[Gate-users] Dose calculation for a CT based voxelized Phantom for Proton beam

[Atiq Ur Rahman]

Dear Gate users,
I am trying to calculate the dose for the CT based Phantom (512x512x361
matrix) using a proton beam. I read dicom images directly and define the HU
to material conversion file.  I am using the vGate.8 virtual machine.
*Problem:* If I define only three materials (vacuum, Air and
TissueEquivalent ) the simulation gives output for 1000 primaries very fast
in a couple of seconds and I can get the output. But if I define one extra
material (any material, I have tried different materials) , let say
(Vacuum, Air, TissueEquvalent, Liver)  the simulation runs for a very very
long time even for 1 primary particle (Actually does not finish even in 10
hours). Can you give me some suggestions to fix the problem. What is the
possible cause of the problem? There seems to be something wrong with my
approach. I have shared my code below.  I have 306 Dicom images put in a
single directory.
Definition of the HUToMat.txt

-2000 -800   Vacuum
-800  -40    Air
-40    200   Blood
200    19000 TissueEquivalent

#CODE
/

*control/execute mac/verbose.mac/gate/geometry/setMaterialDatabase
 data/GateMaterials.db*

*#WorldVolume*









*/gate/world/setMaterial
Vacuum/gate/world/geometry/setXLength           100
cm/gate/world/geometry/setYLength           100
cm/gate/world/geometry/setZLength           100
cm/gate/world/daughters/name
Pat/gate/world/daughters/insert
box/gate/Pat/geometry/setXLength             32
cm/gate/Pat/geometry/setYLength             32
cm/gate/Pat/geometry/setZLength             32 cm*

*#Daughter for DICOM*


*/gate/Pat/daughters/name
Volume/gate/Pat/daughters/insert
 ImageRegularParametrisedVolume #      ImageNestedParametrisedVolume *

*#CoversionFile*
*/gate/Volume/geometry/setHUToMaterialFile       data/HUToMat.txt *




*/gate/Volume/geometry/setImage              New_CODE/data/dcm/1.dcm
#/gate/Volume/placement/setRotationAxis          0 -1
0/gate/Volume/placement/setRotationAngle         90
deg/gate/Volume/setSkipEqualMaterials   1*


*#SIMPLEDOSEActor*










*/gate/actor/addActor
DoseActor  doseDistribution_text/gate/actor/doseDistribution_text/save

 output/Dose_Map_Energy_MeV_1D_5material.root/gate/actor/doseDistribution_text/attachTo
             Volume
#PMMA_Block/gate/actor/doseDistribution_text/stepHitType
random/gate/actor/doseDistribution_text/setSize               300 300 300
mm/gate/actor/doseDistribution_text/setResolution         1280 1
1/gate/actor/doseDistribution_text/enableEdep
 true/gate/actor/doseDistribution_text/enableUncertaintyEdep
true/gate/actor/doseDistribution_text/enableDose
 true/gate/actor/doseDistribution_text/enableUncertaintyDose
true/gate/actor/doseDistribution_text/enableNumberOfHits    true*














*#PhysicsList/gate/physics/addPhysicsList
QGSP_BIC_HP_EMZ#Cuts/gate/physics/Gamma/SetCutInRegion     world 10
mm/gate/physics/Electron/SetCutInRegion    world 10
mm/gate/physics/Positron/SetCutInRegion    world 10
mm/gate/physics/Proton/SetCutInRegion       world 10
mm/gate/physics/Gamma/SetCutInRegion     Pat 1
mm/gate/physics/Electron/SetCutInRegion    Pat 1
mm/gate/physics/Positron/SetCutInRegion    Pat 1
mm/gate/physics/Proton/SetCutInRegion       Pat 1
mm/gate/physics/SetMaxStepSizeInRegion    Pat 1
mm/gate/physics/ActivateStepLimiter proton/gate/physics/displayCuts*






















*/gate/run/initialize/gate/random/setEngineName
MersenneTwister/gate/random/setEngineSeed auto#Source/gate/source/addSource
PBS PencilBeam/gate/source/PBS/setParticleType
proton/gate/source/PBS/setEnergy 90 MeV/gate/source/PBS/setSigmaEnergy .88
MeV/gate/source/PBS/setPosition 0 0 -36.5 cm /gate/source/PBS/setSigmaX 3.0
mm /gate/source/PBS/setSigmaY 3.0 mm #/gate/source/PBS/setRotationAxis 0 1
0#/gate/source/PBS/setRotationAngle 90 deg/gate/source/PBS/setSigmaTheta 20
mrad/gate/source/PBS/setSigmaPhi   20 mrad
/gate/source/PBS/setEllipseXThetaEmittance 40 mm*mrad #40 mm*mrad,
2mm*mrad/gate/source/PBS/setEllipseYPhiEmittance   40 mm*mrad #40 mm*mrad,
2mm*mrad#positive-> converging beam; negative diverging
beam/gate/source/PBS/setEllipseXThetaRotationNorm
positive/gate/source/PBS/setEllipseYPhiRotationNorm
positive/gate/application/setTotalNumberOfPrimaries 1000
/gate/application/start*

*I have dumped this file into single density (.mhd +.raw) format and tried
to read it from a single density file but it has no difference in
performance. Below is the information in the header file.*














*ObjectType = ImageNDims = 3BinaryData = TrueBinaryDataByteOrderMSB =
FalseCompressedData = FalseTransformMatrix = 1 0 0 0 1 0 0 0 1Offset =
-151.494 -36.6564 1115CenterOfRotation = 0 0 0ElementSpacing = 0.589844
0.589844 0.5DimSize = 512 512 361AnatomicalOrientation = ???ElementType =
MET_FLOATElementDataFile = density-ffs-dcm_5mat.raw*

*Please ask me any further details if you feel anything ambiguous.  Your
suggestions and solutions are needed. Thank you in advance!*
*Regards*

*Atiq*
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