[Gate-users] Gate-users Digest, Vol 78, Issue 6

jehangir khan jehangir.kahn at gmail.com
Wed Nov 7 09:16:50 CET 2012 

Dear Gate user!

I am new in this forum as well as new user of Gate simulation , I have been
running Cylindrical PET , and I have recieved output file named as
benchPET.root,   Can someone guide how should I proceed to get Sinograme
to use in reconstruction algorithms to see image.

I shall appreciate your answer
Regards


On Tue, Nov 6, 2012 at 12:00 PM, <
gate-users-request at lists.opengatecollaboration.org> wrote:

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> When replying, please edit your Subject line so it is more specific
> than "Re: Contents of Gate-users digest..."
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>
> Today's Topics:
>
>    1. Annihilation Point (Manuele Calussi)
>    2. Re: Segmentation Violation Error (Lee, Sam (SAM LEE))
>    3. Segmentation Violation Error (Saeed Heidary)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Mon, 5 Nov 2012 14:09:04 +0100
> From: Manuele Calussi <manuele.calussi at gmail.com>
> To: gate-users <gate-users at lists.opengatecollaboration.org>
> Subject: [Gate-users] Annihilation Point
> Message-ID:
>         <CANFn9kULVZoyw_=JEBVH8OY1t+5smHOVTzs-zQVZPY135=
> QKzQ at mail.gmail.com>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Hi Gate-Users
> I have one problem to store in the simulation the annihilation point.
> I simulate one cylindrical scanner PET, where I place one sphere source of
> F18, inside one phantom of water; I want to plot the annihilation point but
> I do not know how to store this type of data in the Root output.
> I saw in the example_ROOT_Analyse, there is a root output file named
> data_PET.root; inside this file, there are some folder and in one of this,
> named Gate, is stored the annihilation point. I want to know how I can
> obtain the same folder in my simulation, using the Root output file,
> because there is not a Gate-macro correlated to the output file
> data_PET.root.
> I post below the part of my Gate-macro where I set the type of the output
> file.
>      ROOT Output format
> #
> /gate/output/root/enable
> #
> /gate/output/root/setFileName MyWork_2
> #
> /gate/output/root/setRootNtupleFlag 1
> #
> /gate/output/root/setRootHitFlag 1
> #
> /gate/output/root/setRootSinglesFlag 1
> #
> /gate/output/root/setRootCoincidencesFlag 1
> #
> /gate/output/root/setSaveRndmFlag 1
> #
> #/gate/output/verbose 2
>
>
> Help me please.
> Best Regards
> Manuele Calussi
> -------------- next part --------------
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>
> ------------------------------
>
> Message: 2
> Date: Mon, 5 Nov 2012 14:46:38 +0000
> From: "Lee, Sam (SAM LEE)" <slee91 at utk.edu>
> To: Manuel Reifegerst <Manuel.Reifegerst at uni-duesseldorf.de>, Gate
>         Mailing List <gate-users at lists.opengatecollaboration.org>
> Subject: Re: [Gate-users] Segmentation Violation Error
> Message-ID:
>         <
> E0BD1EF372F8824EA4717918B50AF3641D1B91B8 at SN2PRD0202MB179.namprd02.prod.outlook.com
> >
>
> Content-Type: text/plain; charset="us-ascii"
>
> Hey,
>
> If your simulation handles high number of photons, it might be possible
> that you need more memory to run the simulation. I once had the similar
> problem, and solved it by running the simulation on a machine with bigger
> memory.
>
> Thanks,
> Sanghyeb(Sam) Lee
>
> PhD Candidate
> Department of Electrical Engineering and Computer Science
> University of Tennessee, Knoxville
> Personal webpage: www.sergeantlee.com
> ________________________________________
> From: gate-users-bounces at lists.opengatecollaboration.org [
> gate-users-bounces at lists.opengatecollaboration.org] on behalf of Manuel
> Reifegerst [Manuel.Reifegerst at uni-duesseldorf.de]
> Sent: 05 November 2012 05:38
> To: Gate Mailing List
> Subject: [Gate-users] Segmentation Violation Error
>
> Hello,
>
> i have an error message in GATE simulations. We have run
> the simulation and always at the end there is this segmentation violation
> error. This is coming up every time i run the simulation, independent of
> the
> parameters (like time or activity) in it.
> Here is shown the bug report, maybe someone have an idea what this means
> and
> how i can fix it:
>
> "---------------------------------------------------------------
>
> [Acquisition-0] Slice 7 from 7 to 8 s [slice=1 s], final stop at 10 s.
