Hojjat Mahani | 21 Jan 09:13 2016
Picon

Energy-Resolution in SPECT (or PET) Imaging

Dear Gaters,

Does anybody has any experience of tracking optical photons (generated in crystal and detected by avalanche photodiodes) in SPECT (or PET) imaging in order to calculate energy resolution of the scanner? If so, I would greatly appreciate it, if you kindly share your experiences.

Thank you in advance,
Hojjat
 


<div><div>
<div dir="ltr">
<span class="">Dear Gaters,</span><br class=""><br class=""><span class="">Does anybody has any experience of tracking optical photons (generated&nbsp;</span><span class="">in crystal and detected by avalanche photodiodes) in SPECT (or PET) imaging in order to&nbsp;</span><span class="">calculate energy resolution of the scanner? If so, I would greatly&nbsp;</span><span class="">appreciate it, if you kindly share your experiences.</span><br class=""><br class=""><span class="">Thank you in advance,</span><br class=""><span class="">Hojjat</span><span></span>
</div>
<div></div>
<div>&nbsp;</div>
<div class="signature">
<div><br></div>
<div><div><br></div></div>
</div>
</div></div>
Lorena Vázquez Canelas | 20 Jan 17:41 2016
Picon

Axial sensitivity PET

Hi all,
I'm doing a simulation of PET and reconstructing image with STIR. I use AMIDE to analyze image.
My question is if someone had used AMIDE to calculate the axial sensitivity and plot it by planes. It should have triangular shape.
I added several ROIs but i don't know how plot it.
Someone has done?
​Thanks in advance​
<div><div dir="ltr">
<div class="gmail_default">Hi all,<br>
</div>
<div class="gmail_default">I'm doing a simulation of PET and reconstructing image with STIR. I use AMIDE to analyze image.<br>
</div>
<div class="gmail_default">My
 question is if someone had used AMIDE to calculate the axial 
sensitivity and plot it by planes. It should have triangular shape.<br><div class="gmail_default">I added several ROIs but i don't know how plot it.<br>
</div>
<div class="gmail_default">Someone has done?<br>
</div>
<div class="gmail_default">&#8203;Thanks in advance&#8203;</div>
</div> 		 	   		  </div></div>
Pawe Kowalski | 20 Jan 10:41 2016
Picon

"Strange" true coincidences in the strip J-PET detector

Dear Gaters, 

I am simulating J-PET detector based on plastic scintillators. This scanner is based on axially arranged scintillating detectors (http://inspirehep.net/record/1346549/files/detector3Daxis.png).
In contrast to traditional PET scanners, proper hit is not caused by the photoelectric effect but by the Compton phenomenon. For example true coincidence is an event in which there are two primary Compton scatterings in two different strips with energy deposition bigger than fixed energy threshold equal 200 keV. There is additional condition that in an event there must be eqactly two Compton scatterings with energy deposition bigger than 10 keV (noise threshold).

True coincidences are selected using following conditions on Gate variables:

  if (h1.eventID==h2.eventID) {
    if (h1.nPhantomCompton==0 and h2.nPhantomCompton==0) {
      if (h1.nCrystalCompton==1 and h2.nCrystalCompton==1) {
        -> TRUE COINCIDENCE
      }
    }
  }
  ...

Algorithm of simple geometric recontruction:
p1 = (h1.posX, h1.posY, h1.posZ)
p2 = (h2.posX, h2.posY, h2.posZ)
t1,t2 - times of two primary Compton scatterings from single annihilation

l=|p1-p1|
dl=(t1-t2) * c
a=dl(2 l)+1/2
p = p1 (1-a) +p2 a // - position of "reconstructed" point

Unfortunatelly, after simple geometric recontruction of only true coincidences, I get some "strange" results. In the attachment there is result of simulation of sphere source with a diameter 1 mm with activity 370 keV placed in (1cm,0,0). The detector is placed in the vacuum. Source of back-to-back gamma quanta with energy 511 keV was used in the simulation.

One can see, that there are some points that lie outside the region with diameter 1 mm and even outside the region with radius equal to 5 cm.
What may be the reason of formation of these coincidences? Number of these strange coincidences is much less than number of proper true coincidences but I would like to find a solution to improve my results. Thank you in advance for your time and your help.

Best regards,
Paweł Kowalski,
National Centre for Nuclear Research
<div><div>
<div>Dear Gaters,&nbsp;</div>
<div><br></div>
<div class="">I am simulating J-PET detector based on plastic scintillators. This scanner is based on axially arranged scintillating detectors (http://inspirehep.net/record/1346549/files/detector3Daxis.png).</div>
<div class="">In contrast to traditional PET scanners, proper hit is not caused by the photoelectric effect but by the Compton phenomenon. For example true coincidence is an event in which there are two primary Compton scatterings in two different strips with energy deposition bigger than fixed energy threshold equal 200 keV. There is additional condition that in an event there must be eqactly two Compton scatterings with energy deposition bigger than 10 keV (noise threshold).</div>
<div class=""><br class=""></div>
<div class="">True coincidences are selected using following conditions on Gate variables:</div>
<div class=""><br class=""></div>
<div class="">&nbsp; if (h1.eventID==h2.eventID) {</div>
<div class="">&nbsp; &nbsp; if (h1.nPhantomCompton==0 and h2.nPhantomCompton==0) {</div>
<div class="">&nbsp; &nbsp; &nbsp; if (h1.nCrystalCompton==1 and h2.nCrystalCompton==1) {</div>
<div class="">&nbsp; &nbsp; &nbsp; &nbsp; -&gt; TRUE COINCIDENCE</div>
<div class="">&nbsp; &nbsp; &nbsp; }</div>
<div class="">&nbsp; &nbsp; }</div>
<div class="">&nbsp; }</div>
<div class="">&nbsp; ...</div>
<div class=""><br class=""></div>
<div class="">Algorithm of simple geometric recontruction:</div>
<div class="">p1 = (h1.posX, h1.posY, h1.posZ)</div>
<div class="">p2 = (h2.posX, h2.posY, h2.posZ)</div>
<div class="">t1,t2 - times of two primary Compton scatterings from single annihilation</div>
<div class=""><br class=""></div>
<div class="">l=|p1-p1|</div>
<div class="">dl=(t1-t2) * c</div>
<div class="">a=dl(2 l)+1/2</div>
<div class="">p = p1 (1-a) +p2 a // - position of "reconstructed" point</div>
<div class=""><br class=""></div>
<div class="">Unfortunatelly, after simple geometric recontruction of only true coincidences, I get some "strange" results. In the attachment there is result of simulation of sphere source with a diameter 1 mm with activity 370 keV placed in (1cm,0,0). The detector is placed in the vacuum. Source of back-to-back gamma quanta with energy 511 keV was used in the simulation.</div>
<div class=""><br class=""></div>
<div class="">One can see, that there are some points that lie outside the region with diameter 1 mm and even outside the region with radius equal to 5 cm.</div>
<div dir="ltr" class="">What may be the reason of formation of these coincidences? Number of these strange coincidences is much less than number of proper true coincidences but I would like to find a solution to improve my results. Thank you in advance for your time and your help.</div>
<div dir="ltr" class=""><br></div>
<div dir="ltr" class="">Best regards,</div>
<div dir="ltr" class="">Pawe&#322; Kowalski,</div>
<div dir="ltr" class="">National Centre for Nuclear Research</div>
</div></div>
Eric Moszczynski | 19 Jan 12:37 2016
Picon

NbOfHits

Hi gate users,

I am using DoseActor and I use to enable the NumberOfHits. My problem is the following : I observed a increase of the number of hit when a interface between two volumes is met. It as an impact on the dose values.

