[Gate-users] Voxelized Phantom
bassim aklan
bassim.aklan at imp.uni-erlangen.de
Thu Jul 25 12:29:01 CEST 2013
Hello Gate's users,
I am facing a problem with the voxelized phantom and source in Gate
v6.1, namely I have segmented a CT data set of nema image quality
phantom in different regions. Now, When I run my macro file, every thing
is fine loaded without any errors. The problem is by saving the data
into root file. It means, the data is not writing into root file,
although the simulation is running. The size of root file remains the
same with increasing of the file size. When I have a look at the root
file, the coincidence tree is empty. Did some one faced such problem
before. I would be thankful if some body can help me with issue. Below
you see the output of my simulation.
Thanks in advance and regards,
bassim
*Simulation output:*
[Core-0] Starting macro main1.mac
[G4] Range Translator
[G4] Range 0 : imageValue in [ 0.000e+00 , 0.000e+00 ] --->
material Air, visibility 0, coulour
(0.000e+00,1.000e+00,0.000e+00,2.000e-01)
[G4] Range 1 : imageValue in [ 5.000e+01 , 5.000e+01 ] --->
material Water, visibility 0, coulour
(1.000e+00,0.000e+00,0.000e+00,2.000e-01)
[G4] Range 2 : imageValue in [ 1.000e+02 , 1.000e+02 ] --->
material PMMA, visibility 0, coulour
(1.961e-01,8.039e-01,1.961e-01,2.000e-01)
[G4] Range 3 : imageValue in [ 2.500e+02 , 2.500e+02 ] --->
material PMMA, visibility 0, coulour
(1.961e-01,8.039e-01,1.961e-01,2.000e-01)
[G4] Range 4 : imageValue in [ 4.500e+02 , 4.500e+02 ] --->
material Glass, visibility 1, coulour
(6.627e-01,6.627e-01,6.627e-01,2.000e-01)
[G4] Range 5 : imageValue in [ 3.500e+02 , 3.500e+02 ] --->
material Lung, visibility 0, coulour
(0.000e+00,0.000e+00,1.000e+00,0.000e+00)
[G4] Range 6 : imageValue in [ 9.500e+02 , 9.500e+02 ] --->
material Water, visibility 0, coulour
(1.000e+00,0.000e+00,0.000e+00,2.000e-01)
[G4] Range 7 : imageValue in [ 1.050e+03 , 1.050e+03 ] --->
material Water, visibility 0, coulour
(1.000e+00,0.000e+00,0.000e+00,2.000e-01)
[G4] Range 8 : imageValue in [ 1.150e+03 , 1.150e+03 ] --->
material Water, visibility 0, coulour
(1.000e+00,0.000e+00,0.000e+00,2.000e-01)
[G4] Range 9 : imageValue in [ 1.250e+03 , 1.250e+03 ] --->
material Water, visibility 0, coulour
(1.000e+00,0.000e+00,0.000e+00,2.000e-01)
[G4] Range 10 : imageValue in [ 1.350e+03 , 1.350e+03 ] --->
material Water, visibility 0, coulour
(1.000e+00,0.000e+00,0.000e+00,2.000e-01)
[G4] Range 11 : imageValue in [ 1.450e+03 , 1.450e+03 ] --->
material Water, visibility 0, coulour
(1.000e+00,0.000e+00,0.000e+00,2.000e-01)
[G4] Header read from 'nema_phantom_downsampled.h33'
[G4] Data file name 'nema_phantom_downsampled.i33'
[G4] Nb of planes: 115
[G4] Nb of pixels per plane: 134 100
[G4] Pixel size: 1.988e+00 2.000e+00
[G4] Slice thickness: 1.500e+00
[G4] Matrix size: 2.664e+02 2.000e+02
[G4] Data type: UNSIGNED INTEGER
[G4]
[G4] nx ny nz: 134 100 115
[G4] dx dy dz: 1.988e+00 2.000e+00 1.500e+00
[G4] Nof Higher level 3
[G4]
[G4] GATE object: 'digitizer/Coincidences'
[G4] Is enabled? Yes
[G4] Coincidence window: 5.900e+00 ns
[G4] Coincidence window jitter: 0.000e+00 ps
[G4] Coincidence offset: 0.000e+00 ps
[G4] Coincidence offset jitter: 0.000e+00 ps
[G4] Min sector diff.: 2
[G4] Input: 'Singles'
[G4] Output: 'Coincidences'
[G4] in GateCoincidencePulseProcessorChain call new
