[gate-users] Re: gate-users Digest, Vol 13, Issue 9
Ananth Ravi
ananth.ravi at sw.ca
Tue Apr 12 16:41:17 CEST 2005
Hi Jose,
I had the similar problem, and discovered that the drivers for my video card
were outdated.
After I corrected this problem the voxelized phantom seems to run fine.
Maybe you should
try and look into updating your drivers.
Hope that helps,
Ananth
----- Original Message -----
From: <gate-users-request at lphe1pet1.epfl.ch>
To: <gate-users at lphe1pet1.epfl.ch>
Sent: Tuesday, April 12, 2005 4:10 AM
Subject: gate-users Digest, Vol 13, Issue 9
> Send gate-users mailing list submissions to
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>
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>
> Please use the GATE's site webmaster e-mail to reach the person
> managing the list.
>
>
> Today's Topics:
>
> 1. Error when using voxelized phantoms (Jose L. Rubio)
> 2. Transportation process in gateHits.dat (Bing Bai)
> 3. Re: Error when using voxelized phantoms (Sebastien JAN)
> 4. Re: Error when using voxelized phantoms (Jose L. Rubio)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Mon, 11 Apr 2005 21:56:08 +0200
> From: "Jose L. Rubio" <jlrubio at die.upm.es>
> Subject: [gate-users] Error when using voxelized phantoms
> To: gate-users at lphe1pet1.epfl.ch
> Message-ID: <425AD658.10009 at die.upm.es>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Hello,
>
> I am trying to run a simulation based on one of the examples distributed
> with GATE, the one in the directory
> "examples/example_PHAMTOM_SOURCE/Voxelized_Phantom_Source", and I get
> the following error when the simulation starts:
>
>
>
****************************************************************************
****
> * G4Track Information: Particle = gamma, Track ID = 2, Parent
> ID = 0
>
>
****************************************************************************
****
>
> Step# X(mm) Y(mm) Z(mm) KinE(MeV) dE(MeV) StepLeng
> TrackLeng NextVolu me ProcName
> 0 59.1 4.83 39.1 0.511 0 0
> 0 voxels _P initStep
> 1 60 5.43 39.1 0.511 0 1.05
> 1.05 voxels _P Transportation
>
> *** Break *** segmentation violation
> Aborted (core dumped)
>
>
> The simulation is using both voxelized phantom and source, based on the
> example files "VoxelizedPhantom.mac" and "VoxelizedSource.mac", and it
> seems that the problem arises from the Voxelized Phantom, as when I
> substitute it for a cylinder the error disappears and the simulation
> runs withou any problem.
>
> I attach the full macro that I am using, just in case it helps, but
> probably the mistake is in the lines related with the phantom:
>
> # Insert a replica-based voxel-matrix geometry
> /gate/world/daughters/insert replicaMatrix
> /gate/replicaMatrix/geometry/insertReader interfile
> /gate/replicaMatrix/interfileReader/insertTranslator range
> /gate/replicaMatrix/interfileReader/rangeTranslator/readTable
> range_vox.dat
> /gate/replicaMatrix/interfileReader/rangeTranslator/describe 1
> # Hoffman Brain Phantom - Interfile format
> /gate/replicaMatrix/interfileReader/readFile hof3.h33
> /gate/replicaMatrix/interfileReader/describe 1
> /gate/replicaMatrix/attachPhantomSD
>
> If anybody knows what I am doing wrong, or has succesfully run a
> simulation with voxelized phantom, I would appreciate any help!
>
> By the way, what is the difference between the object "replicaMatrix"
> and "matrix"? Can the later also be used for reading voxelized phantoms
> from Interfile files?
>
> Thanks in advance!!
