[Gate-users] Sinograms out of Root output

Marc Chamberland MarcChamberland at cmail.carleton.ca
Wed Nov 7 15:35:07 CET 2012 

Hi,

On the Gate website, they provide a link to a utility that can read the Root file and bin the coincidences into Michelograms and projection files. This utility was provided graciously by Ross Schmidtlein and Sadek Nehmeh.

Here's the link: http://www.opengatecollaboration.org/sites/opengatecollaboration.org/files/Bin_GATE_v1.0.c

You'll need to modify the source code to match your scanner.

Marc



__________________________

Marc Chamberland, MSc
PhD candidate
Department of Physics
Carleton University
Ottawa (ON)

Le 2012-11-07 à 4:19 AM, jehangir khan <jehangir.kahn at gmail.com>
 a écrit :

> Dear Gate users!
> 
> 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 Wed, Nov 7, 2012 at 9:19 AM, <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. Re: Annihilation Point (Seb)
>    2. Simulating back-to-back photons with non-collinearity
>       (Jonathan Poon)
>    3. Re: Gate-users Digest, Vol 78, Issue 6 (jehangir khan)
> 
> 
> ----------------------------------------------------------------------
> 
> Message: 1
> Date: Tue, 06 Nov 2012 16:28:04 +0100
> From: Seb <sebastien.jan at cea.fr>
> To: gate-users at lists.opengatecollaboration.org
> Subject: Re: [Gate-users] Annihilation Point
> Message-ID: <50992C84.6010505 at cea.fr>
> Content-Type: text/plain; charset="iso-8859-1"; Format="flowed"
> 
> Hi
> This option is disable since the release 6.0.
> If you want to use it, you need to modify in the code:
> ------------------
> file :GateToRoot.cc
> line 126: m_recordFlag = 0; // Design to embrace obsolete functions
> (histogram, recordVoxels, ...)
> by m_recordFlag =1;
> ------------------
> And then, recompile Gate.
> Cheers
> Seb
> 
> > 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
> >
> >
> > _______________________________________________
> > Gate-users mailing list
> > Gate-users at lists.opengatecollaboration.org
> > http://lists.opengatecollaboration.org/mailman/listinfo/gate-users
> 
> 
> --
> -------------------
> S?bastien JAN, PhD
> Groupe de Recherche en Physique Bio-M?dicale
> CEA - I?BM - Service Hospitalier Fr?d?ric Joliot
> 4 pl. du G?n?ral Leclerc 91401 Orsay
> +33 1 69 86 78 37
> 
> -------------------------------------
> http://www.opengatecollaboration.org/
> -------------------------------------
> 
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> 
> ------------------------------
> 
> Message: 2
> Date: Tue, 6 Nov 2012 16:33:01 -0800
> From: Jonathan Poon <jkpoon at ucdavis.edu>
> To: gate-users <gate-users at lists.opengatecollaboration.org>
> Subject: [Gate-users] Simulating back-to-back photons with
>         non-collinearity
> Message-ID:
>         <CAFTDE3Q=YZcKTdrhiu_i+CLi1WYpxS4WK7qT=VZ_6+YwU5=wzA at mail.gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1
> 
> Hi Everyone,
> 
> I'm looking to simulate a source with no attenuation.  Is it possible
> to enable non-collinearity for back-to-back photons?  Or do I have to
> enable a e+ source inside an attenuating object in order to model
> non-collinearity and positron range?   Thanks for your help!
> 
> Jonathan
> 
> 
> ------------------------------
> 
> Message: 3
> Date: Wed, 7 Nov 2012 09:16:50 +0100
> From: jehangir khan <jehangir.kahn at gmail.com>
> To: gate-users at lists.opengatecollaboration.org
> Subject: Re: [Gate-users] Gate-users Digest, Vol 78, Issue 6
> Message-ID:
>         <CAOK_3n5ayvJY6wfWjQJKJ47yLsoKGzB2yS9gpFXn9oKcX6x6Xw at mail.gmail.com>
> Content-Type: text/plain; charset="iso-8859-1"
> 
> 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:
> 
> > 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. 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 --------------
> > An HTML attachment was scrubbed...
> > URL: <
> > http://lists.opengatecollaboration.org/mailman/private/gate-users/attachments/20121105/1c91d0cf/attachment-0001.html
> > >
> >
> > ------------------------------
> >
> > 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
> > >
> > > -------------- next part --------------
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> > > >
> > >
> > > ------------------------------
> > >
> > > _______________________________________________
> > > Gate-users mailing list
> > > Gate-users at lists.opengatecollaboration.org
> > > http://lists.opengatecollaboration.org/mailman/listinfo/gate-users
> > >
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> > ------------------------------
> >
> > _______________________________________________
> > Gate-users mailing list
> > Gate-users at lists.opengatecollaboration.org
> > http://lists.opengatecollaboration.org/mailman/listinfo/gate-users
> >
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> 
> _______________________________________________
> Gate-users mailing list
> Gate-users at lists.opengatecollaboration.org
> http://lists.opengatecollaboration.org/mailman/listinfo/gate-users
> 
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> *****************************************
> 
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