[gate-users] Re: gate-users Digest, Vol 17, Issue 17
Carey Floyd
cef at deckard.duhs.duke.edu
Thu Aug 11 13:28:05 CEST 2005
This may seem like a silly or leading question but is posted in good
faith with only good intentions. I have been using GEANT4 (not GATE)
for about 20 months now to simulate a unique imaging environment in
which I am using a neutron beam to stimulate characteristic gamma
emission from a target (body). The beam is translated and the target is
rotated to achieve CT as in first generation x-ray CT. Since I am
modeling a tomographic system and am not very experienced with C++, I
was attracted to GATE. It seems, however, that most of my real work
would still have to be at the GEANT4 level and that I would not be able
to benefit much from the excellent work that you have all done to make
it pleasent and easy to modify models in GATE. Am I being stuborn or
would it make sense for me to embrace the new world and try to switch
to GATE? I realize that no one can answer that for certain, but has
anyone had success in using GATE for an application other than
PET/SPECT. Mine is sort of like SPECT with a stimulated source rather
than a naturally radioactive source. The gamma energies are between 300
keV and 6.6 MeV though that should not matter if GATE retains all of
the physical interactions that GEANT4 does. Advice is welcome.
Carey Floyd PhD
Professor of Radiology and Biomedical Engineering
Director of Diagnostic Imaging Track, Medical Physics Program
Duke University
On Aug 11, 2005, at 6:00 AM, gate-users-request at lphe1pet1.epfl.ch wrote:
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> Today's Topics:
>
> 1. Simulation of scintillator and PMT (Yun Dong)
> 2. Variable Substitution (GATE Simulation)
> 3. help on installation on SuSE Linux gcc 3.3.3 (Chen, Yu)
> 4. Re: gate-users Digest, Vol 17, Issue 15 (Christian Wietholt)
> 5. Re: Re: gate-users Digest, Vol 17, Issue 15 (Sebastien JAN)
> 6. Re: Simulation of scintillator and PMT (Sebastien JAN)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Wed, 10 Aug 2005 10:25:38 -0600
> From: Yun Dong <dongyun at iit.edu>
> Subject: [gate-users] Simulation of scintillator and PMT
> To: gate-users at lphe1pet1.epfl.ch
> Message-ID: <11167e41111a76.1111a7611167e4 at iit.edu>
> Content-Type: text/plain; charset=us-ascii
>
> Hi all,
> Is it possible to simulate PET detector by GATE, such as a block of
> 8*8
> crystal coupled by 2*2 PMT with slotted lightguide. I just want to get
> some simulation investigation about performance of scintillator-PMT,
> especially flood field image. Thanks.
>
> Best regards
> Yun Dong
>
>
>
> ------------------------------
>
> Message: 2
> Date: Wed, 10 Aug 2005 15:50:41 -0400
> From: GATE Simulation <peter.bloomfield at camhpet.ca>
> Subject: [gate-users] Variable Substitution
> To: gate-users at lphe1pet1.epfl.ch
> Message-ID: <200508101550.41404.peter.bloomfield at camhpet.ca>
> Content-Type: text/plain; charset="utf-8"
>
>
> Sorry this is a long winded email, and is really for reference.
>
> I have the following setup
> OS - Fedora Core 4
> gcc - gcc (GCC) 4.0.1
> GATE : V2.2.0
> Geant4 : Geant4_7.0_p01
> CLHEP : 1.8.1
> Root : V4.04/02f
>
> Everything compiled and I checked the installation using the PET
> benchmark and all seemed good.
>
> The problem I came across is the passing of alias names and values
> using the -a argument on the Gate command line.
>
> Issuing the following
> Gate -a DATA_FILE junk
> produced the following output
> *************************************************************
> Geant4 version $Name: geant4-07-00-patch-01 $ (23-February-2005)
> Copyright : Geant4 Collaboration
> Reference : NIM A 506 (2003), 250-303
> WWW : http://cern.ch/geant4
> *************************************************************
>
> Time set to (s) 0
> Visualization Manager instantiating...
> Visualization Manager initialising...
> Registering graphics systems...
>
> You have successfully chosen to use the following graphics systems.