> [Acquisition-0]
>
> [Acquisition-0] Slice 8 from 8 to 9 s [slice=1 s], final stop at 10 s.
> [Acquisition-0]
>
> [Acquisition-0] Slice 9 from 9 to 10 s [slice=1 s], final stop at 10 s.
> [Core-0] End of macro benchPET.mac
>
>  *** Break *** segmentation violation
>
>
>
> ===========================================================
> There was a crash.
> This is the entire stack trace of all threads:
> ===========================================================
> #0  0x00007fb476a058be in waitpid () from /lib64/libc.so.6
> #1  0x00007fb47699d736 in do_system () from /lib64/libc.so.6
> #2  0x00007fb47f3c3900 in TUnixSystem::StackTrace() () from
> /home/manuel/gate_user/root/lib/libCore.so
> #3  0x00007fb47f3c6143 in TUnixSystem::DispatchSignals(ESignals) () from
> /home/manuel/gate_user/root/lib/libCore.so
> #4  <signal handler called>
> #5  0x00007fb477192d93 in std::_Rb_tree_increment(std::_Rb_tree_node_base*)
> () from /usr/lib64/libstdc++.so.6
> #6  0x00007fb482a435f6 in GatePhysicsList::~GatePhysicsList() () from
> /home/manuel/gate_user/gate_v6.1/tmp/Linux-g++/Gate/libGate.so
> #7  0x00007fb482a43a09 in GatePhysicsList::~GatePhysicsList() () from
> /home/manuel/gate_user/gate_v6.1/tmp/Linux-g++/Gate/libGate.so
> #8  0x00007fb47c117447 in G4RunManager::~G4RunManager() () from
> /home/manuel/gate_user/geant4.9.3.p02/lib/Linux-g++/libG4run.so
> #9  0x00007fb482a79e99 in GateRunManager::~GateRunManager() () from
> /home/manuel/gate_user/gate_v6.1/tmp/Linux-g++/Gate/libGate.so
> #10 0x0000000000407d24 in main ()
> ===========================================================
>
>
> The lines below might hint at the cause of the crash.
> If they do not help you then please submit a bug report at
> http://root.cern.ch/bugs. Please post the ENTIRE stack trace
> from above as an attachment in addition to anything else
> that might help us fixing this issue.
> ===========================================================
> #5  0x00007fb477192d93 in std::_Rb_tree_increment(std::_Rb_tree_node_base*)
> () from /usr/lib64/libstdc++.so.6
> #6  0x00007fb482a435f6 in GatePhysicsList::~GatePhysicsList() () from
> /home/manuel/gate_user/gate_v6.1/tmp/Linux-g++/Gate/libGate.so
> #7  0x00007fb482a43a09 in GatePhysicsList::~GatePhysicsList() () from
> /home/manuel/gate_user/gate_v6.1/tmp/Linux-g++/Gate/libGate.so
> #8  0x00007fb47c117447 in G4RunManager::~G4RunManager() () from
> /home/manuel/gate_user/geant4.9.3.p02/lib/Linux-g++/libG4run.so
> #9  0x00007fb482a79e99 in GateRunManager::~GateRunManager() () from
> /home/manuel/gate_user/gate_v6.1/tmp/Linux-g++/Gate/libGate.so
> #10 0x0000000000407d24 in main ()
> ===========================================================
>
>
> Speicherschutzverletzung
>
> --------------------------------------------------------"
>
>
> Root version 5.30
> Gate 6.1
> GeAnt 4.9.3 p02
> CLHEP 2.0.4.7
>
> running on Linux openSuse 12.1 (64 bit)
>
>
>
> Thank you in advance for your help!
>
> Best Regards,
>
> Manuel Reifegerst
>
>
>
>
>
> ------------------------------
>
> Message: 3
> Date: Tue, 6 Nov 2012 11:08:34 +0330
> From: Saeed Heidary <saeedheidary79 at gmail.com>
> To: gate-users at lists.opengatecollaboration.org
> Subject: [Gate-users] Segmentation Violation Error
> Message-ID:
>         <CAAwAR=OYcp02ZYjXrT_K6bHZfEdtrQ87uhfqbv2KzTc=
> YJUjOA at mail.gmail.com>
> Content-Type: text/plain; charset="utf-8"
>
> Dear Manuel
> I advise  to install GATE 6.2
> it is more reliable than 6.1!
> regards
> On Mon, Nov 5, 2012 at 2:30 PM, <
> gate-users-request at lists.opengatecollaboration.org> wrote:
>
> > Send Gate-users mailing list submissions to
> >         gate-users at lists.opengatecollaboration.org
> >
> > To subscribe or unsubscribe via the World Wide Web, visit
> >
> http://lists.opengatecollaboration.org/mailman/listinfo/gate-users
> > or, via email, send a message with subject or body 'help' to
> >         gate-users-request at lists.opengatecollaboration.org
> >
> > You can reach the person managing the list at
> >         gate-users-owner at lists.opengatecollaboration.org
> >
> > When replying, please edit your Subject line so it is more specific
> > than "Re: Contents of Gate-users digest..."
> >
> >
> > Today's Topics:
> >
> >    1. Segmentation Violation Error (Manuel Reifegerst)
> >
> >
> > ----------------------------------------------------------------------
> >
> > Message: 1