In my case, i have a volume of Air and a volume of water, my volumes are separated with empty space(vaccum) but I have still this issue.


The NbOfHits file is returning something like this :

Air-NbOfHits.txt


####################################
# Matrix Size= (100,100,12.7)
# Resol      = (1,1,10000)
# VoxelSize  = (100,100,0.00127)
# nbVal      = 10000
####################################
7177
3804
3198
3149
3041
3031
2902
2873
2851
2783
2727
2792
2635
2689
...

3119
3214
3203
3244
3210
3448
3555
3508
3808
3869
3961
4239
4195
4334
4536
4680
4873
5094
5480
5556
5897
6401
6752
7226
7789
8820
9531
11101
16205
61277





 Water-NbOfHits.txt



####################################
# Matrix Size= (100,100,0.1)
# Resol      = (1,1,10000)
# VoxelSize  = (100,100,1e-05)
# nbVal      = 10000
####################################
24318
16180
15217
14737
14504
13996
13681
13616
13279
13387
13239
12871

...

11262
11683
12114
12744
13244
13685
14156
15025
15689
16407
17139
18123
18910
20575
22906
26920
35023
98842







Do you have any ideas ?
Thanks in advance.

Best regards.

<div>
<div>
<p>Hi gate users,<br><br>
I am using DoseActor and I use to enable the NumberOfHits. My problem is the following : I observed a increase of the number of hit when a interface between two volumes is met. It as an impact on the dose values.<br><br>
In my case, i have a volume of Air and a volume of water, my volumes are separated with empty space(vaccum) but I have still this issue.<br></p>
<p><br></p>
<p>The NbOfHits file is returning something like this :<br><br>
Air-NbOfHits.txt</p>
<p><br></p>
<p>####################################
<br>
# Matrix Size= (100,100,12.7)<br>
# Resol&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; = (1,1,10000)<br>
# VoxelSize&nbsp; = (100,100,0.00127)<br>
# nbVal&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; = 10000<br>
#################################### <br>
7177<br>
3804<br>
3198<br>
3149<br>
3041<br>
3031<br>
2902<br>
2873<br>
2851<br>
2783<br>
2727<br>
2792<br>
2635<br>
2689 <br>
...</p>
<p>3119<br>
3214<br>
3203<br>
3244<br>
3210<br>
3448<br>
3555<br>
3508<br>
3808<br>
3869<br>
3961<br>
4239<br>
4195<br>
4334<br>
4536<br>
4680<br>
4873<br>
5094<br>
5480<br>
5556<br>
5897<br>
6401<br>
6752<br>
7226<br>
7789<br>
8820<br>
9531<br>
11101<br>
16205<br>
61277<br></p>
<p><br></p>
<p><br></p>
<p><br></p>
<p><br></p>
<p>&nbsp;Water-NbOfHits.txt</p>
<p><br></p>
<p><br></p>
<p>#################################### <br>
# Matrix Size= (100,100,0.1)<br>
# Resol&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; = (1,1,10000)<br>
# VoxelSize&nbsp; = (100,100,1e-05)<br>
# nbVal&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; = 10000<br>
#################################### <br>
24318<br>
16180<br>
15217<br>
14737<br>
14504<br>
13996<br>
13681<br>
13616<br>
13279<br>
13387<br>
13239<br>
12871<br></p>
<p>...</p>
<p>11262<br>
11683<br>
12114<br>
12744<br>
13244<br>
13685<br>
14156<br>
15025<br>
15689<br>
16407<br>
17139<br>
18123<br>
18910<br>
20575<br>
22906<br>
26920<br>
35023<br>
98842<br></p>
<p><br></p>
<p><br></p>
<p><br></p>
<p><br><br><br>
Do you have any ideas ?<br>
Thanks in advance.<br><br>
Best regards.<br></p>
</div>
</div>
Peyman Sheikhzadeh | 19 Jan 09:31 2016
Picon

maximum ring difference

Hi Gate users,
I want to implement maximum ring difference(MRD=half an Axial FOV) without reconstruction.
Can I use MRD in root output analysis only for sensitivity and NECR calculation without image reconstruction? 
 

Best Regards
-------------------


Peyman Sh
PhD Candidate in Medical Physics


 
<div><div>
<div dir="ltr">
<span class="">Hi Gate users,</span><span></span>
</div>
<div dir="ltr"><span class="">I want to implement maximum ring difference(MRD=half an Axial FOV) without reconstruction.</span></div>
<div dir="ltr"><span class="">Can I use MRD in root output analysis only for sensitivity and NECR calculation without image reconstruction?&nbsp;</span></div>
<div></div>
<div>&nbsp;</div>
<div class="signature">
<div><div class="MsoNormal" dir="RTL"><span><br></span></div></div>
<span>Best Regards</span><br><div><span>-------------------</span></div>
<div><br></div>
<div>
<br><div>
<div class="ecxMsoSubtitle"><span>Peyman Sh</span></div>
<div class="ecxMsoSubtitle"><span>PhD Candidate in Medical Physics</span></div>
<div class="ecxMsoSubtitle"><br></div>
<div class="ecxMsoSubtitle"><br></div>
</div>
</div>
<div class="MsoNormal"><span>&nbsp;</span></div>
</div>
</div></div>
Lorena Vázquez Canelas | 18 Jan 12:35 2016
Picon

Re: Defining a source


Hi again,
Thanks for all yours anwers.
I had the incorrectly defined confinement.
Hopefully this way, the simulation is not so slow.

,

Jared's answer should be fine (I didn't try), but here is an other approach (minimal working example in attachment), very similar, with the "Forbid" command.


On 01/18/2016 10:02 AM, Lorena Vázquez Canelas wrote:
<!-- .ExternalClass .ecxhmmessage P { padding:0px; } .ExternalClass body.ecxhmmessage { font-size:12pt; font-family:Calibri; } -->

<!-- .ExternalClass .ecxhmmessage P { padding:0px; } .ExternalClass body.ecxhmmessage { font-size:12pt; font-family:Calibri; } -->
Hi Gaters,
I'm doing a simulation of image qual¡ty phantom.
I want to build a source with the form that i send in the image: it is a quarter cylinder.
It's possible?

