[gate-users] Re: gate-users Digest, Vol 13, Issue 9
Sebastien JAN
jan at shfj.cea.fr
Tue Apr 12 17:00:20 CEST 2005
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 écrit :
>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were outdated.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
>>*****************************************
>>
>>
>>
>
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