Mohsen Sadat shahabi | 30 Sep 09:45 2014
Picon

surface flux

Hi, Gate users
I want to record all gamma particles that go through a surface or enter a volume either they have interactions(Hit) or do not have any interaction.
can anyone help me to produce this type of output?
best regards
Mohsen
<div><div>
<div dir="ltr">Hi, Gate users</div>
<div dir="ltr">I want to record all gamma particles that go through a surface or enter a volume either they have interactions(Hit) or do not have any interaction.</div>
<div dir="ltr">can anyone help me to produce this type of output?</div>
<div dir="ltr">best regards</div>
<div dir="ltr">Mohsen<br>
</div>
</div></div>
Pedro Correia | 29 Sep 12:33 2014
Picon

Scanner system and coincidences.

Dear Gaters

I wonder if I can use a general scanner system to simulate an experimental setup in which two scintillators
(one LYSO and one BGO) are both read by PMTs, with a gamma source between them, and still have Coincidences
in the root output, or I need to read the Hits/Singles tree separately in Root and build a script to obtain
the coincidences. 

I don’t know if I can use any PET predefined scanner, because the scintillators have different
geometries. 

And instead of one scanner system, what if I have two separated systems, one for each scintillator, I will
still be able to have coincidences between the sensitive detectors of separated scanner systems?

Thank you all

Pedro Correia
PhD Student, University of Aveiro. 
PmB | 26 Sep 21:52 2014
Picon

CLHEP - Link Error

Fellow Gaters,

I am sure I have hit this problem previously, and I can't for the life 
of me recall how to correct it.

I am trying to compile Gate V7.0 and all goes well until linking; I get 
the following error

[100%] Building CXX object 
CMakeFiles/Gate.dir/source/externals/clhep/src/CLHEP/Matrix/Matrix.cc.o
[100%] Building CXX object 
CMakeFiles/Gate.dir/source/externals/clhep/src/CLHEP/RandomObjects/RandomVector.cc.o
[100%] Building CXX object 
CMakeFiles/Gate.dir/source/externals/clhep/src/CLHEP/RandomObjects/RandMultiGauss.cc.o
Linking CXX executable Gate
/usr/bin/ld: cannot find -lCLHEP-2.1.3.1
collect2: ld returned 1 exit status
make[2]: *** [Gate] Error 1
make[1]: *** [CMakeFiles/Gate.dir/all] Error 2
make: *** [all] Error 2

I have defined the following in ccmake

  CLHEP_CONFIG_EXECUTABLE 
/home/peter/Src/GATE/CLHEP/Install/bin/clhep-config
  CLHEP_INCLUDE_DIR /home/peter/Src/GATE/CLHEP/Install/include
  CLHEP_LIBRARY 
/home/peter/Src/GATE/CLHEP/Install/lib64/libCLHEP-2.1.3.1.so

for CLHEP.

Any thoughts will be most appreciated, cheers

Peter

Ali Faiez Taha | 26 Sep 21:18 2014
Picon
Picon

Help on Gate7 segmentation


After compiled and install the programs described in
(http://wiki.opengatecollaboration.org/index.php/New_Compilation_ProcedureV7.0)
 and when execute the Gate, I have the follow erros.

$> Gate princ05_.mac

I am using Rocks Cluster Linux
Kernel :  2.6.32-431.5.1.el6.x86_64 #1 SMP Wed Feb 12 00:41:43 UTC 2014
x86_64 x86_64 x86_64 GNU/Linux

How can I solve this problem ?
Thanks a lot.

===============================================================================

[G4]
[G4] *************************************************************
[G4]  Geant4 version Name: geant4-09-06-patch-03    (14-March-2014)
[G4]                       Copyright : Geant4 Collaboration
[G4]                       Reference : NIM A 506 (2003), 250-303
[G4]                             WWW : http://cern.ch/geant4
[G4] *************************************************************
[G4]
[Core-0] Initialization of geometry
[Core-0] Initialization of physics
[Physic-0] WARNING: manual physic lists are being deprecated.
Please, use physic list builder mechanism instead. Related documentation
can be found at:
http://wiki.opengatecollaboration.org/index.php/Users_Guide_V7.0:Setting_up_the_physics
[Core-0] Initialization of actors
[Core-0]
[Core-0]
**********************************************************************
[Core-0]  GATE version name: gate_v7.0

