiveDecay3.3 used in GEANT4.

This finally should give you  more realistic data about the positron
range, since it takes into account the energy distribution of the
emitted positron.

I hope this helps!

Kind regards,

Uwe Pietrzyk

-----------------------------------------
#
# S O U R C E S
#

# source: ion
/gate/source/addSource        IonSource

/gate/source/IonSource/setActivity        {SourceActivity}


/gate/source/IonSource/gps/type Volume
/gate/source/IonSource/gps/shape Sphere
#/gate/source/IonSource/gps/radius 0.1 mm
/gate/source/IonSource/gps/radius {SourceRad}
/gate/source/IonSource/gps/centre 0.0 0.0 0.0 cm

##
## universal ion source
## with arbitrary halflife
##
/gate/source/IonSource/gps/particle ion
/gate/source/IonSource/gps/ion {Ion_Z_val} {Ion_A_val} 0 0
/gate/source/IonSource/setForcedUnstableFlag true
/gate/source/IonSource/setForcedHalfLife 99999999.0 s
/gate/source/IonSource/gps/energytype Mono
/gate/source/IonSource/gps/monoenergy 0. MeV
/gate/source/IonSource/gps/number 1

/gate/source/IonSource/gps/angtype iso
/gate/source/IonSource/gps/mintheta 0. deg
/gate/source/IonSource/gps/maxtheta 180. deg
/gate/source/IonSource/gps/minphi 0. deg
/gate/source/IonSource/gps/maxphi 360. deg

/gate/source/list

#/gate/source/IonSource/gps/confine source_vol


/----------------------------------------------------------------------
Prof. Dr. Uwe Pietrzyk
Diplom-Physiker
Institut für Neurowissenschaften und Medizin / INM-4
Forschungszentrum Jülich GmbH
52425 Jülich
Tel: +49-2461-61 4763
Fax: +49-2461-61 2820
Mobil: +49-162-103-4871
eMail: U.Pietrzyk <at> fz-juelich.de
http://www.fz-juelich.de/inm/inm-4/DE/Home/home_node.html
&
Bergische Universität Wuppertal
Fakultät für Mathematik und Naturwissenschaften
Büro:  D.08.01
Gaußstr. 20
42097 Wuppertal
Tel: +49-(0)202-439-3523
Fax: +49-(0)202-439-2811
eMail: Uwe.Pietrzyk-QoZ5z9YNi+XRHuS+YikPfA@public.gmane.org
http://www.medizinphysik.uni-wuppertal.de
----------------------------------------------------------------------/





On 17 Nov 2015, at 10:47, Andrea González <andreita_5_92-PkbjNfxxIARBDgjK7y7TUQ@public.gmane.org> wrote:

<!-- .x_hmmessage {margin:0px; padding:0px} body.x_hmmessage {font-size:12pt; font-family:Calibri} -->
Sorry, you are right!
I'm using 22-Na as follows:


/gate/source/addSource na22
/gate/source/na22/setActivity 10000 Bq

/gate/source/na22/gps/particle e+
/gate/source/na22/setForcedUnstableFlag true
/gate/source/na22/setForcedHalfLife 81993600 s
#/gate/source/na22/gps/energytype Mono
#/gate/source/na22/gps/monoenergy 545 keV 
/gate/source/na22/gps/monoenergy 195 keV 


/gate/source/na22/gps/type Plane
/gate/source/na22/gps/shape Circle
/gate/source/na22/gps/radius 0.5 mm

/gate/source/na22/gps/angtype iso
/gate/source/na22/gps/centre 0. 0. 0. cm

/gate/source/list

Do you thing is correct?

My physics list:

#=====================================
#    Electromagnetic  processes
#=====================================



/gate/physics/addProcess RadioactiveDecay

/gate/physics/addProcess PhotoElectric
/gate/physics/processes/PhotoElectric/setModel StandardModel

/gate/physics/addProcess Compton
/gate/physics/processes/Compton/setModel StandardModel

/gate/physics/addProcess GammaConversion
/gate/physics/processes/GammaConversion/setModel StandardModel

/gate/physics/addProcess ElectronIonisation
/gate/physics/processes/ElectronIonisation/setModel StandardModel e-
/gate/physics/processes/ElectronIonisation/setModel StandardModel e+
/gate/physics/processes/ElectronIonisation/setStepFunction e+ 0.2 0.1 mm
/gate/physics/processes/ElectronIonisation/setStepFunction e- 0.2 0.1 mm
/gate/physics/processes/ElectronIonisation/setLinearLossLimit electron 0.01

