[gate-users] Re: gate-users Digest, Vol 13, Issue 12
Ananth Ravi
ananth.ravi at sw.ca
Tue Apr 12 17:06:50 CEST 2005
Hi Sebastien,
I do have good particl tracking, however I am using the tried and tested
version of Gate, the gate_v.1.0.2 with geant4 5.2.p02. But I found
that there was a dependance on the on board video card ram even if
visualization was
turned off. Even with the stable version of GATE.
Regards,
Ananth
----- Original Message -----
From: <gate-users-request at lphe1pet1.epfl.ch>
To: <gate-users at lphe1pet1.epfl.ch>
Sent: Tuesday, April 12, 2005 11:00 AM
Subject: gate-users Digest, Vol 13, Issue 12
> Send gate-users mailing list submissions to
> gate-users at lphe1pet1.epfl.ch
>
> To subscribe or unsubscribe via the World Wide Web, visit
> http://lphe1pet1.epfl.ch/mailman/listinfo/gate-users
>
> Please use the GATE's site webmaster e-mail to reach the person
> managing the list.
>
>
> Today's Topics:
>
> 1. Re: Re: gate-users Digest, Vol 13, Issue 9 (Sebastien JAN)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Tue, 12 Apr 2005 17:00:20 +0200
> From: Sebastien JAN <jan at shfj.cea.fr>
> Subject: Re: [gate-users] Re: gate-users Digest, Vol 13, Issue 9
> To: GATE feedback and helpline for Users
> <gate-users at lphe1pet1.epfl.ch>
> Message-ID: <425BE284.7040108 at shfj.cea.fr>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
>
> Hi Ananth,
>
> Do you have a good particle tracking (without abort or segmentatiopn
> fault) with gate_v1.1.0 or v1.2.0 (version for g4 6 and g4 7) when you
> use a replicaMatrix for your phantom desciption ?
>
> thanks
> seb
>
>
> Ananth Ravi a ecrit :
>
> >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were outdated.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
> >>gate-users at lphe1pet1.epfl.ch
> >>
> >>To subscribe or unsubscribe via the World Wide Web, visit
> >>http://lphe1pet1.epfl.ch/mailman/listinfo/gate-users
> >>
> >>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
> >>gate-users at lphe1pet1.epfl.ch
> >>http://lphe1pet1.epfl.ch/mailman/listinfo/gate-users
> >>
> >>End of gate-users Digest, Vol 13, Issue 9
> >>*****************************************
> >>
> >>
> >>
> >
> >_______________________________________________
> >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 13, Issue 12
> ******************************************
>
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