>
> Regards,
>
> Jose L. Rubio
> -------------- next part --------------
> # G E O M E T R Y : PET for small animal imaging
> #
>
> /gate/geometry/enableAutoUpdate
>
>
> # C Y L I N D R I C A L W I T H E C A T S Y S T E M
> /gate/world/daughters/name ecat
> /gate/world/daughters/insert cylinder
> /gate/ecat/setMaterial Air
> /gate/ecat/geometry/setRmax 145 mm
> /gate/ecat/geometry/setRmin 130 mm
> /gate/ecat/geometry/setHeight 80 mm
> /gate/ecat/vis/forceWireframe
> /gate/geometry/update
>
> # B L O C K
> /gate/ecat/daughters/name block
> /gate/ecat/daughters/insert box
> /gate/block/placement/setTranslation 135 0 0 mm
> /gate/block/geometry/setXLength 10. mm
> /gate/block/geometry/setYLength 19. mm
> /gate/block/geometry/setZLength 19. mm
> /gate/block/setMaterial Air
> /gate/block/vis/forceWireframe
> /gate/block/vis/setColor gray
> /gate/geometry/update
>
>
> # C R Y S T A L
> /gate/block/daughters/name crystal
> /gate/block/daughters/insert box
> /gate/crystal/geometry/setXLength 10. mm
> /gate/crystal/geometry/setYLength 2.2 mm
> /gate/crystal/geometry/setZLength 2.2 mm
> /gate/crystal/placement/setTranslation 0 0 0 mm
> /gate/crystal/setMaterial LSO
> /gate/crystal/vis/setColor yellow
> /gate/geometry/update
>
> # R E P E A T C R Y S T A L
> /gate/crystal/repeaters/insert cubicArray
> /gate/crystal/cubicArray/setRepeatNumberX 1
> /gate/crystal/cubicArray/setRepeatNumberY 8
> /gate/crystal/cubicArray/setRepeatNumberZ 8
> /gate/crystal/cubicArray/setRepeatVector 10. 2.4 2.4 mm
> /gate/geometry/update
>
> # R E P E A T B L O C K
> /gate/block/repeaters/insert linear
> /gate/block/linear/setRepeatNumber 4
> /gate/block/linear/setRepeatVector 0. 0. 19.2 mm
> /gate/block/repeaters/insert ring
> /gate/block/ring/setRepeatNumber 42
>
>
> # A T T A C H S Y S T E M
> /gate/systems/ecat/block/attach block
> /gate/systems/ecat/crystal/attach crystal
>
> # A T T A C H L A Y E R SD
> /gate/crystal/attachCrystalSD
>
>
>
> # V O X E L I Z E D M A T R I X H O F F M A N B R A I N P H A N T O
M
>
> # Insert a replica-based voxel-matrix geometry
> /gate/world/daughters/insert replicaMatrix
> /gate/replicaMatrix/geometry/insertReader interfile
> /gate/replicaMatrix/interfileReader/insertTranslator range
> /gate/replicaMatrix/interfileReader/rangeTranslator/readTable
range_vox.dat
> /gate/replicaMatrix/interfileReader/rangeTranslator/describe 1
> # Hoffman Brain Phantom - Interfile format
> /gate/replicaMatrix/interfileReader/readFile hof3.h33
> /gate/replicaMatrix/interfileReader/describe 1
> /gate/replicaMatrix/attachPhantomSD
>
>
>
>
> #
> # P H Y S I C S
> #
>
>
> # EM P R O C E S S
> /gate/physics/gamma/selectRayleigh inactive
> /gate/physics/gamma/selectPhotoelectric standard
> /gate/physics/gamma/selectCompton standard
>
> # I N A C T I V E S E C O N D A R Y E L E C T R O N S
> /gate/physics/setElectronCut 1. m
>
> # I N A C T I V E X - R A Y S
> /gate/physics/setXRayCut 1. GeV
> /gate/physics/setDeltaRayCut 1. GeV
>
>
> #
> # A C Q U I S I T I O N P A R A M E T E R S - > DIGITIZER &
COINC SHORTER
> #
>
> # A D D E R
> /gate/digitizer/Singles/insert adder
>
> # R E A D O U T
> /gate/digitizer/Singles/insert readout
> /gate/digitizer/Singles/readout/setDepth 1
> /gate/digitizer/Singles/insert blurring
> /gate/digitizer/Singles/blurring/setResolution 0.26
> /gate/digitizer/Singles/blurring/setEnergyOfReference 511. keV
>
> # E N E R G Y C U T
> /gate/digitizer/Singles/insert thresholder
> /gate/digitizer/Singles/thresholder/setThreshold 350. keV
> /gate/digitizer/Singles/insert upholder
> /gate/digitizer/Singles/upholder/setUphold 650. keV
>
>
> # C O I N C I S O R T E R
>
> /gate/digitizer/Coincidences/setWindow 10. ns
>
> /run/initialize
>
>
> #
> # V O X E L S O U R C E B A S E D O N T H E H O F F M A N B R A
I N P H A N T O M
>
> /gate/source/addSource voxel voxel
> /gate/source/voxel/reader/insert interfile
> /gate/source/voxel/interfileReader/translator/insert range
> /gate/source/voxel/interfileReader/rangeTranslator/readTable
act_range_vox.dat
> /gate/source/voxel/interfileReader/rangeTranslator/describe 1