/gate/physics/addProcess Bremsstrahlung
/gate/physics/processes/Bremsstrahlung/setModel StandardModel e-
/gate/physics/processes/Bremsstrahlung/setModel StandardModel e+

/gate/physics/addProcess PositronAnnihilation

/gate/physics/addProcess eMultipleScattering e-
/gate/physics/addProcess eMultipleScattering e+
/gate/physics/addProcess/eMultipleScattering/setModel Urban95Model

/gate/physics/processes/eMultipleScattering/setGeometricalStepLimiterType e- distanceToBoundary
/gate/physics/processes/eMultipleScattering/setGeometricalStepLimiterType e+ distanceToBoundary

#=========
# Options
#=========

/gate/physics/setEMin 0.1 keV
/gate/physics/setEMax 10 GeV


The problem is about the annihilation range of the positrons in PMMA, because it shows a distrubution much broader than it should be...

I really appreciate your help and comments.

Best regards, Andrea.






From: u.pietrzyk-97/bSmCnXvjoK6nBLMlh1Q@public.gmane.org
To: andreita_5_92-PkbjNfxxIARBDgjK7y7TUQ@public.gmane.org
CC: gate-users <at> lists.opengatecollaboration.org
Subject: Re: [Gate-users] Best physics list for positron annihilation.
Date: Mon, 16 Nov 2015 15:40:00 +0000


Dear Andrea,

you didn’t mention the type of problem, but when
you use 22-Na as an ion source you need to specify
the radioactive decay explicitly. In our test and examples,
we use the following:

/gate/physics/addPhysicsList emstandard
/gate/physics/addProcess RadioactiveDecay

and this seems to work fine.
In case you mean something else, please let us know.

Kind regards,

Uwe Pietrzyk

/----------------------------------------------------------------------
Prof. Dr. Uwe Pietrzyk
Diplom-Physiker
Institut für Neurowissenschaften und Medizin / INM-4
Forschungszentrum Jülich GmbH
52425 Jülich
Tel: +49-2461-61 4763
Fax: +49-2461-61 2820
Mobil: +49-162-103-4871
eMail: U.Pietrzyk <at> fz-juelich.de
http://www.fz-juelich.de/inm/inm-4/DE/Home/home_node.html
&
Bergische Universität Wuppertal
Fakultät für Mathematik und Naturwissenschaften
Büro:  D.08.01
Gaußstr. 20
42097 Wuppertal
Tel: +49-(0)202-439-3523
Fax: +49-(0)202-439-2811
eMail: Uwe.Pietrzyk-QoZ5z9YNi+XRHuS+YikPfA@public.gmane.org
http://www.medizinphysik.uni-wuppertal.de
----------------------------------------------------------------------/

On 16 Nov 2015, at 15:58, Andrea González <andreita_5_92-PkbjNfxxIARBDgjK7y7TUQ@public.gmane.org> wrote:

<!-- .x_ExternalClass .x_ecxhmmessage {padding:0px} .x_ExternalClass body.x_ecxhmmessage {font-size:12pt; font-family:Calibri} -->
Hello, I'm trying to simulate positron annihilitaion for 22-Na in PMMA.

I would like to know wich is the best physics list in this case, because I have problems with my list (standard EM).

Thank you very much.

Andrea.


_______________________________________________
Gate-users mailing list
Gate-users <at> lists.opengatecollaboration.org
http://lists.opengatecollaboration.org/mailman/listinfo/gate-users



------------------------------------------------------------------------------------------------
------------------------------------------------------------------------------------------------
Forschungszentrum Juelich GmbH
52425 Juelich
Sitz der Gesellschaft: Juelich
Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498
Vorsitzender des Aufsichtsrats: MinDir Dr. Karl Eugen Huthmacher
Geschaeftsfuehrung: Prof. Dr.-Ing. Wolfgang Marquardt (Vorsitzender),
Karsten Beneke (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt,
Prof. Dr. Sebastian M. Schmidt
------------------------------------------------------------------------------------------------
------------------------------------------------------------------------------------------------