Thanks in advance
 
 


_______________________________________________ Gate-users mailing list Gate-users-ZwoEplunGu2uWGBtOU8ma0fXCdDtWGEhSoIsB4E12gc@public.gmane.org http://lists.opengatecollaboration.org/mailman/listinfo/gate-users

<div><div dir="ltr">
<br>Hi again,<br>Thanks for all yours anwers.<br>I had the incorrectly defined confinement.<br>Hopefully this way, the simulation is not so slow.<br><br><div>,<br><br>
    Jared's answer should be fine (I didn't try), but here is an other
    approach (minimal working example in attachment), very similar, with
    the "Forbid" command.<br><br><br><div class="ecxmoz-cite-prefix">On 01/18/2016 10:02 AM, Lorena V&aacute;zquez
      Canelas wrote:<br>
</div>
    <blockquote cite="mid:DUB113-W240B6113450AFEFA7D406DA5C00@...">
      &lt;!--
.ExternalClass .ecxhmmessage P {
padding:0px;
}

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

--&gt;<div dir="ltr">
<br><div>
          &lt;!--
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padding:0px;
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.ExternalClass body.ecxhmmessage {
font-size:12pt;
font-family:Calibri;
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--&gt;<div dir="ltr">Hi Gaters,<br>
            I'm doing a simulation of image qual&iexcl;ty phantom. <br>
            I want to build a source with the form that i send in the
            image: it is a quarter cylinder.<br>
            It's possible?<br><br>
            Thanks in advance<br><div> <span>&nbsp;</span>
              <div class="ecxinlineImage" unselectable="on"></div>
              <span>&nbsp;</span>
</div>
          </div>
        </div>
      </div>
      <br><br>_______________________________________________
Gate-users mailing list
<a class="ecxmoz-txt-link-abbreviated" href="mailto:Gate-users@...engatecollaboration.org">Gate-users@...</a>
<a class="ecxmoz-txt-link-freetext" href="http://lists.opengatecollaboration.org/mailman/listinfo/gate-users" target="_blank">http://lists.opengatecollaboration.org/mailman/listinfo/gate-users</a>
    </blockquote>
    <br>
</div> 		 	   		  </div></div>
Lorena Vázquez Canelas | 18 Jan 10:02 2016
Picon

Re: Defining a source


<!-- .ExternalClass .ecxhmmessage P { padding:0px; } .ExternalClass body.ecxhmmessage { font-size:12pt; font-family:Calibri; } -->
Hi Gaters,
I'm doing a simulation of image qual¡ty phantom.
I want to build a source with the form that i send in the image: it is a quarter cylinder.
It's possible?

Thanks in advance
 
 
<div><div dir="ltr">
<br><div>

&lt;!--
.ExternalClass .ecxhmmessage P {
padding:0px;
}

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

--&gt;<div dir="ltr">Hi Gaters,<br>I'm doing a simulation of image qual&iexcl;ty phantom. <br>I want to build a source with the form that i send in the image: it is a quarter cylinder.<br> It's possible?<br><br>Thanks in advance<br><div>    <span>&nbsp;</span>    <div class="ecxinlineImage" unselectable="on"></div>    <span>&nbsp;</span>
</div> 		 	   		  </div>
</div> 		 	   		  </div></div>
Michal Knap | 14 Jan 13:35 2016
Picon

Fw: Problem with 'std::bad_alloc'

Hi All,
I'm attaching my whole conversation with David and files below.
Could you please help with solving this issue?
It's a strange bug which causes huge consumption of RAM and gives me  this error message

                            /terminate called after throwing an instance of 'std::bad_alloc'/
                            /  what():  std::bad_alloc/
                             /Przerwane (core dumped)/

My visualization doesn't even start but it is the smallest problem.

I run benchmark simulation just to check if is everything all right with my Gate and it all works (benchmarkSPECT.mac with visualization works fine).

I'm working on ubuntu 14.04 LTS / Geant4.9.6.p04 / Gate_v7.0/ ROOT 5.34.34.
On machine with i5VPRO/2.4GHz/8GB/128 SSD. 

Can anybody help me with this issue?
I'll be very thankful.

Best Regards&Thanks
Michał Knap

13:07 czwartek, 2016-1-14, David Boersma <david.boersma-JAjqph6Yjy84M/bo5TPICw@public.gmane.org> napisał(a):




Hi,

All:

Could other people please have a look at Michał's problem? I could run
his macro (see his previous mail) and Gate indeed consumes excessive
amounts of RAM, but it is not clear to me why that happens. See below
for my observations. I have to work on other things now.


Michał:

Yes, I could run your macro. I disabled all the lines with "/vis" in
them, ran the command "Gate ./minigamma1pointsourceoncollimator.mac" and
then observed in a separate window with "htop" how things were going,
resource-wise.

I ran this on a machine with 16 GiB of RAM, Ubuntu 14.04, Geant
4.9.6.p04. It took about a minute to fill up all the RAM, and then it
started to eat up the swap space. When it had eaten up 90% of the swap
space I killed the program (from within htop; I was not able to kill
Gate with ctrl-C).

I think we can conclude that "something" in Gate is allocating too much
memory. It could be a spectacular memory leak, or it could be some
missconfigured component in your macro that causes excessive resource
consumption. For the latter hypothesis I looked at your macro for
suspicious things, but the most segmented thing I could find was the
"projection" output, and replacing 128*128 by 4*4 did not help at all. I
reduced the time slice from 1s to 0.001s and the time stop from 60s to
0.002s, but that did not seem to change anything either.

Maybe there is some implicit/default setting that is wrong for your
application. I am not an imaging expert (I use gate for radiotherapy),
so maybe someone else has an idea.

I ran it in "gdb" (the GNU debugger) and stopped the program by sending
it a signal, while it was eating memory, and checked with "bt"
(backtrace) in which function it was running at the moment I stopped it.
I repeated this several times and got different backtraces every time,
so this did not provide any useful hints for finding out which part of
the code is responsible.

This is as far as I could get, and the problem is not yet solved. I hope
someone else on the list can take over to help you solve this. Maybe
someone should run it with "valgrind", but that can be pretty time
consuming, and maybe someone actually already knows, that would be much
more efficient.

Good luck,
David B.


