[gate-users] Error when using voxelized phantoms
Sebastien JAN
jan at shfj.cea.fr
Tue Apr 12 10:01:21 CEST 2005
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
>
>
>
>------------------------------------------------------------------------
>
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>
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