Patay Gergely | 4 Aug 15:12 2014
Picon

Re: pthread error on Gate v7.0

Hi,

just edit the CMakeLists.txt file to use the libpthread library:
instead of
TARGET_LINK_LIBRARIES(Gate ${Geant4_LIBRARIES} ${ROOT_LIBRARIES}
${CLHEP_LIBRARIES} ${LIBXML2_LIBRARIES} ${LMF_LIBRARY} ${ECAT7_LIBRARY}
ITKMetaIO itkzlib)
write
TARGET_LINK_LIBRARIES(Gate ${Geant4_LIBRARIES} ${ROOT_LIBRARIES}
${CLHEP_LIBRARIES} ${LIBXML2_LIBRARIES} ${LMF_LIBRARY} ${ECAT7_LIBRARY}
ITKMetaIO itkzlib pthread)

that is, adding 'pthread' to the end of line.

cheers,
  Gergely

--
  Gergely Patay
  Mediso Ltd.

On 2014-08-04 14:57, Tautvydas Strioga wrote:
> Hello All,
>
> Does anyone had similar problem while making Gate V7.0 on Linux (14.04):
>
> "/usr/bin/ld:
> CMakeFiles/Gate.dir/source/digits_hits/src/GateToGPUImageSPECT.cc.o: undefined
> reference to symbol 'pthread_create <at>  <at> GLIBC_2.1'
> //lib/i386-linux-gnu/libpthread.so.0: error adding symbols: DSO missing from
(Continue reading)

Tautvydas Strioga | 4 Aug 14:57 2014
Picon

pthread error on Gate v7.0

Hello All,

Does anyone had similar problem while making Gate V7.0 on Linux (14.04):

"/usr/bin/ld: CMakeFiles/Gate.dir/source/digits_hits/src/GateToGPUImageSPECT.cc.o: undefined reference to symbol 'pthread_create <at> <at> GLIBC_2.1'
//lib/i386-linux-gnu/libpthread.so.0: error adding symbols: DSO missing from command line
collect2: error: ld returned 1 exit status" ??

Could anyone help with this error?
Thanks in advance.


Sincerely,

Tautvydas Strioga


<div><div dir="ltr">
<div>
<div>
<div>
<div>
<div>Hello All, <br><br>
</div>Does anyone had similar problem while making Gate V7.0 on Linux (14.04):<br><br>"/usr/bin/ld: CMakeFiles/Gate.dir/source/digits_hits/src/GateToGPUImageSPECT.cc.o: undefined reference to symbol 'pthread_create <at>  <at> GLIBC_2.1'<br>
//lib/i386-linux-gnu/libpthread.so.0: error adding symbols: DSO missing from command line<br>collect2: error: ld returned 1 exit status" ??<br><br>
</div>Could anyone help with this error?<br>
</div>Thanks in advance.<br><br><br>
</div>Sincerely, <br><br>
</div>Tautvydas Strioga<br><div><div> <div><div><div><div><div>
<br><br>
</div></div></div></div></div>
</div></div>
</div></div>
victor meldrew | 2 Aug 16:12 2014
Picon

Re: Using Generic Repeaters

Hello All,

   I am trying to model a cylindrical pet using generic repeaters. I would like to arrange the modules along a ring and then twist it along the radius. So this involves first a rotation along the scanner z-axis and then along the x-axis. My problem is that is seems like the co-ordinate system is fixed to the scanner. 

For example, for the first module placed along the 3 o'clock, the scanner axes and the axis for the modules coincide. But for a module at, say,  1 o'clock the x-axis is still aligned along the scanner axes while I want it to be the radius line. 

  Does anyone have experience with this? Thanks in advance.