[Core-0]                     Copyright : OpenGATE Collaboration

[Core-0]                     Reference : Phys. Med. Biol. 49 (2004)
4543-4561
[Core-0]                     Reference : Phys. Med. Biol. 56 (2011)
881-901
[Core-0]                     WWW : http://www.opengatecollaboration.org

[Core-0]
**********************************************************************
[Core-0]
[Core-0] You are using Geant4 version 9.6.3
[Core-0] Starting macro princ05_.mac
 CREATED THE COMMAND /gate/systems/cylindricalPET/addAnewRsector
===== XML PATH ====: ./Materials.xml

 *** Break *** segmentation violation

===========================================================
There was a crash.
This is the entire stack trace of all threads:
===========================================================
#0  0x0000003fbdeabf9e in waitpid () from /lib64/libc.so.6
#1  0x0000003fbde3e899 in do_system () from /lib64/libc.so.6
#2  0x00007ff2b4fca548 in TUnixSystem::StackTrace() () from
/state/partition1/home/Gate7/Root/root/lib/libCore.so
#3  0x00007ff2b4fc93c3 in TUnixSystem::DispatchSignals(ESignals) () from
/state/partition1/home/Gate7/Root/root/lib/libCore.so
#4  <signal handler called>
#5  0x0000003fbdf28190 in __strncmp_sse42 () from /lib64/libc.so.6
#6  0x0000003fc9e5e465 in __xmlParserInputBufferCreateFilename () from
/usr/lib64/libxml2.so.2
#7  0x0000003fc9e3380d in xmlNewInputFromFile () from
/usr/lib64/libxml2.so.2
#8  0x0000003fc9e37ac6 in xmlCreateURLParserCtxt () from
/usr/lib64/libxml2.so.2
#9  0x0000003fc9e4ea8e in xmlSAXParseFileWithData () from
/usr/lib64/libxml2.so.2
#10 0x00000000007e6af0 in GateXMLDocument::GateXMLDocument(G4String
const&) ()
#11 0x00000000005c4319 in
GateMaterialDatabase::ReadMaterialFromDBFile(G4String const&) ()
#12 0x00000000005c62fb in GateMaterialDatabase::GetMaterial(G4String
const&) ()
#13 0x00000000005ab808 in GateVVolume::DefineOwnMaterials() ()
#14 0x00000000005a77f0 in GateVolumeMessenger::SetNewValue(G4UIcommand*,
G4String) ()
#15 0x00007ff2b58aec2a in G4UIcommand::DoIt(G4String) () from
/state/partition1/home/Gate7/geant4.9.6.p03-install/lib64/libG4intercoms.so
#16 0x00007ff2b58baa63 in G4UImanager::ApplyCommand(char const*) () from
/state/partition1/home/Gate7/geant4.9.6.p03-install/lib64/libG4intercoms.so
#17 0x00007ff2b58a0ac7 in G4UIbatch::ExecCommand(G4String const&) ()
from
/state/partition1/home/Gate7/geant4.9.6.p03-install/lib64/libG4intercoms.so
#18 0x00007ff2b58a1a4b in G4UIbatch::SessionStart() () from
/state/partition1/home/Gate7/geant4.9.6.p03-install/lib64/libG4intercoms.so
#19 0x00007ff2b58b8cb3 in G4UImanager::ExecuteMacroFile(char const*) ()
from
/state/partition1/home/Gate7/geant4.9.6.p03-install/lib64/libG4intercoms.so
#20 0x00007ff2b58b538f in
G4UIcontrolMessenger::SetNewValue(G4UIcommand*, G4String) () from
/state/partition1/home/Gate7/geant4.9.6.p03-install/lib64/libG4intercoms.so
#21 0x00007ff2b58aec2a in G4UIcommand::DoIt(G4String) () from
/state/partition1/home/Gate7/geant4.9.6.p03-install/lib64/libG4intercoms.so
#22 0x00007ff2b58baa63 in G4UImanager::ApplyCommand(char const*) () from
/state/partition1/home/Gate7/geant4.9.6.p03-install/lib64/libG4intercoms.so
#23 0x00000000004eaf78 in main ()
===========================================================