Den 13/01/2016 kl. 20:26, skrev Michal Knap:
> Hi David,
> It would be really great if you could take a look on my mac file.
> Please see the attachment.
> I'm a little bit confused about this bug.
>
> I will try to try out your idea with much simplified version and will
> return with the results.
>
> Thanks&Regards
> Michał Knap
>
>
>
> 12:00 środa, 2016-1-13, David Boersma <david.boersma-JAjqph6Yjy84M/bo5TPICw@public.gmane.org>
> napisał(a):
>
>
> Hi Michał,
>
> On 2016-01-13 07:04, Michal Knap wrote:
>  > Hi David,
>  > I have only one version of Gate and Geant4 installed - Gate v7.0 and
>  > Geant4.9.6.p04.
>  >
>  > I successfully  run benchmark simulation - benchmarkSPECT, with or
>  > without visualization.
>  >
>  > So it's somthing with my code i think. What can i disable/enable to fix
>  > this bug?
>
> If there is indeed something wrong with your code then we can only help
> you by looking at your code.
>
> So, as I wrote in my previous mail, it would be nice if you could make a
> short and strongly simplified version of your macro which still crashes
> in the same way. Preferably it only uses input data from the examples
> and benchmarks. E.g. you define only a very crude geometry and a gamma
> source, and a number of primaries, no visualization. If that throws the
> same bad_alloc exception, then please send that to us, we can try to
> reproduce and tell you what's wrong. Of course it is possible that the
> problem disappears after you take out certain parts of the macro. If you
> can nail it down to one particular line or set of lines that makes the
> difference between crashing and not crashing, then quote those lines to
> us. That is less helpful the first option, but could still provide a hint.
>
> David B.
>
>
>  >
>  > Best regards
>  > Michał Knap
>  >
>  >
>  > 18:11 wtorek, 2016-1-12, David Boersma <david.boersma-JAjqph6Yjy84M/bo5TPICw@public.gmane.org
> <mailto:david.boersma <at> physics.uu.se>>
>  > napisał(a):
>  >
>  >
>  > Hi Michał,
>  >
>  > Some more simple questions:
>  >
>  > * Can you run macros from the example directory successfully, or do some
>  > of them result in this same error?
>  >
>  >
>  > * Do you have multiple versions of Geant4 and/or Root installed? If yes,
>  > could you check with the following command:
>  >
>  > ldd $(which Gate)
>  >
>  > that your Gate executable gets indeed linked to the same versions as the
>  > ones you configured during installation of Gate? If the versions do not
>  > match: then fix your environment, or reinstall Gate (from scratch).
>  >
>  >
>  >
>  > If these simple questions do not help, then I think the next step is to
>  > make a minimalistic version of your macro that demonstrates the error
>  > you are seeing and post it here on the list, so that other people have a
>  > chance to reproduce this problem. Please also specify how you run the
>  > Gate command (with which options).
>  >
>  > HTH,
>  > David Boersma
>  >
>  > Den 12/01/2016 kl. 17:35, skrev Michal Knap:
>  >  > Hi David,
>  >  > I checked you idea but i use only 50-60% RAM memory.
>  >  > While i'm running simulation i do not use any other apps.
>  >  > Even browser is closed.
>  >  >
>  >  > I have intel i5 vPRO, 8GB RAM, 120 GB SSD
>  >  > Ubuntu 14.04 LTS, Geant4.9.6.p04,Gate7.0,Root 5.34.34
>  >  >
>  >  > Kind regards
>  >  >
>  >  >
>  >  > 17:01 wtorek, 2016-1-12, David Boersma
> <david.boersma-JAjqph6Yjy84M/bo5TPICw@public.gmane.org <mailto:david.boersma-JAjqph6Yjy8aUXJvG02c5w@public.gmane.orgse>
>  > <mailto:david.boersma-JAjqph6Yjy8aUXJvG02c5w@public.gmane.orgse
> <mailto:david.boersma-JAjqph6Yjy84M/bo5TPICw@public.gmane.org>>>
>  >  > napisał(a):
>  >  >
>  >  >
>  >  >
>  >  >
>  >  > Hi Michał,
>  >  >
>  >  > My first guess would be a memory problem. Could you check with some
>  >  > resource monitor ("top" or "htop" on linux, "Activity Monitory" on
>  >  > MacOSX) how much RAM is used on your machine, by which programs?
>  >  >
>  >  > It could be that other programs than GATE (e.g. a web browser) are
> using
>  >  > so much RAM that there is not enough available for your GATE
>  >  > application. Then this is easily solved by quitting those other
> programs.
>  >  >
>  >  > It could be that you configured GATE too optimistically, e.g. using a
>  >  > scoring volume with too many voxels. Then you should either use a more
>  >  > modest configuration, or run on a bigger machine.
>  >  >
>  >  > There are many other possible causes, but these are the easiest
> ones, I
>  >  > can think of. It would be good if you could tell us whether these are
>  >  > already ruled out.
>  >  >
>  >  > Also: when reporting problems and asking for help, it could be helpful
>  >  > if you would add some basic specs about the OS (+version) and the
>  >  > hardware (in particular how much RAM your have). Which version of GATE
>  >  > are you using, with which version of Geant4? How did you install
> it? Did
>  >  > you install it recently or long ago?
>  >  >
>  >  > HTH,
>  >  > David
>  >  >
>  >  > Den 12/01/2016 kl. 15:55, skrev Michal Knap:
>  >  >  > Hi All,
>  >  >  > As i'm trying to simulate a minigammacamera i'm getting this error
>  >  > message.
>  >  >  > I still do not know how to fix this.
>  >  >  > Can anybody know what is wrong?
>  >  >  > //
>  >  >  > /[Acquisition-0] Slice 0 from 0 to 37.5 s [slice=37.5 s], final
>  > stop at
>  >  >  > 150 s./
>  >  >  > /terminate called after throwing an instance of 'std::bad_alloc'/
>  >  >  > /  what():  std::bad_alloc/
>  >  >  > /Przerwane (core dumped)/
>  >  >  > /
>  >  >  > /
>  >  >  > I'll be very thankful for any help.
>  >  >  >
>  >  >  > Thanks in advance
>  >  >  >
>  >  >  > Kind regards
>  >  >  > Michał Knap
>  >  >
>  >  >  >
>  >  >  >
>  >  >  > _______________________________________________
>  >  >  > Gate-users mailing list
>  >  >  > Gate-users-ZwoEplunGu2uWGBtOU8ma0fXCdDtWGEhSoIsB4E12gc@public.gmane.org
> <mailto:Gate-users-ZwoEplunGu2uWGBtOU8ma0fXCdDtWGEhSoIsB4E12gc@public.gmane.org>
>  > <mailto:Gate-users-ZwoEplunGu2uWGBtOU8ma2ZaI6lBa+6R@public.gmane.orgboration.org
> <mailto:Gate-users-ZwoEplunGu2uWGBtOU8ma0fXCdDtWGEhSoIsB4E12gc@public.gmane.org>>
>  >  > <mailto:Gate-users <at> lists.opengatecollaboration.org
> <mailto:Gate-users-ZwoEplunGu2uWGBtOU8ma0fXCdDtWGEhSoIsB4E12gc@public.gmane.org>
>  > <mailto:Gate-users-ZwoEplunGu2uWGBtOU8ma0fXCdDtWGEhSoIsB4E12gc@public.gmane.org
> <mailto:Gate-users <at> lists.opengatecollaboration.org>>>
>  >  >  > http://lists.opengatecollaboration.org/mailman/listinfo/gate-users
>  >  >  >
>  >  > _______________________________________________
>  >  > Gate-users mailing list
>  >  > Gate-users <at> lists.opengatecollaboration.org