  Thanks in advance for any advice,


Victor M.
<div><div dir="ltr">
<span>Hello All,</span><div><br></div>
<div>&nbsp; &nbsp;I am trying to model a cylindrical pet using generic repeaters. I would like to arrange the modules along a ring and then twist it along the radius. So this involves first a rotation along the scanner z-axis and then along the x-axis. My problem is that is seems like the co-ordinate system is fixed to the scanner.&nbsp;</div>
<div><br></div>
<div>For example, for the first module placed along the 3 o'clock, the scanner axes and the axis for the modules coincide. But for a module at, say, &nbsp;1 o'clock the x-axis is still aligned along the scanner axes while I want it to be the radius line.&nbsp;</div>
<div><br></div>
<div>&nbsp; Does anyone have experience with this? Thanks in advance.</div>
<div>
<br>
</div>
<div>&nbsp; Thanks in advance for any advice,</div>
<div><br></div>
<div>
<br>
</div>
<div>Victor M.</div>
</div></div>
leda.lorenzon | 2 Aug 08:55 2014
Picon

Problems with ARFs

Dear Gate-users, 
I’m trying to simulate my SPECT system using Angular Response Functions (ARFs).  I followed the 3 steps described in the “User Guide v7.0”. First I  generated the ARF tables computing  a rectangular source  of Tc99m (140 keV) located at the center of FOV but I don’t understand how much is important the size of the source and the distance from the SPECThead.  In the third step (use of the ARF tables), following the example provided in the folder /examples/example_ARF/ useARFTables.mac, I created only the main headvolume SPECThead, made of air, without any daughters (for example, crystal, shielding,…). The problem is that proceeding in this way I can’t obtain a meaningful image. Could you please tell me what am I doing wrong?

 I also noticed that in the macro example, useARFTables.mac, there is no specification of the energy window. Is this correct?
 
Could you also please tell me the meaning of the following commands?

 /gate/source/ARFSource/gps/ene/type Range 
/gate/source/ARFSource/setMinEnergy 364.5 keV
 /gate/source/ARFSource/setEnergyRange 0. keV 

Thanks all in advance. 

Best regards. 

Leda Lorenzon
<div>Dear Gate-users,&nbsp;<div>I&rsquo;m trying to simulate my SPECT system using Angular Response Functions (ARFs).&nbsp; I followed the 3 steps described in the &ldquo;User Guide v7.0&rdquo;. First I&nbsp; generated the ARF tables computing&nbsp; a rectangular source&nbsp; of Tc99m (140 keV) located at the center of FOV but I don&rsquo;t understand how much is important the size of the source and the distance from the SPECThead.&nbsp; In the third step (use of the ARF tables), following the example provided in the folder /examples/example_ARF/ useARFTables.mac, I created only the main headvolume SPECThead, made of air, without any daughters (for example, crystal, shielding,&hellip;). The problem is that proceeding in this way I can&rsquo;t obtain a meaningful image. Could you please tell me what am I doing wrong?</div>
<div><br></div>
<div>&nbsp;I also noticed that in the macro example, useARFTables.mac, there is no specification of the energy window. Is this correct?</div>
<div>&nbsp;</div>
<div>Could you also please tell me the meaning of the following commands?</div>
<div><br></div>
<div>&nbsp;/gate/source/ARFSource/gps/ene/type Range&nbsp;</div>
<div>/gate/source/ARFSource/setMinEnergy 364.5 keV</div>
<div>&nbsp;/gate/source/ARFSource/setEnergyRange 0. keV&nbsp;</div>
<div><br></div>
<div>Thanks all in advance.&nbsp;</div>
<div><br></div>
<div>Best regards.&nbsp;</div>
<div><br></div>
<div>Leda Lorenzon</div>
</div>
Benoit Soubelet | 31 Jul 09:19 2014
Picon
Picon

Fwd: Modifying a reference Physics List

Hello,

I'm currently working on a project focused on the nuclear interactions of a proton beam.

We are using the reference Physics List QGSP_BIC_HP_EMY, but I would like to turn off some of the processes in order to evaluate the influence of each of them on the energy deposition.

I tried the usual command (/gate/physics/removeProcess [process] [particle]), but the log file and the results are not modified after execution.
The physics list seems to override my choices; even if I'm calling first the list, and then only I'm removing some of the processes.

So, is it possible to amend a reference physics list?