===============================================================================
Ahmed Elmekawy | 26 Sep 21:02 2014
Picon

Interfile Format

Dear All,

I have a problem to attach the analyze format image for the voxelized phantom example and get a data instead of the interfile format in the same example, so I am trying to convert the dicom format to interfile format for the image, I tried by a lot of programs,  but all of them not work, I got a lot of errors,  any idea how the analyze format image work with the voxelized phantom example instead of the interfile format or how I can convert the dicom format to interfile format.


Thanks in Advance.


Regards,
Ahmed
<div><div dir="ltr">
<div>
<div>
<div>Dear All,<br><br>
</div>I have a problem to attach the analyze format image for the voxelized phantom example and get a data&nbsp;<span class=""><span class=""><span class="">instead of</span></span> the interfile format in the same example</span>, so I am trying to convert the dicom format to interfile format for the image, I tried by a lot of programs,&nbsp; but all of them not work, I got a lot of errors,&nbsp; any idea how the analyze format image work with the voxelized phantom example <span class=""><span class=""><span class="">instead of</span></span> the interfile format </span> or how I can convert the dicom format to interfile format.<br><br><br>
</div>Thanks in Advance.<br><br><br>
</div>Regards,<br>Ahmed<br>
</div></div>
Kris Thielemans | 26 Sep 09:23 2014
Picon

2014 STIR Users' & Developers' meeting at MIC, Seattle: call for registration

Dear all

We wish to announce the 2014 STIR User's & Developer's meeting . Thursday
the 13th of November during the 2014 IEEE Nuclear Sciences Symposium &
Medical Imaging Conference (18.30-20.30 . Room 303 . Washington State
Convention Center . Seattle, WA USA). If you are interested in attending
please reserve a place

http://www.eventbrite.co.uk/e/2014-stir-users-developers-meeting-registratio
n-12852519231

The event is free but priority will be given to those that have reserved.
Furthermore, thanks to our generous sponsors, we are able to offer a boxed
dinner for those reserving and coming before 18.15 (please send any dietary
requirements to Charalampos Tsoumpas <C.Tsoumpas@...>.

For up-to-date information, including the programme, please always check
STIR website: http://stir.sf.net

Kris Thielemans
Senior Lecturer at University College London
Institute for Nuclear Medicine, UCL Hospital
235 Euston Road, London NW1 2BU, UK

Taschereau, Richard | 25 Sep 20:13 2014

Hoffman brain phantom

Hello everybody,

I’m looking for a numerical Hoffman brain phantom (I used to have one but it eventually got lost after
several computer failures/upgrades). Does anyone have a copy available for download?

Many thanks,
Richard

P.S. I saw the brain phantom in the examples, but it is not detailed enough.

Richard Taschereau, Ph.D.
Associate Researcher
UCLA Crump Institute for Molecular Imaging
570 Westwood Plaza, Building 114, room 4350-C
Los Angeles, CA 90095-1770
Phone: (310) 825-0697
Fax:     (310) 206-8975

________________________________

IMPORTANT WARNING: This email (and any attachments) is only intended for the use of the person or entity to
which it is addressed, and may contain information that is privileged and confidential. You, the
recipient, are obligated to maintain it in a safe, secure and confidential manner. Unauthorized
redisclosure or failure to maintain confidentiality may subject you to federal and state penalties. If
you are not the intended recipient, please immediately notify us by return email, and delete this message
from your computer.
Zhang,Yuxuan | 25 Sep 20:06 2014

Gate v7.0 optical photon energy output issue

Hi,

 

In the previous versions of Gate (6.2 and older), the energy definition of the

optical photon output is the number of photons that hit the detector. However,

in the newest Gate (v7.0), the energy seems to be changed to the sum of real energy

of each photons (in MeV). I think this change might not be necessary.

 

I am using the optical photons simulation to study the detector design with PMTs and SiPMs.

Both the PMT and SiPM are usually working in photon counting mode in the

PET system and they don't have energy resolution to the incident optical photons.