<div>
<div>
<div><br></div>
<div>Hi Andrea,</div>
<div><br></div>
<div>in your macro you are specifying a source which emits positrons</div>
<div>with a fixed energy! To simulate the range of positrons from</div>
<div>Na-22 decay you better use an ion-source!&nbsp;</div>
<div>Here is the code we use in the EduGATE example &ldquo;Spectro&rdquo;</div>
<div>(see also:&nbsp;<a href="http://www.opengatecollaboration.org/EduGATE">http://www.opengatecollaboration.org/EduGATE</a>)</div>
<div>&amp; see macro file attached to this eMail.</div>
<div><br></div>
<div>In the case of Na-22 the aliases in { } are replaced by</div>
<div><br></div>
<div>Ion_Z_val -&gt; 11</div>
<div>Ion_A_val -&gt; 22</div>
<div><br></div>
<div>NOTE: this is done automatically in the Spectro example</div>
<div>according to the users&rsquo; choice for the Isotope. We simply read</div>
<div>the file:&nbsp;RadioactiveDecay3.3 used in GEANT4.</div>
<div><br></div>
<div>This finally should give you &nbsp;more realistic data about the positron</div>
<div>range, since it takes into account the energy distribution of the</div>
<div>emitted positron.</div>
<div><br></div>
<div>I hope this helps!</div>
<div><br></div>
<div>Kind regards,</div>
<div><br></div>
<div>Uwe Pietrzyk</div>
<div><br></div>
<div>-----------------------------------------</div>
<div>
<div>#</div>
<div>#<span class="x_Apple-tab-span"> </span>S O U R C E S</div>
<div>#</div>
<div><br></div>
<div># source: ion</div>
<div>/gate/source/addSource <span class="x_Apple-tab-span">
</span>&nbsp; &nbsp; &nbsp; &nbsp;IonSource</div>
<div><br></div>
<div>/gate/source/IonSource/setActivity <span class="x_Apple-tab-span">
</span>&nbsp; &nbsp; &nbsp; &nbsp;{SourceActivity}</div>
<div><br></div>
<div><br></div>
<div>/gate/source/IonSource/gps/type<span class="x_Apple-tab-span">
</span>Volume</div>
<div>/gate/source/IonSource/gps/shape<span class="x_Apple-tab-span">
</span>Sphere</div>
<div>#/gate/source/IonSource/gps/radius<span class="x_Apple-tab-span">
</span>0.1 mm</div>
<div>/gate/source/IonSource/gps/radius<span class="x_Apple-tab-span">
</span>{SourceRad}</div>
<div>/gate/source/IonSource/gps/centre <span class="x_Apple-tab-span">
</span>0.0 0.0 0.0 cm</div>
<div><br></div>
<div>##</div>
<div>## universal ion source</div>
<div>## with arbitrary halflife</div>
<div>##</div>
<div>/gate/source/IonSource/gps/particle<span class="x_Apple-tab-span">
</span>ion</div>
<div>/gate/source/IonSource/gps/ion <span class="x_Apple-tab-span">
</span>{Ion_Z_val} {Ion_A_val} 0 0</div>
<div>/gate/source/IonSource/setForcedUnstableFlag <span class="x_Apple-tab-span">
</span>true</div>
<div>/gate/source/IonSource/setForcedHalfLife <span class="x_Apple-tab-span">
</span>99999999.0 s</div>
<div>/gate/source/IonSource/gps/energytype <span class="x_Apple-tab-span">
</span>Mono</div>
<div>/gate/source/IonSource/gps/monoenergy <span class="x_Apple-tab-span">
</span>0. MeV</div>
<div>/gate/source/IonSource/gps/number <span class="x_Apple-tab-span">
</span>1</div>
<div><br></div>
<div>/gate/source/IonSource/gps/angtype<span class="x_Apple-tab-span">
</span>iso</div>
<div>/gate/source/IonSource/gps/mintheta<span class="x_Apple-tab-span">
</span>0. deg</div>
<div>/gate/source/IonSource/gps/maxtheta <span class="x_Apple-tab-span">
</span>180. deg</div>
<div>/gate/source/IonSource/gps/minphi <span class="x_Apple-tab-span">
</span>0. deg</div>
<div>/gate/source/IonSource/gps/maxphi <span class="x_Apple-tab-span">
</span>360. deg</div>
<div><br></div>
<div>/gate/source/list</div>
<div><br></div>
<div>#/gate/source/IonSource/gps/confine <span class="x_Apple-tab-span">
</span>source_vol</div>
<div><br></div>
</div>
<br><div>
<div>
<div><span>/----------------------------------------------------------------------</span></div>
<div>Prof. Dr. Uwe Pietrzyk<br>
Diplom-Physiker<br>
Institut f&uuml;r Neurowissenschaften und Medizin / INM-4<br>
Forschungszentrum J&uuml;lich GmbH<br>
52425 J&uuml;lich<br>
Tel: +49-2461-61 4763<br>
Fax: +49-2461-61 2820<br>
Mobil: +49-162-103-4871<br>
eMail:&nbsp;<a href="mailto:U.Pietrzyk@...">U.Pietrzyk <at> fz-juelich.de</a><br><a href="http://www.fz-juelich.de/inm/inm-4/DE/Home/home_node.html">http://www.fz-juelich.de/inm/inm-4/DE/Home/home_node.html</a><br>
&amp;<br>
Bergische Universit&auml;t Wuppertal<br>
Fakult&auml;t f&uuml;r Mathematik und Naturwissenschaften</div>