Best regards,
 
Benoît Soubelet,
Tel : +41 (0)7 91 38 05 25

"I have a dream today" - Martin Luther King

"You may say I'm a dreamer, but I'm not the only one, I hope someday you will join us, and the world will live as one" - John Lennon


<div><div dir="ltr">Hello,<br><div class="gmail_quote"><div dir="ltr">
<div>
<div>
<div>
<div>
<div><br></div>I'm currently working on a project focused on the nuclear interactions of a proton beam.<br><br>
</div>We are using the reference Physics List QGSP_BIC_HP_EMY, but I would like to turn off some of the processes in order to evaluate the influence of each of them on the energy deposition.<br><br>
</div>I tried the usual command (/gate/physics/removeProcess [process] [particle]), but the log file and the results are not modified after execution.<br>The physics list seems to override my choices; even if I'm calling first the list, and then only I'm removing some of the processes.<br><br>
</div>So, is it possible to amend a reference physics list?<br><br>
</div>Best regards,<br clear="all"><div><div dir="ltr">
<div>&nbsp;</div>Beno&icirc;t Soubelet,<div>

&Eacute;l&egrave;ve-ing&eacute;nieur - Double-dipl&ocirc;me ETHZ/EPFL - Ecole Centrale<br>Mail :&nbsp;<a href="mailto:benoit.soubelet@..." target="_blank">benoit.soubelet@...</a>&nbsp;ou&nbsp;<span><a href="mailto:benoit.soubelet@..." target="_blank">benoit.soubelet@...</a></span> ou <a href="mailto:sbenoit@..." target="_blank">sbenoit@...</a> <br>
</div>
<div>Tel : +41 (0)7 91 38 05 25 <br><br>"I have a dream today" - Martin Luther King</div>

<p>"You
 may say I'm a dreamer, but I'm not the only one, I hope someday you 
will join us, and the world will live as one" - John Lennon</p>
</div></div>
<p></p>
</div></div>

<br>
</div></div>
Amy Meldrum | 29 Jul 21:44 2014

ProductionAndStopping Actor - No output?

Hello all,

I am trying to use actors for the first time in efforts of trying to see where my optical photons are going in my simulations. I am trying to use the ProductionAndStopping actor, but when I run my macro, I do not get any sort of new output for the actors. I specified the filename I'd like the actor data to be saved under (a .txt file), but nothing gets created. Is there an essential step I am missing? I do not know what else to do.


Thank you,

-Amy
<div><div dir="ltr">Hello all,<div><br></div>
<div>I am trying to use actors for the first time in efforts of trying to see where my optical photons are going in my simulations. I am trying to use the ProductionAndStopping actor, but when I run my macro, I do not get any sort of new output for the actors. I specified the filename I'd like the actor data to be saved under (a .txt file), but nothing gets created. Is there an essential step I am missing? I do not know what else to do.</div>
<div><br></div>
<div><br></div>
<div>Thank you,</div>
<div><br></div>
<div>-Amy</div>
</div></div>
Esteban Venialgo | 29 Jul 10:23 2014
Picon
Picon

Rayleigh exception when simulating optical photons

Dear Gate Users,

I get this error when I enable the "OpticalRayleigh" process:
/gate/physics/addProcess OpticalRayleigh


-------- EEEE ------- G4Exception-START -------- EEEE -------
  • G4Exception : ProcMan201
    issued by : G4VProcess::SubtractNumberOfInteractionLengthLeft()
    Negative currentInteractionLength for OpticalRayleigh
  • Event Must Be Aborted **
  • -------- EEEE -------- G4Exception-END --------- EEEE -------



I tried to run the same simulation on Gate6.2 and Gate7.0


Gate6.2: geant4-09-05-patch-01

               root 5.26

               clhep 2.1.1.0

               CentOS release 5.10


Gate7.0:  geant4-09-06-patch-03

                root 5.26

                clhep 2.1.3.1

                CentOS release 5.10



Have someone had the same problem ??


