[gate-users] Error when using voxelized phantoms

Jose L. Rubio jlrubio at die.upm.es
Tue Apr 12 10:10:24 CEST 2005 

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
>> 
>>
>>    
>>
>
>_______________________________________________
>gate-users mailing list
>gate-users at lphe1pet1.epfl.ch
>http://lphe1pet1.epfl.ch/mailman/listinfo/gate-users
>
>
>  
>

More information about the Gate-users mailing list