<div>B&uuml;ro: &nbsp;D.08.01<br>
Gau&szlig;str. 20<br>
42097 Wuppertal<br>
Tel: +49-(0)202-439-3523<br>
Fax: +49-(0)202-439-2811<br>
eMail:&nbsp;<a href="mailto:Uwe.Pietrzyk@...">Uwe.Pietrzyk@...</a><br><a href="http://www.medizinphysik.uni-wuppertal.de/">http://www.medizinphysik.uni-wuppertal.de</a><br>
----------------------------------------------------------------------/</div>
</div>
</div>
<div><br class="x_webkit-block-placeholder"></div>
<div><br></div>
<div></div>
</div>
<div>
<div></div>
<div><br></div>
<div><br></div>
<br><div>
<div>On 17 Nov 2015, at 10:47, Andrea Gonz&aacute;lez &lt;<a href="mailto:andreita_5_92@...">andreita_5_92@...</a>&gt; wrote:</div>
<br class="x_Apple-interchange-newline"><blockquote type="cite">
&lt;!--
.x_hmmessage 
	{margin:0px;
	padding:0px}
body.x_hmmessage
	{font-size:12pt;
	font-family:Calibri}
--&gt;
<div class="x_hmmessage">
<div dir="ltr">Sorry, you are right!
<div>I'm using 22-Na as follows:</div>
<div>
<div><br></div>
<div><br></div>
<div><span>/gate/source/addSource na22</span></div>
<div>/gate/source/na22/setActivity 10000 Bq</div>
<div><br></div>
<div>/gate/source/na22/gps/particle e+</div>
<div>/gate/source/na22/setForcedUnstableFlag true</div>
<div>/gate/source/na22/setForcedHalfLife 81993600 s</div>
<div>#/gate/source/na22/gps/energytype Mono</div>
<div>#/gate/source/na22/gps/monoenergy 545 keV&nbsp;</div>
<div>/gate/source/na22/gps/monoenergy 195 keV&nbsp;</div>
<div><br></div>
<div><br></div>
<div>/gate/source/na22/gps/type Plane</div>
<div>/gate/source/na22/gps/shape Circle</div>
<div>/gate/source/na22/gps/radius 0.5 mm</div>
<div><br></div>
<div>/gate/source/na22/gps/angtype iso</div>
<div>/gate/source/na22/gps/centre 0. 0. 0. cm</div>
<div><br></div>
<div>/gate/source/list</div>
</div>
<div><br></div>
<div>Do you thing is correct?</div>
<div><br></div>
<div>My physics list:</div>
<div><br></div>
<div>
<div>#=====================================</div>
<div># &nbsp; &nbsp;Electromagnetic &nbsp;processes</div>
<div>#=====================================</div>
<div><br></div>
<div><br></div>
<div><br></div>
<div>/gate/physics/addProcess RadioactiveDecay</div>
<div><br></div>
<div>/gate/physics/addProcess PhotoElectric</div>
<div>/gate/physics/processes/PhotoElectric/setModel StandardModel</div>
<div><br></div>
<div>/gate/physics/addProcess Compton</div>
<div>/gate/physics/processes/Compton/setModel StandardModel</div>
<div><br></div>
<div>/gate/physics/addProcess GammaConversion</div>
<div>/gate/physics/processes/GammaConversion/setModel StandardModel</div>
<div><br></div>
<div>/gate/physics/addProcess ElectronIonisation</div>
<div>/gate/physics/processes/ElectronIonisation/setModel StandardModel e-</div>
<div>/gate/physics/processes/ElectronIonisation/setModel StandardModel e+</div>
<div>/gate/physics/processes/ElectronIonisation/setStepFunction e+ 0.2 0.1 mm</div>
<div>/gate/physics/processes/ElectronIonisation/setStepFunction e- 0.2 0.1 mm</div>
<div>/gate/physics/processes/ElectronIonisation/setLinearLossLimit electron 0.01</div>
<div><br></div>
<div>/gate/physics/addProcess Bremsstrahlung</div>
<div>/gate/physics/processes/Bremsstrahlung/setModel StandardModel e-</div>
<div>/gate/physics/processes/Bremsstrahlung/setModel StandardModel e+</div>
<div><br></div>
<div>/gate/physics/addProcess PositronAnnihilation</div>
<div><br></div>
<div>/gate/physics/addProcess eMultipleScattering e-</div>
<div>/gate/physics/addProcess eMultipleScattering e+</div>
<div>/gate/physics/addProcess/eMultipleScattering/setModel Urban95Model</div>
<div><br></div>
<div>/gate/physics/processes/eMultipleScattering/setGeometricalStepLimiterType e- distanceToBoundary</div>
<div>/gate/physics/processes/eMultipleScattering/setGeometricalStepLimiterType e+ distanceToBoundary</div>
<div><br></div>
<div>#=========</div>
<div># Options</div>
<div>#=========</div>
<div><br></div>
<div>/gate/physics/setEMin 0.1 keV</div>
<div>/gate/physics/setEMax 10 GeV</div>
<div><br></div>
</div>
<div><br></div>
<div>The problem is about the annihilation range of the positrons in PMMA, because it shows a distrubution much broader than it should be...</div>
<div><br></div>
<div>I really appreciate your help and comments.</div>
<div><br></div>
<div>Best regards, Andrea.</div>
<div><br></div>
<div><br></div>
<div><br></div>
<div><br></div>
<div><br></div>
<div>
<br><div>