The new change in the Gate 7.0 of output the absolute energy instead of the photon counts

for the optical simulation make the such study more difficult.

 

If this change is necessary for other applications such as florescence study or something else,

maybe it is better to add a switch to let user to select the output mode between the absolute

energy and the number of count.

 

 

<div>
<div>
<div>
<p>Hi,</p>
<p>&nbsp;</p>
<p>In the&nbsp;previous versions of Gate (6.2 and older), the energy&nbsp;definition<a></a> of the</p>
<p>optical photon output is the number of photons that hit the detector. However,</p>
<p>in the newest Gate (v7.0<a></a><a></a><a></a><a></a><a></a><a></a><a></a><a></a>), the energy seems to be&nbsp;changed&nbsp;to the sum of real energy</p>
<p>of each photons (in MeV<a></a><a></a><a></a><a></a><a></a><a></a><a></a><a></a>). I think this change might not be necessary.</p>
<p>&nbsp;</p>
<p>I am using the optical photons simulation to study the detector design with&nbsp;PMTs<a></a><a></a><a></a><a></a><a></a><a></a><a></a><a></a> and SiPMs<a></a><a></a><a></a><a></a><a></a><a></a><a></a><a></a>.</p>
<p>Both the PMT and&nbsp;SiPM<a></a><a></a><a></a><a></a><a></a><a></a><a></a><a></a> are usually working in photon counting mode in the</p>
<p>PET system and&nbsp;they don't have energy resolution to the incident optical photons.</p>
<p>The new change in the Gate 7.0&nbsp;of output the absolute energy instead of the photon counts</p>
<p>for the optical&nbsp;simulation<a></a><a></a><a></a> make the such study more difficult.
</p>
<p>&nbsp;</p>
<p>If this change is necessary for other applications such as&nbsp;florescence<a></a><a></a><a></a><a></a><a></a> study or&nbsp;something<a></a><a></a> else,</p>
<p>maybe it is better to add a switch&nbsp;to let user&nbsp;to select the output&nbsp;mode between the absolute</p>
<p>energy and&nbsp;the number of&nbsp;count.</p>
<p>&nbsp;</p>
<p>&nbsp;</p>
<p></p>
</div>
</div>
</div>
shahrokh nasseri | 25 Sep 09:38 2014
Picon

Using variance reduction techniques (splitting and Russian roulette) for selective (daughter) volumes?

Hi GATE users

How can restrict variance reduction techniques in the certain volume?
Or in other words, how can I use variance reduction techniques for
selective volumes (daughter volumes)?
In GATE manual, it is mentioned to use volume Filter (volumeFilter),
but this filter is not worked with processes module in physics. For
example, I want to use splitting in water phantom, how can I do?
In other hands, if I use the following command, splitting is
activated/occurred in the world volume and all children of world
volume, but I want to split events only in water phantom.
/gate/physics/processes/Bremsstrahlung/activateSplitting e- 1000

Thanks a lot for your comments.
Shahrokh
Amy Meldrum | 24 Sep 18:26 2014

Multiple Sources - How GATE Chooses

Gate Users,

I am hoping someone can clarify something for me that I cannot seem to find in the Users Guide. If I define multiple sources in a simulation, and then use the /setTotalNumberOfPrimaries command to set the number of primary particles run, Does GATE randomly choose between the defined sources as to which one starts the next primary particle? And if so, does each source have an equal probability of being chosen?

Thank you,

-Amy
<div><div dir="ltr">Gate Users,<div><br></div>
<div>I am hoping someone can clarify something for me that I cannot seem to find in the Users Guide. If I define multiple sources in a simulation, and then use the /setTotalNumberOfPrimaries command to set the number of primary particles run, Does GATE randomly choose between the defined sources as to which one starts the next primary particle? And if so, does each source have an equal probability of being chosen?</div>
<div><br></div>
<div>Thank you,</div>
<div><br></div>
<div>-Amy</div>
</div></div>
Ali User | 23 Sep 11:14 2014
Picon

some simple question about geometry, material and visualization

Hi dear Gate users

I have just started to use vGate (virtual Gate) and have some problems that I don't know how to solve them. here are my problems:

