[Gate-users] Gate-users Digest, Vol 182, Issue 6
Atiq Ur Rahman
atiqchep at gmail.com
Thu Jul 8 05:57:00 CEST 2021
Dear users,
In my previous email, the text formatting was a bit weird. I am combining
my both emails.
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 ,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 361 Dicom images put in a single directory.
You can reproduce my problem using downloading the code directly:
https://drive.google.com/drive/folders/1r2LPzE7KLZX0-kfVTNaQyWADLgelVdR9?usp=sharing
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 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 HUToMat.txt
/gate/Volume/geometry/setImage 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
Dose_Map_Energy_MeV_1D_5material.root
/gate/actor/doseDistribution_text/attachTo Volume
/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
/gate/source/PBS/setEllipseXThetaRotationNorm positive
/gate/source/PBS/setEllipseYPhiRotationNorm positive
/gate/application/setTotalNumberOfPrimaries 1000
/gate/application/start
I have dumped this file into a 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 = Image
NDims = 3
BinaryData = True
BinaryDataByteOrderMSB = False
CompressedData = False
TransformMatrix = 1 0 0 0 1 0 0 0 1
Offset = -151.494 -36.6564 1115
CenterOfRotation = 0 0 0
ElementSpacing = 0.589844 0.589844 0.5
DimSize = 512 512 361
AnatomicalOrientation = ???
ElementType = MET_FLOAT
ElementDataFile = density-ffs-dcm_5mat.raw
Please ask me for any further details if you feel anything ambiguous.
Your suggestions and solutions are needed. Thank you in advance!
Regards
Atiq
On Fri, Jul 9, 2021 at 4:54 AM <
gate-users-request at lists.opengatecollaboration.org> wrote:
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> Today's Topics:
>
> 1. Dose calculation for a CT based voxelized Phantom for Proton
> beam (Atiq Ur Rahman)
> 2. Re: (Reproduce my problem) (Atiq Ur Rahman)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Thu, 8 Jul 2021 04:05:23 +0200
> From: Atiq Ur Rahman <atiqchep at gmail.com>
> To: gate-users at lists.opengatecollaboration.org
> Subject: [Gate-users] Dose calculation for a CT based voxelized
> Phantom for Proton beam
> Message-ID:
> <CAEQ5BgcpvqOn1wL9PXnKCFOQXCwke4m=
> AYTO16REJ1A1rAbVyg at mail.gmail.com>
> Content-Type: text/plain; charset="utf-8"
>
> 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*
> -------------- next part --------------
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> ------------------------------
>
> Message: 2
> Date: Thu, 8 Jul 2021 04:46:15 +0200
> From: Atiq Ur Rahman <atiqchep at gmail.com>
> To: gate-users at lists.opengatecollaboration.org
> Subject: Re: [Gate-users] (Reproduce my problem)
> Message-ID:
> <CAEQ5BgcDHXXqf-wu3gK3dFdWPq=_
> yziUZiMMd9ik1D6pcgsvew at mail.gmail.com>
> Content-Type: text/plain; charset="utf-8"
>
> Dear Users,
> Anyone who wants to reproduce my problem can directly go to google drive.
> Here is the link to the problem.
>
> https://drive.google.com/drive/folders/1r2LPzE7KLZX0-kfVTNaQyWADLgelVdR9?usp=sharing
> Regards
> Atiq
>
> On Thu, Jul 8, 2021 at 4:05 AM Atiq Ur Rahman <atiqchep at gmail.com> wrote:
>
> > 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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> ------------------------------
>
> End of Gate-users Digest, Vol 182, Issue 6
> ******************************************
>
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