From: <a href="mailto:u.pietrzyk@...">u.pietrzyk@...</a><br>
To: <a href="mailto:andreita_5_92@...">andreita_5_92@...</a><br>
CC: <a href="mailto:gate-users@...">gate-users <at> lists.opengatecollaboration.org</a><br>
Subject: Re: [Gate-users] Best physics list for positron annihilation.<br>
Date: Mon, 16 Nov 2015 15:40:00 +0000<br><br><div><br></div>
<div>Dear Andrea,</div>
<div><br></div>
<div>you didn&rsquo;t mention the type of problem, but when</div>
<div>you use 22-Na as an ion source you need to specify</div>
<div>the radioactive decay explicitly. In our test and examples,</div>
<div>we use the following:</div>
<div><br></div>
<div>
<div>/gate/physics/addPhysicsList emstandard</div>
<div>/gate/physics/addProcess RadioactiveDecay</div>
</div>
<div><br></div>
<div>and this seems to work fine.</div>
<div>In case you mean something else, please let us know.</div>
<div><br></div>
<div>Kind regards,</div>
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<div>Uwe Pietrzyk</div>
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<div>Prof. Dr. Uwe Pietrzyk<br>
Diplom-Physiker<br>
Institut f&uuml;r Neurowissenschaften und Medizin / INM-4<br>
Forschungszentrum J&uuml;lich GmbH<br>
52425 J&uuml;lich<br>
Tel: +49-2461-61 4763<br>
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eMail:&nbsp;<a href="mailto:U.Pietrzyk@...">U.Pietrzyk <at> fz-juelich.de</a><br><a href="http://www.fz-juelich.de/inm/inm-4/DE/Home/home_node.html" target="_blank">http://www.fz-juelich.de/inm/inm-4/DE/Home/home_node.html</a><br>
&amp;<br>
Bergische Universit&auml;t Wuppertal<br>
Fakult&auml;t f&uuml;r Mathematik und Naturwissenschaften</div>
<div>B&uuml;ro: &nbsp;D.08.01<br>
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<div>On 16 Nov 2015, at 15:58, Andrea Gonz&aacute;lez &lt;<a href="mailto:andreita_5_92@...">andreita_5_92@...</a>&gt; wrote:</div>
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<div dir="ltr">Hello, I'm trying to simulate positron annihilitaion for 22-Na in PMMA.
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<br><div>I would like to know wich is the best physics list in this case, because I have problems with my list (standard EM).</div>
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<div>Thank you very much.</div>
<div><br></div>
<div>Andrea.</div>
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Gmane