> # Hoffman Brain Phantom - Interfile format
> /gate/source/voxel/interfileReader/readFile hof3.h33
> /gate/source/voxel/interfileReader/verbose 1
> /gate/source/voxel/setType backtoback
> /gate/source/voxel/gps/particle gamma
> /gate/source/voxel/gps/energytype Mono
> /gate/source/voxel/gps/monoenergy 511. keV
> /gate/source/voxel/gps/angtype iso
> /gate/source/voxel/setPosition -128. -128. -55 mm
> /gate/source/voxel/dump 1
>
>
> #
> # O U T P U T -> ROOT ; ASCII ; ECAT7 ; SEED
> #
> # C H A N G E T H E S E E D (1) O R N O T (0)
> /gate/output/root/setSaveRndmFlag 1
>
> # S E T U P - R O O T _ F I L E
> /gate/output/root/setFileName YourROOTOutPut
>
> /gate/output/root/setRootSinglesAdderFlag 0
> #/gate/output/root/setRootSinglesCrystalblurringFlag 0
> /gate/output/root/setRootSinglesReadoutFlag 0
>
> /gate/output/root/setRootHitFlag 1
> /gate/output/root/setRootSinglesFlag 1
> /gate/output/root/setRootNtupleFlag 1
> /gate/output/root/setRootCoincidencesFlag 1
>
> # S E T U P - A S C I I _ F I L E
>
> /gate/output/ascii/setOutFileSinglesAdderFlag 0
> /gate/output/ascii/setOutFileSinglesReadoutFlag 0
> /gate/output/ascii/setOutFileSinglesBlurringFlag 0
> /gate/output/ascii/setOutFileSinglesThresholderFlag 0
> /gate/output/ascii/setOutFileSinglesUpholderFlag 0
> /gate/output/ascii/setOutFileSinglesFlag 0
> /gate/output/ascii/setOutFileHitsFlag 0
> /gate/output/ascii/setOutFileCoincidencesFlag 0
>
>
> # S T A R T
> /gate/application/setTimeSlice 1. s
> /gate/application/setTimeStart 0. s
> /gate/application/setTimeStop 1. s
> /gate/application/startDAQ
>
>
> ------------------------------
>
> Message: 2
> Date: Mon, 11 Apr 2005 13:42:50 -0700 (PDT)
> From: Bing Bai <bbai at sipi.usc.edu>
> Subject: [gate-users] Transportation process in gateHits.dat
> To: gate-users at lphe1pet1.epfl.ch
> Message-ID: <Pine.GSO.4.60.0504111334550.26139 at biron.usc.edu>
> Content-Type: TEXT/PLAIN; charset=US-ASCII; format=flowed
>
> Hi,
>
> When checking the gateHits.dat generated from my PET scanner simulation, I
> found a small portion of the hits are labelled as "Transportation" and the
> energy deposited is not zero. Are these so called "special hit" in user's
> manual Chap 8.1, when a particle moves from one volume to another?
> If so why the energy deposit is non-zero? (according to the user manual it
> should deposit zero energy.)
> And I found some hits in the same file with zero energy deposit, but are
> labelled as other process such as Compton.
>
> Thanks,
> Bing
>
> ------------------------------
>
> Message: 3
> Date: Tue, 12 Apr 2005 10:01:21 +0200
> From: Sebastien JAN <jan at shfj.cea.fr>
> Subject: Re: [gate-users] Error when using voxelized phantoms
> To: GATE feedback and helpline for Users
> <gate-users at lphe1pet1.epfl.ch>
> Message-ID: <425B8051.8 at shfj.cea.fr>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
>
> Hi Jose,
>
> What is your Gate version ?
>
> sebastien
>
>
>
> Jose L. Rubio a ecrit :
>
> > Hello,
> >
> > I am trying to run a simulation based on one of the examples
> > distributed with GATE, the one in the directory
> > "examples/example_PHAMTOM_SOURCE/Voxelized_Phantom_Source", and I get
> > the following error when the simulation starts:
> >
> >
> >
****************************************************************************
****
> >
> > * G4Track Information: Particle = gamma, Track ID = 2, Parent
> > ID = 0
> >
> >
****************************************************************************
****
> >
> >
> > Step# X(mm) Y(mm) Z(mm) KinE(MeV) dE(MeV) StepLeng
> > TrackLeng NextVolu me ProcName
> > 0 59.1 4.83 39.1 0.511 0
> > 0 0 voxels _P initStep
> > 1 60 5.43 39.1 0.511 0 1.05
> > 1.05 voxels _P Transportation
> > *** Break *** segmentation violation
> > Aborted (core dumped)
> >
> >
> > The simulation is using both voxelized phantom and source, based on
> > the example files "VoxelizedPhantom.mac" and "VoxelizedSource.mac",
> > and it seems that the problem arises from the Voxelized Phantom, as
> > when I substitute it for a cylinder the error disappears and the
> > simulation runs withou any problem.