GateCoincidenceDigiMaker
[G4] in GateVCoincidencePulseProcessor call new GateCoincidenceDigiMaker
[G4]
[G4] GATE object: 'digitizer/finalCoinc'
[G4] Is enabled? Yes
[G4] Nb of elements: 1
[G4] 'digitizer/finalCoinc/deadtime'
[G4] Attached to: 'digitizer'
[G4] Output: 'finalCoinc'
[G4] in GateVCoincidencePulseProcessor call new GateCoincidenceDigiMaker
[G4] GateSourceVoxellizedMessenger::SetNewValue
[G4] Range Translator
[G4] Range 0 : imageValue in [ 5.000e+01 , 5.000e+01 ] --->
activity (Bq) 4.200e+07
[G4] Range 1 : imageValue in [ 1.150e+03 , 1.150e+03 ] --->
activity (Bq) 9.478e+04
[G4] Range 2 : imageValue in [ 1.250e+03 , 1.250e+03 ] --->
activity (Bq) 4.373e+04
[G4] Range 3 : imageValue in [ 1.350e+03 , 1.350e+03 ] --->
activity (Bq) 1.956e+04
[G4] Range 4 : imageValue in [ 1.450e+03 , 1.450e+03 ] --->
activity (Bq) 8.901e+03
[G4] GateSourceVoxelImageReader::ReadFile : fileName:
nema_phantom_downsampled.h33
[G4] Header read from 'nema_phantom_downsampled.h33'
[G4] Data file name 'nema_phantom_downsampled.i33'
[G4] Nb of planes: 115
[G4] Nb of pixels per plane: 134 100
[G4] Pixel size: 1.988e+00 2.000e+00
[G4] Slice thickness: 1.500e+00
[G4] Matrix size: 2.664e+02 2.000e+02
[G4] Data type: UNSIGNED INTEGER
[G4]
[G4] GateSourceVoxellizedMessenger::SetNewValue
[G4] Source ---------------> voxel_brain
[G4] ID : 0
[G4] type : backtoback
[G4] startTime (s) : 0.000e+00
[G4] time (s) : 0.000e+00
[G4] forcedUnstable : 1
[G4] forcedLifetime (s) : 9.502e+03
[G4] verboseLevel : 0
[G4] -----------------------
[G4] Voxel reader ----------> number of voxels : 980645
[G4] total activity (Bq) : 4.115e+13
[G4] position (mm) : 0.000e+00 0.000e+00 0.000e+00
[G4] voxel size (mm) : 1.988e+00 2.000e+00 1.500e+00
[G4] Source --------------> voxel_brain
[G4] ID : 0
[G4] type : backtoback
[G4] activity (Bq) : 0.000e+00
[G4] startTime (s) : 0.000e+00
[G4] time (s) : 0.000e+00
[G4] forcedUnstable : 1
[G4] forcedHalfLife (s) : 6.586e+03
[G4] verboseLevel : 0
[G4] relative to vol : World
[G4] ----------------------
[G4]
[G4] GPS info ---------------->
[G4] particle : gamma
[G4] SourcePosType : Point
[G4] Shape : NULL
[G4] halfx,halfy,halfz (mm) : 0.000e+00 0.000e+00 0.000e+00
[G4] Radius (mm) : 0.000e+00
[G4] CentreCoords (mm) : 0.000e+00 0.000e+00 0.000e+00
[G4] EnergyDisType : Mono
[G4] AngleDisType : iso
[G4] MinTheta, MaxTheta (deg) : 0.000e+00 1.800e+02
[G4] MinPhi, MaxPhi (deg) : 0.000e+00 3.600e+02
[G4] --------------------------
[G4]
[G4] GateSourceMgr::ListSources: List of the sources in the source manager
[G4] Source ---------------> voxel_brain
[G4] ID : 0
[G4] type : backtoback
[G4] startTime (s) : 0.000e+00
[G4] time (s) : 0.000e+00
[G4] forcedUnstable : 1
[G4] forcedLifetime (s) : 9.502e+03
[G4] verboseLevel : 0
[G4] -----------------------
[Acquisition-0]
[Acquisition-0] ============= Source initialization =============
[Acquisition-0]
[Acquisition-0] ============= Acquisition starts! =============
[Acquisition-0] Simulation start time = 0 sec
[Acquisition-0] Simulation end time = 240 sec
[Acquisition-0] Simulation will have = 1 run(s)
[Acquisition-0]
--
Bassim Aklan, MSc.
Institute of Medical Physics - Section for MR Imaging
University of Erlangen-Nuremberg
Henkestr. 91
91052 Erlangen, Germany
phone: +49-(0)9131/85-25545
bassim.aklan at imp.uni-erlangen.de
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