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 <div class="gmail_quote">On Tue, Nov 6, 2012 at 12:00 PM, <<a href="mailto:gate-users-request@lists.opengatecollaboration.org" target="_blank">gate-users-request@lists.opengatecollaboration.org</a>> wrote: <blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Send Gate-users mailing list submissions to <a href="mailto:gate-users@lists.opengatecollaboration.org">gate-users@lists.opengatecollaboration.org</a> To subscribe or unsubscribe via the World Wide Web, visit <a href="http://lists.opengatecollaboration.org/mailman/listinfo/gate-users" target="_blank">http://lists.opengatecollaboration.org/mailman/listinfo/gate-users</a> or, via email, send a message with subject or body 'help' to <a href="mailto:gate-users-request@lists.opengatecollaboration.org">gate-users-request@lists.opengatecollaboration.org</a> You can reach the person managing the list at <a href="mailto:gate-users-owner@lists.opengatecollaboration.org">gate-users-owner@lists.opengatecollaboration.org</a> When replying, please edit your Subject line so it is more specific than "Re: Contents of Gate-users digest..." 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 <<a href="mailto:manuele.calussi@gmail.com">manuele.calussi@gmail.com</a>> To: gate-users <<a href="mailto:gate-users@lists.opengatecollaboration.org">gate-users@lists.opengatecollaboration.org</a>> Subject: [Gate-users] Annihilation Point Message-ID: <CANFn9kULVZoyw_=JEBVH8OY1t+5smHOVTzs-zQVZPY135=<a href="mailto:QKzQ@mail.gmail.com">QKzQ@mail.gmail.com</a>> 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 -------------- An HTML attachment was scrubbed... URL: <<a href="http://lists.opengatecollaboration.org/mailman/private/gate-users/attachments/20121105/1c91d0cf/attachment-0001.html" target="_blank">http://lists.opengatecollaboration.org/mailman/private/gate-users/attachments/20121105/1c91d0cf/attachment-0001.html</a>> ------------------------------ Message: 2 Date: Mon, 5 Nov 2012 14:46:38 +0000 From: "Lee, Sam (SAM LEE)" <<a href="mailto:slee91@utk.edu">slee91@utk.edu</a>> To: Manuel Reifegerst <<a href="mailto:Manuel.Reifegerst@uni-duesseldorf.de">Manuel.Reifegerst@uni-duesseldorf.de</a>>, Gate Mailing List <<a href="mailto:gate-users@lists.opengatecollaboration.org">gate-users@lists.opengatecollaboration.org</a>> Subject: Re: [Gate-users] Segmentation Violation Error Message-ID: <<a href="mailto:E0BD1EF372F8824EA4717918B50AF3641D1B91B8@SN2PRD0202MB179.namprd02.prod.outlook.com">E0BD1EF372F8824EA4717918B50AF3641D1B91B8@SN2PRD0202MB179.namprd02.prod.outlook.com</a>> 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: <a href="http://www.sergeantlee.com" target="_blank">www.sergeantlee.com</a> ________________________________________ From: <a href="mailto:gate-users-bounces@lists.opengatecollaboration.org">gate-users-bounces@lists.opengatecollaboration.org</a> [<a href="mailto:gate-users-bounces@lists.opengatecollaboration.org">gate-users-bounces@lists.opengatecollaboration.org</a>] on behalf of Manuel Reifegerst [<a href="mailto:Manuel.Reifegerst@uni-duesseldorf.de">Manuel.Reifegerst@uni-duesseldorf.de</a>] 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 <a href="http://root.cern.ch/bugs" target="_blank">http://root.cern.ch/bugs</a>. 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 <<a href="mailto:saeedheidary79@gmail.com">saeedheidary79@gmail.com</a>> To: <a href="mailto:gate-users@lists.opengatecollaboration.org">gate-users@lists.opengatecollaboration.org</a> Subject: [Gate-users] Segmentation Violation Error Message-ID: <CAAwAR=OYcp02ZYjXrT_K6bHZfEdtrQ87uhfqbv2KzTc=<a href="mailto:YJUjOA@mail.gmail.com">YJUjOA@mail.gmail.com</a>> 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, < <a href="mailto:gate-users-request@lists.opengatecollaboration.org">gate-users-request@lists.opengatecollaboration.org</a>> wrote: > Send Gate-users mailing list submissions to > <a href="mailto:gate-users@lists.opengatecollaboration.org">gate-users@lists.opengatecollaboration.org</a> > > To subscribe or unsubscribe via the World Wide Web, visit > <a href="http://lists.opengatecollaboration.org/mailman/listinfo/gate-users" target="_blank">http://lists.opengatecollaboration.org/mailman/listinfo/gate-users</a> > or, via email, send a message with subject or body 'help' to > <a href="mailto:gate-users-request@lists.opengatecollaboration.org">gate-users-request@lists.opengatecollaboration.org</a> > > You can reach the person managing the list at > <a href="mailto:gate-users-owner@lists.opengatecollaboration.org">gate-users-owner@lists.opengatecollaboration.org</a> > > 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 <<a href="mailto:Manuel.Reifegerst@uni-duesseldorf.de">Manuel.Reifegerst@uni-duesseldorf.de</a>> > To: Gate Mailing List <<a href="mailto:gate-users@lists.opengatecollaboration.org">gate-users@lists.opengatecollaboration.org</a>> > Subject: [Gate-users] Segmentation Violation Error > Message-ID: <<a href="mailto:5097970B.10702@uni-duesseldorf.de">5097970B.10702@uni-duesseldorf.de</a>> > 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 > <a href="http://root.cern.ch/bugs" target="_blank">http://root.cern.ch/bugs</a>. 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 > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: < > <a href="http://lists.opengatecollaboration.org/mailman/private/gate-users/attachments/20121105/4fda65b4/attachment-0001.html" target="_blank">http://lists.opengatecollaboration.org/mailman/private/gate-users/attachments/20121105/4fda65b4/attachment-0001.html</a> > > > > ------------------------------ > > _______________________________________________ > Gate-users mailing list > <a href="mailto:Gate-users@lists.opengatecollaboration.org">Gate-users@lists.opengatecollaboration.org</a> > <a href="http://lists.opengatecollaboration.org/mailman/listinfo/gate-users" target="_blank">http://lists.opengatecollaboration.org/mailman/listinfo/gate-users</a> > > End of Gate-users Digest, Vol 78, Issue 5 > ***************************************** > -------------- next part -------------- An HTML attachment was scrubbed... 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