             Esteban,




<div>
    Dear Gate Users,<br><br>
    I get this error when I enable the "OpticalRayleigh" process:<br>
    /gate/physics/addProcess OpticalRayleigh<br><br><br>
    -------- EEEE ------- G4Exception-START -------- EEEE -------
    <ul>
<li>G4Exception : ProcMan201<br>
        issued by : G4VProcess::SubtractNumberOfInteractionLengthLeft()<br>
        Negative currentInteractionLength for OpticalRayleigh</li>
      <li>Event Must Be Aborted **≤/li>
      <li>-------- EEEE -------- G4Exception-END --------- EEEE -------</li>
    </ul>
<p><br></p>
    <p><br></p>
    <p>I tried to run the same simulation on Gate6.2 and Gate7.0</p>
    <p><br></p>
    <p>Gate6.2: geant4-09-05-patch-01</p>
    <p>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; root 5.26</p>
    <p>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; clhep 2.1.1.0</p>
    <p>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; CentOS release 5.10<br></p>
    <p><br></p>
    <p>Gate7.0:&nbsp; geant4-09-06-patch-03</p>
    <p>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; root 5.26</p>
    <p>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; clhep 2.1.3.1</p>
    <p>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; CentOS release 5.10<br></p>
    <p><br></p>
    <p><br></p>
    <p>Have someone had the same problem ??</p>
    <p><br></p>
    <p>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Esteban,<br></p>
    <p><br></p>
    <p><br></p>
    <p><br></p>
  </div>
Amy Meldrum | 23 Jul 17:05 2014

Simulating Beta Particles - Problems

Hello all,

I am trying to simulate a beta source with plastic scintillators and counting the photons that make it to a PMT. However, there are some aspects of my initial results that do not make sense to me, and do not seem correct.

The beta sources I have tried to simulate include C-14, Cl-36, and Sr-90/Y-90. For all of these isotopes, my 'pulse height spectrum' I get at my PMT is very highly skewed to the left - many, many instances of detecting only a handful of optical photons that were produced, and very few 'counts' of higher energy pulses. Related to this issue is that the max number of photons I seem to collect at my PMT per parent particle is extremely low compared to what is likely generated by the beta particle. For example, the maximum photons I collect from Cl-36 is about 2% of the maximum number of photons that are generated from the scintillator. I feel like There should be at least SOME instances where more than 2% of the originally generated photons from a parent particle are collected at the PMT.

And lastly, my simulated data for C-14 compares fairly well against my experimental data despite some of these issues. Yet my simulated data for Cl-36 and Sr-90/Y-90 are vastly different from my experimental data. I suspect it might have something to do with how my beta source is being defined. Has anyone simulated Cl-36 or Sr-90/Y-90? 

I have tried so many things to try and correct my simulations to be more like my experimental data, but I am running out of ideas. Any help or advice for these problems I'm having would be greatly appreciated. I am trying to use these simulations for my graduate research.

-Amy M
<div><div dir="ltr">Hello all,<div><br></div>
<div>I am trying to simulate a beta source with plastic scintillators and counting the photons that make it to a PMT. However, there are some aspects of my initial results that do not make sense to me, and do not seem correct.</div>
<div><br></div>
<div>The beta sources I have tried to simulate include C-14, Cl-36, and Sr-90/Y-90. For all of these isotopes, my 'pulse height spectrum' I get at my PMT is very highly skewed to the left - many, many instances of detecting only a handful of optical photons that were produced, and very few 'counts' of higher energy pulses. Related to this issue is that the max number of photons I seem to collect at my PMT per parent particle is extremely low compared to what is likely generated by the beta particle. For example, the maximum photons I collect from Cl-36 is about 2% of the maximum number of photons that are generated from the scintillator. I feel like There should be at least SOME instances where more than 2% of the originally generated photons from a parent particle are collected at the PMT.</div>
<div><br></div>
<div>And lastly, my simulated data for C-14 compares fairly well against my experimental data despite some of these issues. Yet my simulated data for Cl-36 and Sr-90/Y-90 are vastly different from my experimental data. I suspect it might have something to do with how my beta source is being defined. Has anyone simulated Cl-36 or Sr-90/Y-90?&nbsp;<br><br>I have tried so many things to try and correct my simulations to be more like my experimental data, but I am running out of ideas. Any help or advice for these problems I'm having would be greatly appreciated. I am trying to use these simulations for my graduate research.</div>
<div><br></div>
<div>-Amy M</div>
</div></div>
E. Khakifirooz | 23 Jul 16:08 2014
Picon

Editor for JAPE

Hello,

Is there any special editor for Jape files? Actually writing codes for them, in my case huge codes, can be really error-prone without any special editor.