> Current available graphics systems are:
> DAWNFILE (DAWNFILE)
> VRML1FILE (VRML1FILE)
> VRML2FILE (VRML2FILE)
> OpenGLImmediateX (OGLIX)
> OpenGLStoredX (OGLSX)
> /control/alias junk "junk"
> . . .
>
> the /control/alias line is incorrect, it should read
> /control/alias DATA_FILE "junk"
>
> I corrected this in the Gate source code by changing the line
> G4String newCommand = G4String("/control/alias ") + argv[++nextArg] +
> " \"" + argv[++nextArg] + "\"";
> to
> G4String AliasName = argv[++nextArg] ;
> G4String AliasValue = argv[++nextArg] ;
> G4String newCommand = G4String("/control/alias ") + AliasName + " \""
> + AliasValue + "\"";
>
> I do not know what the difference is between the two pieces of code
> but a compilation warning
> Gate.cc:184: warning: operation on ‘nextArg’ may be undefined
> no longer appeared on compilation with the code change, and so I
> assume that it is a compiler 'problem'.
>
> Can anyone else throw some light on this,
>
>
> Cheers
>
>
> Peter
>
>
>
>
>
>
> ------------------------------
>
> Message: 3
> Date: Wed, 10 Aug 2005 18:43:31 -0400
> From: "Chen, Yu" <Yu.Chen at umassmed.edu>
> Subject: [gate-users] help on installation on SuSE Linux gcc 3.3.3
> To: "GATE feedback and helpline for Users"
> <gate-users at lphe1pet1.epfl.ch>
> Message-ID:
>
> <782EA7F07D3AA342AC5124CF24C70D780150E7DA at edunivmail04.ad.umassmed.edu>
>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Hi,
>
> When I try to make Gate in SuSE Linux gcc 3.3.3:
>
> Reading specs from /usr/lib64/gcc-lib/x86_64-suse-linux/3.3.3/specs
> Configured with: ../configure --enable-threads=posix --prefix=/usr
> --with-local-prefix=/usr/local --infodir=/usr/share/info
> --mandir=/usr/share/man --enable-languages=c,c++,f77,objc,java,ada
> --disable-checking --libdir=/usr/lib64 --enable-libgcj
> --with-gxx-include-dir=/usr/include/g++ --with-slibdir=/lib64
> --with-system-zlib --enable-shared --enable-__cxa_atexit
> x86_64-suse-linux
> Thread model: posix
> gcc version 3.3.3 (SuSE Linux)
>
> the error occurred:
>
> Creating/replacing object files in ./tmp/Linux-g++/Gate/libGate.a ...
> ar: creating ./tmp/Linux-g++/Gate/libGate.a
> Compiling Gate.cc ...
> Using granular libraries ...
> Linking Gate ...
> /usr/lib64/gcc-lib/x86_64-suse-linux/3.3.3/../../../../x86_64-suse-
> linux/bin/ld: cannot find -lXt
> collect2: ld returned 1 exit status
> make: *** [bin/Linux-g++/Gate] Error 1
>
>
> What can I do?
>
> Yu
>
> Yu Chen, Ph.D.
> University of Massachusetts Medical School
> Division of Nuclear Medicine
> 55 Lake Avenue North
> Worcester, MA 01655-0243
> Phone: (508) 856-6123
> Fax: (508) 856-4572
>
>
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> ------------------------------
>
> Message: 4
> Date: Thu, 11 Aug 2005 09:02:10 +0000
> From: Christian Wietholt <cwietholt at nhri.org.tw>
> Subject: [gate-users] Re: gate-users Digest, Vol 17, Issue 15
> To: gate-users at lphe1pet1.epfl.ch
> Message-ID: <200508110902.10395.cwietholt at nhri.org.tw>
> Content-Type: text/plain; charset=iso-8859-1
>
>> Message: 3
>> Date: Wed, 10 Aug 2005 16:20:43 +0000
>> From: Christian Wietholt <cwietholt at nhri.org.tw>
>> Subject: [gate-users] spblurring folow-up
>> To: gate-users at lphe1pet1.epfl.ch
>> Message-ID: <200508101620.43733.cwietholt at nhri.org.tw>
>> Content-Type: text/plain; charset=iso-8859-1
>>
>
> Dear all,
>
> Yesterday I posted below message about my troubles with the spblurring
> functionality in Gate. After getting really desperate I decided this
> morning
> to take a look at the source code. I made the following changes to
> GateSpblurring.cc
>
> I changed line 77 from :
>
> G4double PzNew = Pz;
>
> to
>
> G4double PzNew = G4RandGauss::shoot(Pz,m_spresolution/2.35);
>
> After some testing, it seems to have resolved the problems I mentioned
> below.