Attachment (GateMaterials.db): application/octet-stream, 22 KiB
Attachment (Materials.xml): text/xml, 2173 bytes
<div><div>
<div><div><div>
<div><span>Hi All,</span></div>
<div><span>I'm attaching my whole conversation with David and files below.</span></div>
<div>Could you please help with solving this issue?</div>
<div dir="ltr">It's a strange bug&nbsp;which causes&nbsp;huge consumption of RAM and gives me&nbsp;<span class="yiv3203938371">&nbsp;this error message</span>
</div>
<div dir="ltr"><span class="yiv3203938371"><br clear="none"></span></div>
<div dir="ltr"><span class="yiv3203938371">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;/terminate called after throwing an instance of 'std::bad_alloc'/</span></div>
<span class="yiv3203938371">&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;/&nbsp; what():&nbsp; std::bad_alloc/</span><br clear="none" class="yiv3203938371"><div dir="ltr"><span>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;/Przerwane (core dumped)/</span></div>
<div dir="ltr"><br clear="none"></div>
<div dir="ltr">My visualization doesn't even start but it is the smallest problem.</div>
<div dir="ltr"><br></div>
<div dir="ltr">I run benchmark simulation just to check if is everything all right with my Gate and it all works (benchmarkSPECT.mac with visualization works fine).</div>
<div dir="ltr"><br></div>
<div dir="ltr">I'm working on ubuntu 14.04 LTS / Geant4.9.6.p04 / Gate_v7.0/ ROOT 5.34.34.</div>
<div dir="ltr">On machine with i5VPRO/2.4GHz/8GB/128 SSD.&nbsp;</div>
<div class="yiv3203938371qtdSeparateBR"><br></div>
<div class="yiv3203938371qtdSeparateBR">Can anybody help me with this issue?</div>
<div class="yiv3203938371qtdSeparateBR">I'll be very thankful.</div>
<div class="yiv3203938371qtdSeparateBR"><br></div>
<div class="yiv3203938371qtdSeparateBR">Best Regards&amp;Thanks</div>
<div class="yiv3203938371qtdSeparateBR">Micha&#322; Knap<br clear="none"><br clear="none">
</div>  </div></div></div>
<div class=".yiv3203938371yahoo_quoted"> <div> <div> <div dir="ltr"> 13:07 czwartek, 2016-1-14, David Boersma &lt;david.boersma@...&gt; napisa&#322;(a):<br clear="none">
</div>  <br clear="none"><br clear="none"><div class="qtdSeparateBR">
<br><br>
</div>
<div class="yiv3203938371yqt8973136228"><div class="yiv3203938371y_msg_container">Hi,<br clear="none"><br clear="none">All:<br clear="none"><br clear="none">Could other people please have a look at Micha&#322;'s problem? I could run <br clear="none">his macro (see his previous mail) and Gate indeed consumes excessive <br clear="none">amounts of RAM, but it is not clear to me why that happens. See below <br clear="none">for my observations. I have to work on other things now.<br clear="none"><br clear="none"><br clear="none">Micha&#322;:<br clear="none"><br clear="none">Yes, I could run your macro. I disabled all the lines with "/vis" in <br clear="none">them, ran the command "Gate ./minigamma1pointsourceoncollimator.mac" and <br clear="none">then observed in a separate window with "htop" how things were going, <br clear="none">resource-wise.<br clear="none"><br clear="none">I ran this on a machine with 16 GiB of RAM, Ubuntu 14.04, Geant <br clear="none">4.9.6.p04. It took about a minute to fill up all the RAM, and then it <br clear="none">started to eat up the swap space. When it had eaten up 90% of the swap <br clear="none">space I killed the program (from within htop; I was not able to kill <br clear="none">Gate with ctrl-C).<br clear="none"><br clear="none">I think we can conclude that "something" in Gate is allocating too much <br clear="none">memory. It could be a spectacular memory leak, or it could be some <br clear="none">missconfigured component in your macro that causes excessive resource <br clear="none">consumption. For the latter hypothesis I looked at your macro for <br clear="none">suspicious things, but the most segmented thing I could find was the <br clear="none">"projection" output, and replacing 128*128 by 4*4 did not help at all. I <br clear="none">reduced the time slice from 1s to 0.001s and the time stop from 60s to <br clear="none">0.002s, but that did not seem to change anything either.<br clear="none"><br clear="none">Maybe there is some implicit/default setting that is wrong for your <br clear="none">application. I am not an imaging expert (I use gate for radiotherapy), <br clear="none">so maybe someone else has an idea.<br clear="none"><br clear="none">I ran it in "gdb" (the GNU debugger) and stopped the program by sending <br clear="none">it a signal, while it was eating memory, and checked with "bt" <br clear="none">(backtrace) in which function it was running at the moment I stopped it. <br clear="none">I repeated this several times and got different backtraces every time, <br clear="none">so this did not provide any useful hints for finding out which part of <br clear="none">the code is responsible.<br clear="none"><br clear="none">This is as far as I could get, and the problem is not yet solved. I hope <br clear="none">someone else on the list can take over to help you solve this. Maybe <br clear="none">someone should run it with "valgrind", but that can be pretty time <br clear="none">consuming, and maybe someone actually already knows, that would be much <br clear="none">more efficient.<br clear="none"><br clear="none">Good luck,<br clear="none">David B.<br clear="none"><br clear="none"><br clear="none">Den 13/01/2016 kl. 20:26, skrev Michal Knap:<br clear="none">&gt; Hi David,<br clear="none">&gt; It would be really great if you could take a look on my mac file.<br clear="none">&gt; Please see the attachment.<br clear="none">&gt; I'm a little bit confused about this bug.<br clear="none">&gt;<br clear="none">&gt; I will try to try out your idea with much simplified version and will<br clear="none">&gt; return with the results.<br clear="none">&gt;<br clear="none">&gt; Thanks&amp;Regards<br clear="none">&gt; Micha&#322; Knap<br clear="none">&gt;<br clear="none">&gt;<br clear="none">&gt;<br clear="none">&gt; 12:00 &#347;roda, 2016-1-13, David Boersma &lt;<a rel="nofollow" shape="rect" ymailto="mailto:david.boersma@..." target="_blank" href="mailto:david.boersma@...">david.boersma@...</a>&gt;<br clear="none">&gt; napisa&#322;(a):<br clear="none">&gt;<br clear="none">&gt;<br clear="none">&gt; Hi Micha&#322;,<br clear="none">&gt;<br clear="none">&gt; On 2016-01-13 07:04, Michal Knap wrote:<br clear="none">&gt;&nbsp; &gt; Hi David,<br clear="none">&gt;&nbsp; &gt; I have only one version of Gate and Geant4 installed - Gate v7.0 and<br clear="none">&gt;&nbsp; &gt; Geant4.9.6.p04.<br clear="none">&gt;&nbsp; &gt;<br clear="none">&gt;&nbsp; &gt; I successfully&nbsp; run benchmark simulation - benchmarkSPECT, with or<br clear="none">&gt;&nbsp; &gt; without visualization.<br clear="none">&gt;&nbsp; &gt;<br clear="none">&gt;&nbsp; &gt; So it's somthing with my code i think. What can i disable/enable to fix<br clear="none">&gt;&nbsp; &gt; this bug?