> > Date: Mon, 05 Nov 2012 11:38:03 +0100
> > From: Manuel Reifegerst <Manuel.Reifegerst at uni-duesseldorf.de>
> > To: Gate Mailing List <gate-users at lists.opengatecollaboration.org>
> > Subject: [Gate-users] Segmentation Violation Error
> > Message-ID: <5097970B.10702 at uni-duesseldorf.de>
> > Content-Type: text/plain; charset="iso-8859-15"; Format="flowed"
> >
> > Hello,
> >
> > i have an error message in GATE simulations. We have run
> > the simulation and always at the end there is this segmentation violation
> > error. This is coming up every time i run the simulation, independent of
> > the
> > parameters (like time or activity) in it.
> > Here is shown the bug report, maybe someone have an idea what this means
> > and
> > how i can fix it:
> >
> > "---------------------------------------------------------------
> >
> > [Acquisition-0] Slice 7 from 7 to 8 s [slice=1 s], final stop at 10 s.
> > [Acquisition-0]
> >
> > [Acquisition-0] Slice 8 from 8 to 9 s [slice=1 s], final stop at 10 s.
> > [Acquisition-0]
> >
> > [Acquisition-0] Slice 9 from 9 to 10 s [slice=1 s], final stop at 10 s.
> > [Core-0] End of macro benchPET.mac
> >
> >   *** Break *** segmentation violation
> >
> >
> >
> > ===========================================================
> > There was a crash.
> > This is the entire stack trace of all threads:
> > ===========================================================
> > #0  0x00007fb476a058be in waitpid () from /lib64/libc.so.6
> > #1  0x00007fb47699d736 in do_system () from /lib64/libc.so.6
> > #2  0x00007fb47f3c3900 in TUnixSystem::StackTrace() () from
> > /home/manuel/gate_user/root/lib/libCore.so
> > #3  0x00007fb47f3c6143 in TUnixSystem::DispatchSignals(ESignals) () from
> > /home/manuel/gate_user/root/lib/libCore.so
> > #4  <signal handler called>
> > #5  0x00007fb477192d93 in
> std::_Rb_tree_increment(std::_Rb_tree_node_base*)
> > () from /usr/lib64/libstdc++.so.6
> > #6  0x00007fb482a435f6 in GatePhysicsList::~GatePhysicsList() () from
> > /home/manuel/gate_user/gate_v6.1/tmp/Linux-g++/Gate/libGate.so
> > #7  0x00007fb482a43a09 in GatePhysicsList::~GatePhysicsList() () from
> > /home/manuel/gate_user/gate_v6.1/tmp/Linux-g++/Gate/libGate.so
> > #8  0x00007fb47c117447 in G4RunManager::~G4RunManager() () from
> > /home/manuel/gate_user/geant4.9.3.p02/lib/Linux-g++/libG4run.so
> > #9  0x00007fb482a79e99 in GateRunManager::~GateRunManager() () from
> > /home/manuel/gate_user/gate_v6.1/tmp/Linux-g++/Gate/libGate.so
> > #10 0x0000000000407d24 in main ()
> > ===========================================================
> >
> >
> > The lines below might hint at the cause of the crash.
> > If they do not help you then please submit a bug report at
> > http://root.cern.ch/bugs. Please post the ENTIRE stack trace
> > from above as an attachment in addition to anything else
> > that might help us fixing this issue.
> > ===========================================================
> > #5  0x00007fb477192d93 in
> std::_Rb_tree_increment(std::_Rb_tree_node_base*)
> > () from /usr/lib64/libstdc++.so.6
> > #6  0x00007fb482a435f6 in GatePhysicsList::~GatePhysicsList() () from
> > /home/manuel/gate_user/gate_v6.1/tmp/Linux-g++/Gate/libGate.so
> > #7  0x00007fb482a43a09 in GatePhysicsList::~GatePhysicsList() () from
> > /home/manuel/gate_user/gate_v6.1/tmp/Linux-g++/Gate/libGate.so
> > #8  0x00007fb47c117447 in G4RunManager::~G4RunManager() () from
> > /home/manuel/gate_user/geant4.9.3.p02/lib/Linux-g++/libG4run.so
> > #9  0x00007fb482a79e99 in GateRunManager::~GateRunManager() () from
> > /home/manuel/gate_user/gate_v6.1/tmp/Linux-g++/Gate/libGate.so
> > #10 0x0000000000407d24 in main ()
> > ===========================================================
> >
> >
> > Speicherschutzverletzung
> >
> > --------------------------------------------------------"
> >
> >
> > Root version 5.30
> > Gate 6.1
> > GeAnt 4.9.3 p02
> > CLHEP 2.0.4.7
> >
> > running on Linux openSuse 12.1 (64 bit)
> >
> >
> >
> > Thank you in advance for your help!
> >
> > Best Regards,
> >
> > Manuel Reifegerst
> >
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> >
> > _______________________________________________
> > Gate-users mailing list
> > Gate-users at lists.opengatecollaboration.org
> > http://lists.opengatecollaboration.org/mailman/listinfo/gate-users
> >
> > End of Gate-users Digest, Vol 78, Issue 5
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