> >
> > I attach the full macro that I am using, just in case it helps, but
> > probably the mistake is in the lines related with the phantom:
> >
> > # Insert a replica-based voxel-matrix geometry
> > /gate/world/daughters/insert replicaMatrix
> > /gate/replicaMatrix/geometry/insertReader interfile
> > /gate/replicaMatrix/interfileReader/insertTranslator range
> > /gate/replicaMatrix/interfileReader/rangeTranslator/readTable
> > range_vox.dat
> > /gate/replicaMatrix/interfileReader/rangeTranslator/describe 1
> > # Hoffman Brain Phantom - Interfile format
> > /gate/replicaMatrix/interfileReader/readFile hof3.h33
> > /gate/replicaMatrix/interfileReader/describe 1
> > /gate/replicaMatrix/attachPhantomSD
> >
> > If anybody knows what I am doing wrong, or has succesfully run a
> > simulation with voxelized phantom, I would appreciate any help!
> >
> > By the way, what is the difference between the object "replicaMatrix"
> > and "matrix"? Can the later also be used for reading voxelized
> > phantoms from Interfile files?
> >
> > Thanks in advance!!
> >
> > Regards,
> >
> > Jose L. Rubio
> >
> >------------------------------------------------------------------------
> >
> ># G E O M E T R Y : PET for small animal imaging
> >#
> >
> >/gate/geometry/enableAutoUpdate
> >
> >
> ># C Y L I N D R I C A L W I T H E C A T S Y S T E M
> >/gate/world/daughters/name ecat
> >/gate/world/daughters/insert cylinder
> >/gate/ecat/setMaterial Air
> >/gate/ecat/geometry/setRmax 145 mm
> >/gate/ecat/geometry/setRmin 130 mm
> >/gate/ecat/geometry/setHeight 80 mm
> >/gate/ecat/vis/forceWireframe
> >/gate/geometry/update
> >
> ># B L O C K
> >/gate/ecat/daughters/name block
> >/gate/ecat/daughters/insert box
> >/gate/block/placement/setTranslation 135 0 0 mm
> >/gate/block/geometry/setXLength 10. mm
> >/gate/block/geometry/setYLength 19. mm
> >/gate/block/geometry/setZLength 19. mm
> >/gate/block/setMaterial Air
> >/gate/block/vis/forceWireframe
> >/gate/block/vis/setColor gray
> >/gate/geometry/update
> >
> >
> ># C R Y S T A L
> >/gate/block/daughters/name crystal
> >/gate/block/daughters/insert box
> >/gate/crystal/geometry/setXLength 10. mm
> >/gate/crystal/geometry/setYLength 2.2 mm
> >/gate/crystal/geometry/setZLength 2.2 mm
> >/gate/crystal/placement/setTranslation 0 0 0 mm
> >/gate/crystal/setMaterial LSO
> >/gate/crystal/vis/setColor yellow
> >/gate/geometry/update
> >
> ># R E P E A T C R Y S T A L
> >/gate/crystal/repeaters/insert cubicArray
> >/gate/crystal/cubicArray/setRepeatNumberX 1
> >/gate/crystal/cubicArray/setRepeatNumberY 8
> >/gate/crystal/cubicArray/setRepeatNumberZ 8
> >/gate/crystal/cubicArray/setRepeatVector 10. 2.4 2.4 mm
> >/gate/geometry/update
> >
> ># R E P E A T B L O C K
> >/gate/block/repeaters/insert linear
> >/gate/block/linear/setRepeatNumber 4
> >/gate/block/linear/setRepeatVector 0. 0. 19.2 mm
> >/gate/block/repeaters/insert ring
> >/gate/block/ring/setRepeatNumber 42
> >
> >
> ># A T T A C H S Y S T E M
> >/gate/systems/ecat/block/attach block
> >/gate/systems/ecat/crystal/attach crystal
> >
> ># A T T A C H L A Y E R SD
> >/gate/crystal/attachCrystalSD
> >
> >
> >
> ># V O X E L I Z E D M A T R I X H O F F M A N B R A I N P H A N T
O M
> >
> ># Insert a replica-based voxel-matrix geometry
> >/gate/world/daughters/insert replicaMatrix
> >/gate/replicaMatrix/geometry/insertReader interfile
> >/gate/replicaMatrix/interfileReader/insertTranslator range