<br clear="none">&gt;<br clear="none">&gt; If there is indeed something wrong with your code then we can only help<br clear="none">&gt; you by looking at your code.<br clear="none">&gt;<br clear="none">&gt; So, as I wrote in my previous mail, it would be nice if you could make a<br clear="none">&gt; short and strongly simplified version of your macro which still crashes<br clear="none">&gt; in the same way. Preferably it only uses input data from the examples<br clear="none">&gt; and benchmarks. E.g. you define only a very crude geometry and a gamma<br clear="none">&gt; source, and a number of primaries, no visualization. If that throws the<br clear="none">&gt; same bad_alloc exception, then please send that to us, we can try to<br clear="none">&gt; reproduce and tell you what's wrong. Of course it is possible that the<br clear="none">&gt; problem disappears after you take out certain parts of the macro. If you<br clear="none">&gt; can nail it down to one particular line or set of lines that makes the<br clear="none">&gt; difference between crashing and not crashing, then quote those lines to<br clear="none">&gt; us. That is less helpful the first option, but could still provide a hint.<br clear="none">&gt;<br clear="none">&gt; David B.<br clear="none">&gt;<br clear="none">&gt;<br clear="none">&gt;&nbsp; &gt;<br clear="none">&gt;&nbsp; &gt; Best regards<br clear="none">&gt;&nbsp; &gt; Micha&#322; Knap<br clear="none">&gt;&nbsp; &gt;<br clear="none">&gt;&nbsp; &gt;<br clear="none">&gt;&nbsp; &gt; 18:11 wtorek, 2016-1-12, David Boersma &lt;<a rel="nofollow" shape="rect" ymailto="mailto:david.boersma <at> physics.uu.se" target="_blank" href="mailto:david.boersma@...">david.boersma@...</a><br clear="none">&gt; &lt;mailto:<a rel="nofollow" shape="rect" ymailto="mailto:david.boersma@..." target="_blank" href="mailto:david.boersma@...">david.boersma <at> physics.uu.se</a>&gt;&gt;<br clear="none">&gt;&nbsp; &gt; napisa&#322;(a):<br clear="none">&gt;&nbsp; &gt;<br clear="none">&gt;&nbsp; &gt;<br clear="none">&gt;&nbsp; &gt; Hi Micha&#322;,<br clear="none">&gt;&nbsp; &gt;<br clear="none">&gt;&nbsp; &gt; Some more simple questions:<br clear="none">&gt;&nbsp; &gt;<br clear="none">&gt;&nbsp; &gt; * Can you run macros from the example directory successfully, or do some<br clear="none">&gt;&nbsp; &gt; of them result in this same error?<br clear="none">&gt;&nbsp; &gt;<br clear="none">&gt;&nbsp; &gt;<br clear="none">&gt;&nbsp; &gt; * Do you have multiple versions of Geant4 and/or Root installed? If yes,<br clear="none">&gt;&nbsp; &gt; could you check with the following command:<br clear="none">&gt;&nbsp; &gt;<br clear="none">&gt;&nbsp; &gt; ldd $(which Gate)<br clear="none">&gt;&nbsp; &gt;<br clear="none">&gt;&nbsp; &gt; that your Gate executable gets indeed linked to the same versions as the<br clear="none">&gt;&nbsp; &gt; ones you configured during installation of Gate? If the versions do not<br clear="none">&gt;&nbsp; &gt; match: then fix your environment, or reinstall Gate (from scratch).<br clear="none">&gt;&nbsp; &gt;<br clear="none">&gt;&nbsp; &gt;<br clear="none">&gt;&nbsp; &gt;<br clear="none">&gt;&nbsp; &gt; If these simple questions do not help, then I think the next step is to<br clear="none">&gt;&nbsp; &gt; make a minimalistic version of your macro that demonstrates the error<br clear="none">&gt;&nbsp; &gt; you are seeing and post it here on the list, so that other people have a<br clear="none">&gt;&nbsp; &gt; chance to reproduce this problem. Please also specify how you run the<br clear="none">&gt;&nbsp; &gt; Gate command (with which options).<br clear="none">&gt;&nbsp; &gt;<br clear="none">&gt;&nbsp; &gt; HTH,<br clear="none">&gt;&nbsp; &gt; David Boersma<br clear="none">&gt;&nbsp; &gt;<br clear="none">&gt;&nbsp; &gt; Den 12/01/2016 kl. 17:35, skrev Michal Knap:<br clear="none">&gt;&nbsp; &gt;&nbsp; &gt; Hi David,<br clear="none">&gt;&nbsp; &gt;&nbsp; &gt; I checked you idea but i use only 50-60% RAM memory.<br clear="none">&gt;&nbsp; &gt;&nbsp; &gt; While i'm running simulation i do not use any other apps.<br clear="none">&gt;&nbsp; &gt;&nbsp; &gt; Even browser is closed.<br clear="none">&gt;&nbsp; &gt;&nbsp; &gt;<br clear="none">&gt;&nbsp; &gt;&nbsp; &gt; I have intel i5 vPRO, 8GB RAM, 120 GB SSD<br clear="none">&gt;&nbsp; &gt;&nbsp; &gt; Ubuntu 14.04 LTS, Geant4.9.6.p04,Gate7.0,Root 5.34.34<br clear="none">&gt;&nbsp; &gt;&nbsp; &gt;<br clear="none">&gt;&nbsp; &gt;&nbsp; &gt; Kind regards<br clear="none">&gt;&nbsp; &gt;&nbsp; &gt;<br clear="none">&gt;&nbsp; &gt;&nbsp; &gt;<br clear="none">&gt;&nbsp; &gt;&nbsp; &gt; 17:01 wtorek, 2016-1-12, David Boersma<br clear="none">&gt; &lt;<a rel="nofollow" shape="rect" ymailto="mailto:david.boersma@..." target="_blank" href="mailto:david.boersma <at> physics.uu.se">david.boersma@...</a> &lt;mailto:<a rel="nofollow" shape="rect" ymailto="mailto:david.boersma@..." target="_blank" href="mailto:david.boersma@...">david.boersma@...se</a>&gt;<br clear="none">&gt;&nbsp; &gt; &lt;mailto:<a rel="nofollow" shape="rect" ymailto="mailto:david.boersma@..." target="_blank" href="mailto:david.boersma@...">david.boersma@...se</a><br clear="none">&gt; &lt;mailto:<a rel="nofollow" shape="rect" ymailto="mailto:david.boersma@..." target="_blank" href="mailto:david.boersma@...">david.boersma@...</a>&gt;&gt;&gt;<br clear="none">&gt;&nbsp; &gt;&nbsp; &gt; napisa&#322;(a):<br clear="none">&gt;&nbsp; &gt;&nbsp; &gt;<br clear="none">&gt;&nbsp; &gt;&nbsp; &gt;<br clear="none">&gt;&nbsp; &gt;&nbsp; &gt;<br clear="none">&gt;&nbsp; &gt;&nbsp; &gt;<br clear="none">&gt;&nbsp; &gt;&nbsp; &gt; Hi Micha&#322;,<br clear="none">&gt;&nbsp; &gt;&nbsp; &gt;<br clear="none">&gt;&nbsp; &gt;&nbsp; &gt; My first guess would be a memory problem. Could you check with some<br clear="none">&gt;&nbsp; &gt;&nbsp; &gt; resource monitor ("top" or "htop" on linux, "Activity Monitory" on<br clear="none">&gt;&nbsp; &gt;&nbsp; &gt; MacOSX) how much RAM is used on your machine, by which programs?<br clear="none">&gt;&nbsp; &gt;&nbsp; &gt;<br clear="none">&gt;&nbsp; &gt;&nbsp; &gt; It could be that other programs than GATE (e.g. a web browser) are<br clear="none">&gt; using<br clear="none">&gt;&nbsp; &gt;&nbsp; &gt; so much RAM that there is not enough available for your GATE<br clear="none">&gt;&nbsp; &gt;&nbsp; &gt; application. Then this is easily solved by quitting those other<br clear="none">&gt; programs.<br clear="none">&gt;&nbsp; &gt;&nbsp; &gt;<br clear="none">&gt;&nbsp; &gt;&nbsp; &gt; It could be that you configured GATE too optimistically, e.g. using a<br clear="none">&gt;&nbsp; &gt;&nbsp; &gt; scoring volume with too many voxels. Then you should either use a more<br clear="none">&gt;&nbsp; &gt;&nbsp; &gt; modest configuration, or run on a bigger machine.<br clear="none">&gt;&nbsp; &gt;&nbsp; &gt;<br clear="none">&gt;&nbsp; &gt;&nbsp; &gt; There are many other possible causes, but these are the easiest<br clear="none">&gt; ones, I<br clear="none">&gt;&nbsp; &gt;&nbsp; &gt; can think of. It would be good if you could tell us whether these are<br clear="none">&gt;&nbsp; &gt;&nbsp; &gt; already ruled out.