thanks
--
Best Regards,
 
Ehsan Khakifirooz
<div><div dir="ltr">Hello,<div><br></div>
<div>Is there any special editor for Jape files? Actually writing codes for them, in my case huge codes, can be really error-prone without any special editor.<br clear="all"><div><br></div>
<div>thanks</div>-- <br><div>Best Regards,</div>
<div>&nbsp;</div>
<div>Ehsan Khakifirooz</div>
</div>
</div></div>
Mikhail Polkovnikov | 23 Jul 13:42 2014
Picon

Re: mixing physics lists builders (Psoroulas Serena)

Dear Serena,

For mixed approach you can register physics list like QGSP_BIC_HP and 
then add or remove particular process using
/gate/physics/addProcess, /gate/physics/removeProcess.

http://wiki.opengatecollaboration.org/index.php/Users_Guide_V6.2:Setting_up_the_physics

Best regards,
Mikhail

Psoroulas Serena | 23 Jul 09:49 2014
Picon

mixing physics lists builders

Dear all,

 

for a proton therapy simulation we are investigating the impact of several lists and parameters on our pencil beams. We would in particular like to use a physics list with high precision on low-energy neutrons (like QGSP_BIC_HP), but at the same time we have observed that this list uses the EMoption = 0 (i.e. the settings of the emstandard EM physics list). We would instead like to use a more “mixed approach”, either using the settings of emstandandard_opt3 physics list, or those of empenelope. Is there a way to do it using the physics list builders? Or would any command /gate/physics/addPhysicsList overwrite the settings of a previous command of the similar kind?

 

Thank you

Yours faithfully

Serena

 

__________________________________________
PSI - Paul Scherrer Institut

Mrs. Dr. Serena Psoroulas

Scientific officer – Beam technologies development

Centre for Proton Therapy

WMSA/C13
5232 Villigen PSI

Switzerland

Phone +41 56 310 56 79

serena.psoroulas-QlBsmsa8rgI@public.gmane.org

p-therapie.web.psi.ch

 

<div><div class="WordSection1">
<p class="MsoNormal">Dear all,<p></p></p>
<p class="MsoNormal"><p>&nbsp;</p></p>
<p class="MsoNormal"><span lang="EN-US">for a proton therapy simulation we are investigating the impact of several lists and parameters on our pencil beams. We would in particular like to use a physics list with high precision on low-energy neutrons (like QGSP_BIC_HP), but at the same time we have observed that this list uses the EMoption = 0 (i.e. the settings of the emstandard EM physics list). We would instead like to use a more &ldquo;mixed approach&rdquo;, either using the settings of emstandandard_opt3 physics list, or those of empenelope. Is there a way to do it using the physics list builders? Or would any command /gate/physics/addPhysicsList overwrite the settings of a previous command of the similar kind?<p></p></span></p>
<p class="MsoNormal"><span lang="EN-US"><p>&nbsp;</p></span></p>
<p class="MsoNormal"><span lang="EN-US">Thank you<p></p></span></p>
<p class="MsoNormal"><span lang="EN-US">Yours faithfully<p></p></span></p>
<p class="MsoNormal"><span lang="EN-US">Serena<p></p></span></p>
<p class="MsoNormal"><span lang="EN-US"><p>&nbsp;</p></span></p>
<p class="MsoNormal"><span lang="EN-US">__________________________________________<br>PSI - Paul Scherrer Institut <p></p></span></p>
<p class="MsoNormal"><span lang="EN-US">Mrs. Dr. Serena Psoroulas<p></p></span></p>
<p class="MsoNormal"><span lang="EN-US">Scientific officer &ndash; Beam technologies development<br><br><p></p></span></p>
<p class="MsoNormal"><span lang="EN-US">Centre for Proton Therapy<p></p></span></p>
<p class="MsoNormal"><span lang="EN-US">WMSA/C13<br>5232 Villigen PSI<p></p></span></p>
<p class="MsoNormal"><span>Switzerland<br><br>Phone +41 56 310 56 79 <p></p></span></p>
<p class="MsoNormal"><span>serena.psoroulas@...</span><span><p></p></span></p>
<p class="MsoNormal"><span><a href="http://p-therapie.web.psi.ch/">p-therapie.web.psi.ch</a><p></p></span></p>
<p class="MsoNormal"><p>&nbsp;</p></p>
</div></div>

Gmane