> >/gate/replicaMatrix/interfileReader/rangeTranslator/readTable
range_vox.dat
> >/gate/replicaMatrix/interfileReader/rangeTranslator/describe 1
> ># Hoffman Brain Phantom - Interfile format
> >/gate/replicaMatrix/interfileReader/readFile hof3.h33
> >/gate/replicaMatrix/interfileReader/describe 1
> >/gate/replicaMatrix/attachPhantomSD
> >
> >
> >
> >
> >#
> ># P H Y S I C S
> >#
> >
> >
> ># EM P R O C E S S
> >/gate/physics/gamma/selectRayleigh inactive
> >/gate/physics/gamma/selectPhotoelectric standard
> >/gate/physics/gamma/selectCompton standard
> >
> ># I N A C T I V E S E C O N D A R Y E L E C T R O N S
> >/gate/physics/setElectronCut 1. m
> >
> ># I N A C T I V E X - R A Y S
> >/gate/physics/setXRayCut 1. GeV
> >/gate/physics/setDeltaRayCut 1. GeV
> >
> >
> >#
> ># A C Q U I S I T I O N P A R A M E T E R S - > DIGITIZER &
COINC SHORTER
> >#
> >
> ># A D D E R
> >/gate/digitizer/Singles/insert adder
> >
> ># R E A D O U T
> >/gate/digitizer/Singles/insert readout
> >/gate/digitizer/Singles/readout/setDepth 1
> >/gate/digitizer/Singles/insert blurring
> >/gate/digitizer/Singles/blurring/setResolution 0.26
> >/gate/digitizer/Singles/blurring/setEnergyOfReference 511. keV
> >
> ># E N E R G Y C U T
> >/gate/digitizer/Singles/insert thresholder
> >/gate/digitizer/Singles/thresholder/setThreshold 350. keV
> >/gate/digitizer/Singles/insert upholder
> >/gate/digitizer/Singles/upholder/setUphold 650. keV
> >
> >
> ># C O I N C I S O R T E R
> >
> >/gate/digitizer/Coincidences/setWindow 10. ns
> >
> >/run/initialize
> >
> >
> >#
> ># V O X E L S O U R C E B A S E D O N T H E H O F F M A N B R
A I N P H A N T O M
> >
> >/gate/source/addSource voxel voxel
> >/gate/source/voxel/reader/insert interfile
> >/gate/source/voxel/interfileReader/translator/insert range
> >/gate/source/voxel/interfileReader/rangeTranslator/readTable
act_range_vox.dat
> >/gate/source/voxel/interfileReader/rangeTranslator/describe 1
> ># Hoffman Brain Phantom - Interfile format
> >/gate/source/voxel/interfileReader/readFile hof3.h33
> >/gate/source/voxel/interfileReader/verbose 1
> >/gate/source/voxel/setType backtoback
> >/gate/source/voxel/gps/particle gamma
> >/gate/source/voxel/gps/energytype Mono
> >/gate/source/voxel/gps/monoenergy 511. keV
> >/gate/source/voxel/gps/angtype iso
> >/gate/source/voxel/setPosition -128. -128. -55 mm
> >/gate/source/voxel/dump 1
> >
> >
> >#
> ># O U T P U T -> ROOT ; ASCII ; ECAT7 ; SEED
> >#
> ># C H A N G E T H E S E E D (1) O R N O T (0)
> >/gate/output/root/setSaveRndmFlag 1
> >
> ># S E T U P - R O O T _ F I L E
> >/gate/output/root/setFileName YourROOTOutPut
> >
> >/gate/output/root/setRootSinglesAdderFlag 0
> >#/gate/output/root/setRootSinglesCrystalblurringFlag 0
> >/gate/output/root/setRootSinglesReadoutFlag 0
> >
> >/gate/output/root/setRootHitFlag 1
> >/gate/output/root/setRootSinglesFlag 1
> >/gate/output/root/setRootNtupleFlag 1
> >/gate/output/root/setRootCoincidencesFlag 1
> >
> ># S E T U P - A S C I I _ F I L E
> >
> >/gate/output/ascii/setOutFileSinglesAdderFlag 0
> >/gate/output/ascii/setOutFileSinglesReadoutFlag 0
> >/gate/output/ascii/setOutFileSinglesBlurringFlag 0
> >/gate/output/ascii/setOutFileSinglesThresholderFlag 0
> >/gate/output/ascii/setOutFileSinglesUpholderFlag 0
> >/gate/output/ascii/setOutFileSinglesFlag 0
> >/gate/output/ascii/setOutFileHitsFlag 0