<br clear="none">&gt;&nbsp; &gt;&nbsp; &gt;<br clear="none">&gt;&nbsp; &gt;&nbsp; &gt; Also: when reporting problems and asking for help, it could be helpful<br clear="none">&gt;&nbsp; &gt;&nbsp; &gt; if you would add some basic specs about the OS (+version) and the<br clear="none">&gt;&nbsp; &gt;&nbsp; &gt; hardware (in particular how much RAM your have). Which version of GATE<br clear="none">&gt;&nbsp; &gt;&nbsp; &gt; are you using, with which version of Geant4? How did you install<br clear="none">&gt; it? Did<br clear="none">&gt;&nbsp; &gt;&nbsp; &gt; you install it recently or long ago?<br clear="none">&gt;&nbsp; &gt;&nbsp; &gt;<br clear="none">&gt;&nbsp; &gt;&nbsp; &gt; HTH,<br clear="none">&gt;&nbsp; &gt;&nbsp; &gt; David<br clear="none">&gt;&nbsp; &gt;&nbsp; &gt;<br clear="none">&gt;&nbsp; &gt;&nbsp; &gt; Den 12/01/2016 kl. 15:55, skrev Michal Knap:<br clear="none">&gt;&nbsp; &gt;&nbsp; &gt;&nbsp; &gt; Hi All,<br clear="none">&gt;&nbsp; &gt;&nbsp; &gt;&nbsp; &gt; As i'm trying to simulate a minigammacamera i'm getting this error<br clear="none">&gt;&nbsp; &gt;&nbsp; &gt; message.<br clear="none">&gt;&nbsp; &gt;&nbsp; &gt;&nbsp; &gt; I still do not know how to fix this.<br clear="none">&gt;&nbsp; &gt;&nbsp; &gt;&nbsp; &gt; Can anybody know what is wrong?<br clear="none">&gt;&nbsp; &gt;&nbsp; &gt;&nbsp; &gt; //<br clear="none">&gt;&nbsp; &gt;&nbsp; &gt;&nbsp; &gt; /[Acquisition-0] Slice 0 from 0 to 37.5 s [slice=37.5 s], final<br clear="none">&gt;&nbsp; &gt; stop at<br clear="none">&gt;&nbsp; &gt;&nbsp; &gt;&nbsp; &gt; 150 s./<br clear="none">&gt;&nbsp; &gt;&nbsp; &gt;&nbsp; &gt; /terminate called after throwing an instance of 'std::bad_alloc'/<br clear="none">&gt;&nbsp; &gt;&nbsp; &gt;&nbsp; &gt; /&nbsp; what():&nbsp; std::bad_alloc/<br clear="none">&gt;&nbsp; &gt;&nbsp; &gt;&nbsp; &gt; /Przerwane (core dumped)/<br clear="none">&gt;&nbsp; &gt;&nbsp; &gt;&nbsp; &gt; /<br clear="none">&gt;&nbsp; &gt;&nbsp; &gt;&nbsp; &gt; /<br clear="none">&gt;&nbsp; &gt;&nbsp; &gt;&nbsp; &gt; I'll be very thankful for any help.<br clear="none">&gt;&nbsp; &gt;&nbsp; &gt;&nbsp; &gt;<br clear="none">&gt;&nbsp; &gt;&nbsp; &gt;&nbsp; &gt; Thanks in advance<br clear="none">&gt;&nbsp; &gt;&nbsp; &gt;&nbsp; &gt;<br clear="none">&gt;&nbsp; &gt;&nbsp; &gt;&nbsp; &gt; Kind regards<br clear="none">&gt;&nbsp; &gt;&nbsp; &gt;&nbsp; &gt; Micha&#322; Knap<br clear="none">&gt;&nbsp; &gt;&nbsp; &gt;<br clear="none">&gt;&nbsp; &gt;&nbsp; &gt;&nbsp; &gt;<br clear="none">&gt;&nbsp; &gt;&nbsp; &gt;&nbsp; &gt;<br clear="none">&gt;&nbsp; &gt;&nbsp; &gt;&nbsp; &gt; _______________________________________________<br clear="none">&gt;&nbsp; &gt;&nbsp; &gt;&nbsp; &gt; Gate-users mailing list<br clear="none">&gt;&nbsp; &gt;&nbsp; &gt;&nbsp; &gt; <a rel="nofollow" shape="rect" ymailto="mailto:Gate-users@..." target="_blank" href="mailto:Gate-users@...">Gate-users@...</a><br clear="none">&gt; &lt;mailto:<a rel="nofollow" shape="rect" ymailto="mailto:Gate-users@..." target="_blank" href="mailto:Gate-users@...">Gate-users@...</a>&gt;<br clear="none">&gt;&nbsp; &gt; &lt;mailto:<a rel="nofollow" shape="rect" ymailto="mailto:Gate-users@..." target="_blank" href="mailto:Gate-users@...">Gate-users@...boration.org</a><br clear="none">&gt; &lt;mailto:<a rel="nofollow" shape="rect" ymailto="mailto:Gate-users@..." target="_blank" href="mailto:Gate-users@...">Gate-users@...</a>&gt;&gt;<br clear="none">&gt;&nbsp; &gt;&nbsp; &gt; &lt;mailto:<a rel="nofollow" shape="rect" ymailto="mailto:Gate-users@..." target="_blank" href="mailto:Gate-users@...">Gate-users <at> lists.opengatecollaboration.org</a><br clear="none">&gt; &lt;mailto:<a rel="nofollow" shape="rect" ymailto="mailto:Gate-users@...oration.org" target="_blank" href="mailto:Gate-users@...aboration.org">Gate-users@...</a>&gt;<br clear="none">&gt;&nbsp; &gt; &lt;mailto:<a rel="nofollow" shape="rect" ymailto="mailto:Gate-users@..." target="_blank" href="mailto:Gate-users@...">Gate-users@...</a><br clear="none">&gt; &lt;mailto:<a rel="nofollow" shape="rect" ymailto="mailto:Gate-users@..." target="_blank" href="mailto:Gate-users@...">Gate-users <at> lists.opengatecollaboration.org</a>&gt;&gt;&gt;<br clear="none">&gt;&nbsp; &gt;&nbsp; &gt;&nbsp; &gt; <a rel="nofollow" shape="rect" target="_blank" href="http://lists.opengatecollaboration.org/mailman/listinfo/gate-users">http://lists.opengatecollaboration.org/mailman/listinfo/gate-users</a><br clear="none">&gt;&nbsp; &gt;&nbsp; &gt;&nbsp; &gt;<br clear="none">&gt;&nbsp; &gt;&nbsp; &gt; _______________________________________________<br clear="none">&gt;&nbsp; &gt;&nbsp; &gt; Gate-users mailing list<br clear="none">&gt;&nbsp; &gt;&nbsp; &gt; <a rel="nofollow" shape="rect" ymailto="mailto:Gate-users@..." target="_blank" href="mailto:Gate-users@...">Gate-users <at> lists.opengatecollaboration.org</a><div class="yiv3203938371yqt3640601787">
<br clear="none">&gt; &lt;mailto:<a rel="nofollow" shape="rect" ymailto="mailto:Gate-users@...ration.org" target="_blank" href="mailto:Gate-users@...boration.org">Gate-users@...</a>&gt;<br clear="none">&gt;&nbsp; &gt; &lt;mailto:<a rel="nofollow" shape="rect" ymailto="mailto:Gate-users@..." target="_blank" href="mailto:Gate-users@...">Gate-users <at> lists.opengatecollaboration.org</a><br clear="none">&gt; &lt;mailto:<a rel="nofollow" shape="rect" ymailto="mailto:Gate-users@...laboration.org" target="_blank" href="mailto:Gate-users@...ollaboration.org">Gate-users <at> lists.opengatecollaboration.org</a>&gt;&gt;<br clear="none">&gt;<br clear="none">&gt;&nbsp; &gt;&nbsp; &gt; &lt;mailto:<a rel="nofollow" shape="rect" ymailto="mailto:Gate-users@..." target="_blank" href="mailto:Gate-users@...">Gate-users@...</a><br clear="none">&gt; &lt;mailto:<a rel="nofollow" shape="rect" ymailto="mailto:Gate-users <at> lists.opengatecollaboration.org" target="_blank" href="mailto:Gate-users@...">Gate-users@...org</a>&gt;<br clear="none">&gt;&nbsp; &gt; &lt;mailto:<a rel="nofollow" shape="rect" ymailto="mailto:Gate-users@..." target="_blank" href="mailto:Gate-users@...">Gate-users <at> lists.opengatecollaboration.org</a><br clear="none">&gt; &lt;mailto:<a rel="nofollow" shape="rect" ymailto="mailto:Gate-users@..." target="_blank" href="mailto:Gate-users@...">Gate-users <at> lists.opengatecollaboration.org</a>&gt;&gt;&gt;<br clear="none">&gt;&nbsp; &gt;<br clear="none">&gt;&nbsp; &gt;&nbsp; &gt; <a rel="nofollow" shape="rect" target="_blank" href="http://lists.opengatecollaboration.org/mailman/listinfo/gate-users">http://lists.opengatecollaboration.org/mailman/listinfo/gate-users</a><br clear="none">&gt;&nbsp; &gt;&nbsp; &gt;<br clear="none">&gt;&nbsp; &gt;<br clear="none">&gt;&nbsp; &gt;<br clear="none">&gt;<br clear="none">&gt;<br clear="none">
</div>
<br clear="none"><br clear="none">
</div></div>  </div> </div>  </div>
</div></div>
‪Hadis Shahrabi‬ ‪ | 13 Jan 15:35 2016
Picon

