[gate-users] Error when using voxelized phantoms
Sebastien JAN
jan at shfj.cea.fr
Tue Apr 12 12:24:46 CEST 2005
ok, there is probably a bug with the particle tracking inside the
replicaMatrix volume. We will try to fix it ASAP.
sebastien
Jose L. Rubio a écrit :
> 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 écrit :
>>
>>
>>
>>> 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
>>>
>>>
>>>
>>
>>
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>
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