> >/gate/output/ascii/setOutFileCoincidencesFlag 0
> >
> >
> ># S T A R T
> >/gate/application/setTimeSlice 1. s
> >/gate/application/setTimeStart 0. s
> >/gate/application/setTimeStop 1. s
> >/gate/application/startDAQ
> >
> >
> >
> >------------------------------------------------------------------------
> >
> >_______________________________________________
> >gate-users mailing list
> >gate-users at lphe1pet1.epfl.ch
> >http://lphe1pet1.epfl.ch/mailman/listinfo/gate-users
> >
> >
>
>
> ------------------------------
>
> Message: 4
> Date: Tue, 12 Apr 2005 10:10:24 +0200
> From: "Jose L. Rubio" <jlrubio at die.upm.es>
> Subject: Re: [gate-users] Error when using voxelized phantoms
> To: GATE feedback and helpline for Users
> <gate-users at lphe1pet1.epfl.ch>
> Message-ID: <425B8270.8060808 at die.upm.es>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
> Hi Sebastien,
>
> I am using GATE-1.2.0 with Geant4.7.0.p01. I have tried the same
> simulation both under cygwin/windows and under Ubuntu 5.04 (Debian based
> distribution).
>
> Any idea? :-)
>
> Thaks!
>
> Jose
>
> >Hi Jose,
> >
> >What is your Gate version ?
> >
> >sebastien
> >
> >
> >
> >Jose L. Rubio a ecrit :
> >
> >
> >
> >>Hello,
> >>
> >>I am trying to run a simulation based on one of the examples
> >>distributed with GATE, the one in the directory
> >>"examples/example_PHAMTOM_SOURCE/Voxelized_Phantom_Source", and I get
> >>the following error when the simulation starts:
> >>
> >>
>
>>**************************************************************************
******
> >>
> >> * G4Track Information: Particle = gamma, Track ID = 2, Parent
> >>ID = 0
> >>
>
>>**************************************************************************
******
> >>
> >>
> >> Step# X(mm) Y(mm) Z(mm) KinE(MeV) dE(MeV) StepLeng
> >>TrackLeng NextVolu me ProcName
> >> 0 59.1 4.83 39.1 0.511 0
> >>0 0 voxels _P initStep
> >> 1 60 5.43 39.1 0.511 0 1.05
> >>1.05 voxels _P Transportation
> >> *** Break *** segmentation violation
> >> Aborted (core dumped)
> >>
> >>
> >>The simulation is using both voxelized phantom and source, based on
> >>the example files "VoxelizedPhantom.mac" and "VoxelizedSource.mac",
> >>and it seems that the problem arises from the Voxelized Phantom, as
> >>when I substitute it for a cylinder the error disappears and the
> >>simulation runs withou any problem.
> >>
> >>I attach the full macro that I am using, just in case it helps, but
> >>probably the mistake is in the lines related with the phantom:
> >>
> >> # Insert a replica-based voxel-matrix geometry
> >> /gate/world/daughters/insert replicaMatrix
> >> /gate/replicaMatrix/geometry/insertReader interfile
> >> /gate/replicaMatrix/interfileReader/insertTranslator range
> >> /gate/replicaMatrix/interfileReader/rangeTranslator/readTable
> >>range_vox.dat
> >> /gate/replicaMatrix/interfileReader/rangeTranslator/describe 1
> >> # Hoffman Brain Phantom - Interfile format
> >> /gate/replicaMatrix/interfileReader/readFile hof3.h33
> >> /gate/replicaMatrix/interfileReader/describe 1
> >> /gate/replicaMatrix/attachPhantomSD
> >>
> >>If anybody knows what I am doing wrong, or has succesfully run a
> >>simulation with voxelized phantom, I would appreciate any help!
> >>
> >>By the way, what is the difference between the object "replicaMatrix"
> >>and "matrix"? Can the later also be used for reading voxelized
> >>phantoms from Interfile files?