Filter on particle type

Hello
I have a question 
source in my simulation is proton
To obtain only the neutron dose in the phantom what  command i use?
What is the purpose of the filter on particle type in radiotherapy applications?kill or add?
I look forward to your reply

<div><div>
<div dir="ltr" class="">Hello</div>
<div dir="ltr" class="">I have a question&nbsp;</div>
<div dir="ltr" class="">source in my simulation is proton</div>
<div dir="ltr" class="">To obtain only the neutron dose in the phantom what &nbsp;command i use?<br class="">
</div>
<div dir="ltr" class="">What is the purpose of the filter on particle type in radiotherapy applications?kill or add?</div>
<div dir="ltr" class="">I look forward to your reply</div>
<div class="" dir="ltr"><br></div>
</div></div>
Michal Knap | 12 Jan 15:55 2016
Picon

Problem with 'std::bad_alloc'

Hi All,
As i'm trying to simulate a minigammacamera i'm getting this error message. 
I still do not know how to fix this.
Can anybody know what is wrong?
 
[Acquisition-0] Slice 0 from 0 to 37.5 s [slice=37.5 s], final stop at 150 s.
terminate called after throwing an instance of 'std::bad_alloc'
  what():  std::bad_alloc
Przerwane (core dumped)

I'll be very thankful for any help.

Thanks in advance

Kind regards
Michał Knap
<div><div>
<div class=""><span class="">Hi All,</span></div>
<div class=""><span class="">As i'm trying to simulate a minigammacamera i'm getting this error message.&nbsp;</span></div>
<div class=""><span class="">I still do not know how to fix this.</span></div>
<div class=""><span class="">Can anybody know what is wrong?</span></div>
<div class="">&nbsp;</div>
<div class=""><span class="">[Acquisition-0] Slice 0 from 0 to 37.5 s [slice=37.5 s], final stop at 150 s.</span></div>
<div class=""><span class="">terminate called after throwing an instance of 'std::bad_alloc'</span></div>
<div class=""><span class="">&nbsp; what(): &nbsp;std::bad_alloc</span></div>
<div class=""><span class="">Przerwane (core dumped)</span></div>
<div dir="ltr" class=""><br class=""></div>
<div dir="ltr" class=""><span class="">I'll be very thankful for any help.</span></div>
<div dir="ltr" class=""><span class=""><br></span></div>
<div dir="ltr" class=""><span class="">Thanks in advance</span></div>
<div dir="ltr" class=""><br></div>
<div dir="ltr" class=""><span>Kind regards</span></div>
<div dir="ltr" class=""><span>Micha&#322; Knap</span></div>
</div></div>
Andreas Franz Resch | 11 Jan 16:28 2016
Picon

Re: Problem with custom physic lists in Gate v7.1

Am 08.01.2016 17:34, schrieb Maitz, Charles Anthony:
> Hello Andreas,
> 
> I have similar problems.  On my end, the custom physics list is still
> working, but using the addPhysicsList command results in an empty
> output, despite stating the processes are enabled.  My root file has
> no hits.  Unfortunately, I have no solution.  I tried to post on this
> previously, but my only email addresses can't reach the listserv
> (gmail and outlook).
> 
> Good luck!
> -charlie
> 
> 
> Charles A. Maitz, DVM, PhD, DACVR-RO
> Assistant Professor of Radiation Oncology
> Department of Veterinary Medicine & Surgery
> International Institute of Nano & Molecular Medicine
> University of Missouri - Columbia
> maitzc@...
> 
> 
> 
> -----Original Message-----
> From: gate-users-bounces@...
> [mailto:gate-users-bounces@...]
On Behalf
> Of Andreas Franz Resch
> Sent: Friday, January 08, 2016 10:14 AM
> To: gate-users@...
> Subject: [Gate-users] Problem with custom physic lists in Gate v7.1
> 
> Hi all,
> 
> since Gate v7 it is possible to define the physics list with the
> standard G4 physics lists like e.g.:
> 
> /gate/physics/addPhysicsList QGSP_BIC_HP
> 
> However, using a custom physics List like in versions older than 7 or
> given in the radiotherapy example 4 (Gate v7.1):
> 
> /gate/physics/addProcess IonInelastic
> /gate/physics/processes/IonInelastic/setModel G4BinaryLightIonReaction
> /gate/physics/processes/IonInelastic/setModel G4LEDeuteronInelastic
> deuteron /gate/physics/processes/IonInelastic/setModel
> G4LETritonInelastic triton
> 
> does not work for me (Geant4 10.1). Using the example physics lists
> produces no error, but also an empty output although Gate shows the
> physics processes as enabled and initialized.
> 
> Has somebody else also faced similar problems? I saw that the custom
> physics lists in the radiotherapy examples in the development branch
> disappeared - is this a known issue or just a problem of my particular
> implementation?
> 
> Cheers,
> Andreas
> _______________________________________________
> Gate-users mailing list
> Gate-users@...
> http://lists.opengatecollaboration.org/mailman/listinfo/gate-users

Hi Charlie,

seems to be exactly the same problem as mine. Meanwhile I found a 
workaround. I created my own reference physics list in Geant4 which I 
then call with Gate
(/gate/physics/addPhysicsList MY_REF_PHYSICSLIST). Unfortunately this is 
difficult and time consuming, but is the easiest solution for me right 
now, although I cannot recommend it in general. Anyway, if you need, I 
can send you an instruction how to do it.

Cheers,
Andreas

Gmane