[Gate-users] Attenuation issue with voxellized phantom

[Thibaut Merlin]

Dear all

I'm trying to simulate a PET acquisition with respiratory motion from  
a voxellized phantom, using NCAT datasets and the RTphantom module on  
Gate v6.2. The simulation appears to run well, but when I  
reconstructed the image from a 60s acquisition, it seems that no  
attenuation occurred during my simulation (the image was reconstructed  
without attenuation correction meaning that low attenuating regions,  
as the lungs for example, should appear hot. But it is not the case as  
it can be seen in the image provided).

I didn't see any issue about positioning of the phantom when I enabled  
visualisation. In addition, running the simulation with all the  
regions set to "Air" in the range.dat file led to the same results,  
suggesting that the voxellized phantom is indeed not taken into  
account. Using different navigators (regularMatrix, compressedMatrix,  
parameterizedBoxMatrix) didn't change the results.

Script files related to the phantom are posted below. Thanks in  
advance for any help you could provide me !

Best regards,
Thibaut




------------------------------------------------------------------
           Phantom.mac
------------------------------------------------------------------

# Choose a phantom volume name
/gate/world/daughters/name ncat

# Use a voxelized navigator
/gate/world/daughters/insert regularMatrix
/gate/ncat/geometry/insertReader interfile

/gate/RTPhantom/insert RTVPhantom
/gate/RTVPhantom/AttachTo ncat
/gate/RTVPhantom/SetNumberOfFrames 150
/gate/RTVPhantom/SetTimePerFrame 0.1 s
/gate/RTVPhantom/verbose 0
/gate/RTVPhantom/setHeaderFileName data/phantom_p1_128x83x47.h33
/gate/ncat/interfileReader/insertTranslator range
/gate/ncat/interfileReader/rangeTranslator/readTable data/range.dat
/gate/ncat/interfileReader/rangeTranslator/describe 1
/gate/ncat/placement/setTranslation  0. 0. 0. mm
/gate/RTVPhantom/setBaseFileName data/phantom_p1_128x83x47
#/gate/ncat/vis/forceSolid
#/gate/ncat/vis/setColor Blue

/gate/ncat/attachVoxelPhantomSD




------------------------------------------------------------------
          Source.mac
------------------------------------------------------------------


/gate/source/addSource voxel voxel
/gate/source/voxel/reader/insert interfile

/gate/RTVPhantom/AttachToSource voxel
/gate/source/voxel/interfileReader/translator/insert range
/gate/source/voxel/interfileReader/rangeTranslator/readTable  
data/activites.dat
/gate/source/voxel/interfileReader/rangeTranslator/describe 1
#/gate/source/voxel/interfileReader/SetTimeActivityTablesFrom  
TimeActivity_Tables.dat   # (TACS)
/gate/source/voxel/interfileReader/SetTimeSampling 0.1 s


# The default position of the voxellized source is in the 1^{st}
# quarter. So the voxellized source has to be shifted over half its
# dimension (dimension = dimImgXYZ * dimVoxXYZ)in the negative  
direction on each axis
/gate/source/voxel/setPosition   -256 -166 -94 mm


/gate/source/voxel/setType backtoback
/gate/source/voxel/gps/particle gamma
/gate/source/voxel/setForcedUnstableFlag true
/gate/source/voxel/setForcedHalfLife 6586.2 s
/gate/source/voxel/gps/energytype Mono
/gate/source/voxel/gps/monoenergy 0.511 MeV
#/gate/source/voxel/gps/confine NULL
/gate/source/voxel/gps/angtype iso
/gate/source/voxel/dump 0
/gate/source/voxel/verbose 0

/gate/source/list




------------------------------------------------------------------
               phantom_header.h33
------------------------------------------------------------------
!matrix size [1] := 128
!matrix size [2] := 83
!name of data file := data/phantom_p1_128x83x47_atn_1.bin
!number format := unsigned integer
imagedata byte order := LITTLEENDIAN
scaling factor (mm/pixel) [1] := +4.000000e+00
scaling factor (mm/pixel) [2] := +4.000000e+00
!number of slices := 47
slice thickness (pixels) := +4.000000e+00




------------------------------------------------------------------
              range.dat
------------------------------------------------------------------

13
0 0 Air false 0.0 0.0 0.0 0.0 1.0
1 1 Lung true 0. 255. 0. 1.0
10 10 Body false 1.0 1.0 1.0 1.0
20 20 RibBone true 255. 255. 255. 1.0
40 40 SpineBone true 255. 255. 255. 1.0
60 60 Breast true 0. 255. 255. 1.0
70 70 Spleen true 25. 120. 45. 1.0
100 100 Blood true 255. 0. 0. 1.0
110 110 Heart true 255. 120. 45. 1.0
120 120 Liver true 25. 12. 45. 1.0
130 130 Kidney true 40. 12. 45. 1.0
170 170 Breast true 25. 200. 45. 1.0
180 180 Breast true 25. 200. 45. 1.0




------------------------------------------------------------------
              activites.dat
------------------------------------------------------------------

13
0 0 0
1 1 82
10 10 138
20 20 68
40 40 420
60 60 276
70 70 434
100 100 395
110 110 400
120 120 488
130 130 524
170 170 3427
180 180 979
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