I tried to define a geometry after I defined the directory of the materials, but Gate stopped running.
here is my macro:

Idle> /gate/geometry/setMaterialDatabase /home/gate/Progs/Gate//gate_v6.2/Materials.xml
Idle> gate/world/daughters/name H
Idle> gate/world/daughters/insert box
/home/gate/Progs/Gate/gate_v6.2/source/geometry/src/GateMaterialDatabase.cc (l.132): GateMaterialDatabase: could not find the definition for material 'Vacuum' in material files
gate <at> vgate:~$ 

even when I changed the directory from "Materials.xml" to "GateMaterials.db", some warnings appeared as follow:


Idle> /gate/geometry/setMaterialDatabase /home/gate/Progs/Gate/gate_v6.2/GateMaterials.db
Idle> gate/world/daughters/name H
Idle> gate/world/daughters/insert box
I/O warning : failed to load external entity "Materials.xml"
I/O warning: Discard the previous warning if your simulation doesn't transport OPTICAL PHOTONS. 
Otherwise, please copy the Materials.xml file from the gate-source directory in the directory where you run your main macro.

I ignored the warning and continued entering commands, but I faced similar problem when I set "water" for material:  

Idle> /gate/geometry/setMaterialDatabase /home/gate/Progs/Gate/gate_v6.2/GateMaterials.db
Idle> gate/world/daughters/name H
Idle> gate/world/daughters/insert box
I/O warning : failed to load external entity "Materials.xml"
I/O warning: Discard the previous warning if your simulation doesn't transport OPTICAL PHOTONS. 
Otherwise, please copy the Materials.xml file from the gate-source directory in the directory where you run your main macro.
Idle> gate/H/geometry/setXLength 10. cm
Idle> gate/H/geometry/setYLength 20. cm
Idle> gate/H/geometry/setZLength 30. cm
Idle> gate/H/setMaterial water
/home/gate/Progs/Gate/gate_v6.2/source/geometry/src/GateMaterialDatabase.cc (l.132): GateMaterialDatabase: could not find the definition for material 'water' in material files
gate <at> vgate:~$ 

once again, when I replaced "water" with "LSO", warning message appeared: 
 

Idle> /gate/geometry/setMaterialDatabase /home/gate/Progs/Gate/gate_v6.2/GateMaterials.db
Idle> gate/world/daughters/name H
Idle> gate/world/daughters/insert box
I/O warning : failed to load external entity "Materials.xml"
I/O warning: Discard the previous warning if your simulation doesn't transport OPTICAL PHOTONS. 
Otherwise, please copy the Materials.xml file from the gate-source directory in the directory where you run your main macro.
Idle> gate/H/geometry/setXLength 10. cm
Idle> gate/H/geometry/setYLength 20. cm
Idle> gate/H/geometry/setZLength 30. cm
Idle> gate/H/setMaterial LSO
I/O warning : failed to load external entity "Materials.xml"
I/O warning: Discard the previous warning if your simulation doesn't transport OPTICAL PHOTONS. 
Otherwise, please copy the Materials.xml file from the gate-source directory in the directory where you run your main macro.

I also tried to visualize the volume created, but after I entered the following commands it did not work and no graphical volume was shown.