> I was hoping for some comments, just to verify if I am doing anything
> wrong
> with this change.
>
> I would appreciate your input.
>
> Best Regards,
>
> Christian
>
>> Dear all,
>>
>> I know I have been posting a lot about the spblurring functionality in
>> Gate, and I apologize for any unnecessary posts. As I mentioned in a
>> previous post, the blurring does not have any effect on the globalPosZ
>> variable in gateSingles.dat file. But, when I want to create an image
>> from
>> the ASCII output for a 0 degree projection, don't I use globalPosZ as
>> the
>> value for the ordinate, and the globalPosY as the value for the
>> abscissa in
>> the projection image. Please correct me if I am wrong. If spblurring
>> does
>> not have any effect on globalPosZ, how can I create a representative
>> projection image?
>>
>> In my simulation I simulated a pointsource projecting through a 5mm
>> pinhole
>> which should result in a projected disc of 10mm radius. I did
>> spblurring of
>> 0mm and 30mm (30mm is just for demonstrating the effect).
>> Below please find the distribution values of globalPosX, Y, and Z in
>> gateSingles.dat. Btw. I get similar results in Gate 1 & 2.
>>
>> for a 0 degree simulation: Here I think x is just the depth of the
>> Single
>> in the detector and does not play a role in the image formation, but
>> Y and
>> Z should be the image coordinates.
>>
>> spblurring 0mm:
>> average var stdev
>> X 242.491 3.228 1.797
>> Y 0.528 70.873 8.419
>> Z 0.140 91.875 9.585
>>
>> spblurring 30mm:
>> average var stdev
>> X 241.315 176.202 13.274
>> Y 1.332 258.672 16.083
>> Z 0.140 91.875 9.585
>>
>> (for Z I think the stdev should be similar to the stdev of Y)
>>
>> I would appreciate any comments or corrections to this line of
>> thoughts.
>> I am looking forward to hearing from you.
>>
>> Best Regards,
>>
>> Christian
>>
>> ------------------------------
>>
>
> ------------------------------
>
> Message: 5
> Date: Thu, 11 Aug 2005 10:25:25 +0200
> From: Sebastien JAN <jan at shfj.cea.fr>
> Subject: Re: [gate-users] Re: gate-users Digest, Vol 17, Issue 15
> To: cwietholt at nhri.org.tw, GATE feedback and helpline for Users
> <gate-users at lphe1pet1.epfl.ch>
> Message-ID: <42FB0B75.8020109 at shfj.cea.fr>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
>
>
> Hi Christian,
>
> Of course, you can do that if you want to blur the Z coordinate.
> Actually, this coordinate is the depth of interaction in the crystal
> and
> it is not measured in pet or spect systems. This is why Pznew is equal
> to Pz in the basic code.
>
> Cheers
> Seb
>
> Christian Wietholt a écrit:
>>> Message: 3
>>> Date: Wed, 10 Aug 2005 16:20:43 +0000
>>> From: Christian Wietholt <cwietholt at nhri.org.tw>
>>> Subject: [gate-users] spblurring folow-up
>>> To: gate-users at lphe1pet1.epfl.ch
>>> Message-ID: <200508101620.43733.cwietholt at nhri.org.tw>
>>> Content-Type: text/plain; charset=iso-8859-1
>>>
>>
>>
>> Dear all,
>>
>> Yesterday I posted below message about my troubles with the spblurring
>> functionality in Gate. After getting really desperate I decided this
>> morning
>> to take a look at the source code. I made the following changes to
>> GateSpblurring.cc
>>
>> I changed line 77 from :
>>
>> G4double PzNew = Pz;
>>
>> to
>>
>> G4double PzNew = G4RandGauss::shoot(Pz,m_spresolution/2.35);
>>
>> After some testing, it seems to have resolved the problems I
>> mentioned below.