> >>
> >>Thanks in advance!!
> >>
> >>Regards,
> >>
> >> Jose L. Rubio
> >>
> >>------------------------------------------------------------------------
> >>
> >># G E O M E T R Y : PET for small animal imaging
> >>#
> >>
> >>/gate/geometry/enableAutoUpdate
> >>
> >>
> >># C Y L I N D R I C A L W I T H E C A T S Y S T E M
> >>/gate/world/daughters/name ecat
> >>/gate/world/daughters/insert cylinder
> >>/gate/ecat/setMaterial Air
> >>/gate/ecat/geometry/setRmax 145 mm
> >>/gate/ecat/geometry/setRmin 130 mm
> >>/gate/ecat/geometry/setHeight 80 mm
> >>/gate/ecat/vis/forceWireframe
> >>/gate/geometry/update
> >>
> >># B L O C K
> >>/gate/ecat/daughters/name block
> >>/gate/ecat/daughters/insert box
> >>/gate/block/placement/setTranslation 135 0 0 mm
> >>/gate/block/geometry/setXLength 10. mm
> >>/gate/block/geometry/setYLength 19. mm
> >>/gate/block/geometry/setZLength 19. mm
> >>/gate/block/setMaterial Air
> >>/gate/block/vis/forceWireframe
> >>/gate/block/vis/setColor gray
> >>/gate/geometry/update
> >>
> >>
> >># C R Y S T A L
> >>/gate/block/daughters/name crystal
> >>/gate/block/daughters/insert box
> >>/gate/crystal/geometry/setXLength 10. mm
> >>/gate/crystal/geometry/setYLength 2.2 mm
> >>/gate/crystal/geometry/setZLength 2.2 mm
> >>/gate/crystal/placement/setTranslation 0 0 0 mm
> >>/gate/crystal/setMaterial LSO
> >>/gate/crystal/vis/setColor yellow
> >>/gate/geometry/update
> >>
> >># R E P E A T C R Y S T A L
> >>/gate/crystal/repeaters/insert cubicArray
> >>/gate/crystal/cubicArray/setRepeatNumberX 1
> >>/gate/crystal/cubicArray/setRepeatNumberY 8
> >>/gate/crystal/cubicArray/setRepeatNumberZ 8
> >>/gate/crystal/cubicArray/setRepeatVector 10. 2.4 2.4 mm
> >>/gate/geometry/update
> >>
> >># R E P E A T B L O C K
> >>/gate/block/repeaters/insert linear
> >>/gate/block/linear/setRepeatNumber 4
> >>/gate/block/linear/setRepeatVector 0. 0. 19.2 mm
> >>/gate/block/repeaters/insert ring
> >>/gate/block/ring/setRepeatNumber 42
> >>
> >>
> >># A T T A C H S Y S T E M
> >>/gate/systems/ecat/block/attach block
> >>/gate/systems/ecat/crystal/attach crystal
> >>
> >># A T T A C H L A Y E R SD
> >>/gate/crystal/attachCrystalSD
> >>
> >>
> >>
> >># V O X E L I Z E D M A T R I X H O F F M A N B R A I N P H A N T
O M
> >>
> >># Insert a replica-based voxel-matrix geometry
> >>/gate/world/daughters/insert replicaMatrix
> >>/gate/replicaMatrix/geometry/insertReader interfile
> >>/gate/replicaMatrix/interfileReader/insertTranslator range
> >>/gate/replicaMatrix/interfileReader/rangeTranslator/readTable
range_vox.dat
> >>/gate/replicaMatrix/interfileReader/rangeTranslator/describe 1
> >># Hoffman Brain Phantom - Interfile format
> >>/gate/replicaMatrix/interfileReader/readFile hof3.h33
> >>/gate/replicaMatrix/interfileReader/describe 1
> >>/gate/replicaMatrix/attachPhantomSD
> >>
> >>
> >>
> >>
> >>#
> >># P H Y S I C S
> >>#
> >>
> >>
> >># EM P R O C E S S
> >>/gate/physics/gamma/selectRayleigh inactive
> >>/gate/physics/gamma/selectPhotoelectric standard
> >>/gate/physics/gamma/selectCompton standard
> >>
> >># I N A C T I V E S E C O N D A R Y E L E C T R O N S
> >>/gate/physics/setElectronCut 1. m
> >>
> >># I N A C T I V E X - R A Y S
> >>/gate/physics/setXRayCut 1. GeV
> >>/gate/physics/setDeltaRayCut 1. GeV
> >>
> >>
> >>#
> >># A C Q U I S I T I O N P A R A M E T E R S - > DIGITIZER &
COINC SHORTER
> >>#
> >>