Idle> gate/H/vis/setColor red    
Idle> gate/H/vis/forceWireframe


I would be grateful to guide me.
Thank you so much of your time 
<div><div dir="ltr">
<div>Hi dear Gate users</div>
<div><br></div>
<div>I have just started to use vGate (virtual Gate) and have some problems that I don't know how to solve them. here are my problems:</div>
<div><br></div>
<div>I tried to define a geometry after I defined the directory of the materials, but Gate stopped running.</div>
<div>here is my macro:</div>
<div><br></div>
<div>
<div>Idle&gt; /gate/geometry/setMaterialDatabase /home/gate/Progs/Gate//gate_v6.2/Materials.xml</div>
<div>Idle&gt; gate/world/daughters/name H</div>
<div>Idle&gt; gate/world/daughters/insert box</div>
<div>/home/gate/Progs/Gate/gate_v6.2/source/geometry/src/GateMaterialDatabase.cc (l.132): GateMaterialDatabase: could not find the definition for material 'Vacuum' in material files</div>
<div>gate <at> vgate:~$&nbsp;</div>
</div>
<div><br></div>
<div>even when I changed the directory from "Materials.xml" to "GateMaterials.db", some warnings appeared as follow:</div>
<div><br></div>
<div><br></div>
<div>
<div>Idle&gt; /gate/geometry/setMaterialDatabase /home/gate/Progs/Gate/gate_v6.2/GateMaterials.db</div>
<div>Idle&gt; gate/world/daughters/name H</div>
<div>Idle&gt; gate/world/daughters/insert box</div>
<div>I/O warning : failed to load external entity "Materials.xml"</div>
<div>I/O warning: Discard the previous warning if your simulation doesn't transport OPTICAL PHOTONS.&nbsp;</div>
<div>Otherwise, please copy the Materials.xml file from the gate-source directory in the directory where you run your main macro.</div>
<div><br></div>
<div>I ignored the warning and continued entering commands, but I faced similar problem when I set "water" for material: &nbsp;</div>
</div>
<div><br></div>
<div>
<div>Idle&gt; /gate/geometry/setMaterialDatabase /home/gate/Progs/Gate/gate_v6.2/GateMaterials.db</div>
<div>Idle&gt; gate/world/daughters/name H</div>
<div>Idle&gt; gate/world/daughters/insert box</div>
<div>I/O warning : failed to load external entity "Materials.xml"</div>
<div>I/O warning: Discard the previous warning if your simulation doesn't transport OPTICAL PHOTONS.&nbsp;</div>
<div>Otherwise, please copy the Materials.xml file from the gate-source directory in the directory where you run your main macro.</div>
<div>Idle&gt; gate/H/geometry/setXLength 10. cm</div>
<div>Idle&gt; gate/H/geometry/setYLength 20. cm</div>
<div>Idle&gt; gate/H/geometry/setZLength 30. cm</div>
<div>Idle&gt; gate/H/setMaterial water</div>
<div>/home/gate/Progs/Gate/gate_v6.2/source/geometry/src/GateMaterialDatabase.cc (l.132): GateMaterialDatabase: could not find the definition for material 'water' in material files</div>
<div>gate <at> vgate:~$&nbsp;</div>
</div>
<div><br></div>
<div>once again, when I replaced "water" with "LSO", warning message appeared:&nbsp;</div>
<div>&nbsp;</div>
<div><br></div>
<div>
<div>Idle&gt; /gate/geometry/setMaterialDatabase /home/gate/Progs/Gate/gate_v6.2/GateMaterials.db</div>
<div>Idle&gt; gate/world/daughters/name H</div>
<div>Idle&gt; gate/world/daughters/insert box</div>
<div>I/O warning : failed to load external entity "Materials.xml"</div>
<div>I/O warning: Discard the previous warning if your simulation doesn't transport OPTICAL PHOTONS.&nbsp;</div>
<div>Otherwise, please copy the Materials.xml file from the gate-source directory in the directory where you run your main macro.</div>
<div>Idle&gt; gate/H/geometry/setXLength 10. cm</div>
<div>Idle&gt; gate/H/geometry/setYLength 20. cm</div>
<div>Idle&gt; gate/H/geometry/setZLength 30. cm</div>
<div>Idle&gt; gate/H/setMaterial LSO</div>
<div>I/O warning : failed to load external entity "Materials.xml"</div>
<div>I/O warning: Discard the previous warning if your simulation doesn't transport OPTICAL PHOTONS.&nbsp;</div>
<div>Otherwise, please copy the Materials.xml file from the gate-source directory in the directory where you run your main macro.</div>
<div><br></div>
<div>I also tried to visualize the volume created, but after I entered the following commands it did not work and no graphical volume was shown.<br>
</div>
<div><br></div>
<div>Idle&gt; gate/H/vis/setColor red &nbsp; &nbsp;</div>
<div>Idle&gt; gate/H/vis/forceWireframe</div>
</div>
<div><br></div>
<div><br></div>
<div>I would be grateful to guide me.</div>
<div>Thank you so much of your time&nbsp;</div>
</div></div>

Gmane