>> I was hoping for some comments, just to verify if I am doing anything
>> wrong
>> with this change.
>>
>> I would appreciate your input.
>>
>> Best Regards,
>>
>> Christian
>>
>>
>>> Dear all,
>>>
>>> I know I have been posting a lot about the spblurring functionality
>>> in
>>> Gate, and I apologize for any unnecessary posts. As I mentioned in a
>>> previous post, the blurring does not have any effect on the
>>> globalPosZ
>>> variable in gateSingles.dat file. But, when I want to create an
>>> image from
>>> the ASCII output for a 0 degree projection, don't I use globalPosZ
>>> as the
>>> value for the ordinate, and the globalPosY as the value for the
>>> abscissa in
>>> the projection image. Please correct me if I am wrong. If spblurring
>>> does
>>> not have any effect on globalPosZ, how can I create a representative
>>> projection image?
>>>
>>> In my simulation I simulated a pointsource projecting through a 5mm
>>> pinhole
>>> which should result in a projected disc of 10mm radius. I did
>>> spblurring of
>>> 0mm and 30mm (30mm is just for demonstrating the effect).
>>> Below please find the distribution values of globalPosX, Y, and Z in
>>> gateSingles.dat. Btw. I get similar results in Gate 1 & 2.
>>>
>>> for a 0 degree simulation: Here I think x is just the depth of the
>>> Single
>>> in the detector and does not play a role in the image formation, but
>>> Y and
>>> Z should be the image coordinates.
>>>
>>> spblurring 0mm:
>>> average var stdev
>>> X 242.491 3.228 1.797
>>> Y 0.528 70.873 8.419
>>> Z 0.140 91.875 9.585
>>>
>>> spblurring 30mm:
>>> average var stdev
>>> X 241.315 176.202 13.274
>>> Y 1.332 258.672 16.083
>>> Z 0.140 91.875 9.585
>>>
>>> (for Z I think the stdev should be similar to the stdev of Y)
>>>
>>> I would appreciate any comments or corrections to this line of
>>> thoughts.
>>> I am looking forward to hearing from you.
>>>
>>> Best Regards,
>>>
>>> Christian
>>>
>>> ------------------------------
>>>
>>
>> _______________________________________________
>> gate-users mailing list
>> gate-users at lphe1pet1.epfl.ch
>> http://lphe1pet1.epfl.ch/mailman/listinfo/gate-users
>>
>>
>
>
>
> ------------------------------
>
> Message: 6
> Date: Thu, 11 Aug 2005 11:00:52 +0200
> From: Sebastien JAN <jan at shfj.cea.fr>
> Subject: Re: [gate-users] Simulation of scintillator and PMT
> To: GATE feedback and helpline for Users
> <gate-users at lphe1pet1.epfl.ch>
> Message-ID: <42FB13C4.9020104 at shfj.cea.fr>
> Content-Type: text/plain; charset=us-ascii; format=flowed
>
>
>
> Hi,
>
>> Hi all,
>> Is it possible to simulate PET detector by GATE, such as a block of
>> 8*8
>> crystal coupled by 2*2 PMT with slotted lightguide.
>
> you can simulate the crystal block but remenber that we can not
> simulate
> directly the scintillation and the light collection.
> You can try to mimic the light collection system with the digitizer
> chain (see usersguide for details)
>
> regards
> seb
>
>
> I just want to get
>> some simulation investigation about performance of scintillator-PMT,
>> especially flood field image. Thanks.
>>
>> Best regards
>> Yun Dong
>>
>>
>> _______________________________________________
>> gate-users mailing list
>> gate-users at lphe1pet1.epfl.ch
>> http://lphe1pet1.epfl.ch/mailman/listinfo/gate-users
>>
>>
>
>
> ------------------------------
>
> _______________________________________________
> gate-users mailing list
> gate-users at lphe1pet1.epfl.ch
> http://lphe1pet1.epfl.ch/mailman/listinfo/gate-users
>
> End of gate-users Digest, Vol 17, Issue 17
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