> >># A D D E R
> >>/gate/digitizer/Singles/insert adder
> >>
> >># R E A D O U T
> >>/gate/digitizer/Singles/insert readout
> >>/gate/digitizer/Singles/readout/setDepth 1
> >>/gate/digitizer/Singles/insert blurring
> >>/gate/digitizer/Singles/blurring/setResolution 0.26
> >>/gate/digitizer/Singles/blurring/setEnergyOfReference 511. keV
> >>
> >># E N E R G Y C U T
> >>/gate/digitizer/Singles/insert thresholder
> >>/gate/digitizer/Singles/thresholder/setThreshold 350. keV
> >>/gate/digitizer/Singles/insert upholder
> >>/gate/digitizer/Singles/upholder/setUphold 650. keV
> >>
> >>
> >># C O I N C I S O R T E R
> >>
> >>/gate/digitizer/Coincidences/setWindow 10. ns
> >>
> >>/run/initialize
> >>
> >>
> >>#
> >># V O X E L S O U R C E B A S E D O N T H E H O F F M A N B R
A I N P H A N T O M
> >>
> >>/gate/source/addSource voxel voxel
> >>/gate/source/voxel/reader/insert interfile
> >>/gate/source/voxel/interfileReader/translator/insert range
> >>/gate/source/voxel/interfileReader/rangeTranslator/readTable
act_range_vox.dat
> >>/gate/source/voxel/interfileReader/rangeTranslator/describe 1
> >># Hoffman Brain Phantom - Interfile format
> >>/gate/source/voxel/interfileReader/readFile hof3.h33
> >>/gate/source/voxel/interfileReader/verbose 1
> >>/gate/source/voxel/setType backtoback
> >>/gate/source/voxel/gps/particle gamma
> >>/gate/source/voxel/gps/energytype Mono
> >>/gate/source/voxel/gps/monoenergy 511. keV
> >>/gate/source/voxel/gps/angtype iso
> >>/gate/source/voxel/setPosition -128. -128. -55 mm
> >>/gate/source/voxel/dump 1
> >>
> >>
> >>#
> >># O U T P U T -> ROOT ; ASCII ; ECAT7 ; SEED
> >>#
> >># C H A N G E T H E S E E D (1) O R N O T (0)
> >>/gate/output/root/setSaveRndmFlag 1
> >>
> >># S E T U P - R O O T _ F I L E
> >>/gate/output/root/setFileName YourROOTOutPut
> >>
> >>/gate/output/root/setRootSinglesAdderFlag 0
> >>#/gate/output/root/setRootSinglesCrystalblurringFlag 0
> >>/gate/output/root/setRootSinglesReadoutFlag 0
> >>
> >>/gate/output/root/setRootHitFlag 1
> >>/gate/output/root/setRootSinglesFlag 1
> >>/gate/output/root/setRootNtupleFlag 1
> >>/gate/output/root/setRootCoincidencesFlag 1
> >>
> >># S E T U P - A S C I I _ F I L E
> >>
> >>/gate/output/ascii/setOutFileSinglesAdderFlag 0
> >>/gate/output/ascii/setOutFileSinglesReadoutFlag 0
> >>/gate/output/ascii/setOutFileSinglesBlurringFlag 0
> >>/gate/output/ascii/setOutFileSinglesThresholderFlag 0
> >>/gate/output/ascii/setOutFileSinglesUpholderFlag 0
> >>/gate/output/ascii/setOutFileSinglesFlag 0
> >>/gate/output/ascii/setOutFileHitsFlag 0
> >>/gate/output/ascii/setOutFileCoincidencesFlag 0
> >>
> >>
> >># S T A R T
> >>/gate/application/setTimeSlice 1. s
> >>/gate/application/setTimeStart 0. s
> >>/gate/application/setTimeStop 1. s
> >>/gate/application/startDAQ
> >>
> >>
> >>
> >>------------------------------------------------------------------------
> >>
> >>_______________________________________________
> >>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
> >
> >
> >
> >
>
>
>
> ------------------------------
>
> _______________________________________________
> gate-users mailing list
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> http://lphe1pet1.epfl.ch/mailman/listinfo/gate-users
>
> End of gate-users Digest, Vol 13, Issue 9
> *****************************************
>
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