[Gate-users] Dose actor voxel precision issue
Matthew Strugari
matthew.strugari at dal.ca
Mon Jun 1 21:17:12 CEST 2020
Thank you, Julia and Eng. Pharaon, for your responses.
Julia, I’m glad to hear I’m not the only one experiencing this issue. I was under the impression that setVoxelSize was the preferred method instead of using setResolution although I was just on the ReadTheDocs and found the following (which I have not yet verified):
* If you would like the dose actor to use exactly the same voxels as the input image, then the safest way to configure this is with setResolution. Otherwise, when setting voxelsize, rounding errors may cause the dosels to be slightly different, in particular in cases where the voxel size is not a nice round number (e.g. 1.03516 mm on a dimension with 512 voxels). Such undesired rounding effects have been observed Gate release 7.2 and may be fixed in a later release.
Eng. Pharaon, I am using the “DoseActor”. I would suspect that the results you are experiencing are due to a different effect than what is discussed above. Of course, different Monte Carlo packages are based on different code and different data. Have you tried using a different physics list (see https://geant4.web.cern.ch/node/146), such as empenelope or emlowenergy? The emlivermore physics list uses the G4LivermoreIonisationModel for e- below 100 keV and I wonder if this could be related to your deviated observations above 100 keV. I think this would be a good place to start since you have already implemented cuts and step limits into your simulation.
Best wishes,
Matthew
--
Matthew Strugari
Biomedical Translational Imaging Centre - BIOTIC,
5890 University Ave,
Halifax, NS, B3K 6R8
From: "Eng. M Pharaon" <pharaon_m at hotmail.com>
Date: Saturday, May 30, 2020 at 16:29
To: Matthew Strugari <matthew.strugari at dal.ca>, "gate-users at lists.opengatecollaboration.org" <gate-users at lists.opengatecollaboration.org>
Subject: Re: Dose actor voxel precision issue
CAUTION: The Sender of this email is not from within Dalhousie.
Dear Matthew
What type of dose actor you are using ? Because I'm facing a problem with dose by region actor and my whole project is depending on solving this problem so I could have accurate results .
When I use this actor on low energies, such as 0.01 Mev , the deposited energy results are good and I could confirm from mhd output file that all the energy has been located in the source origin.
But when I use energies for example from 0.3 to 2 Mev, I get results lower than they should be compared to the same voxel phantom results that has been simulated using mcnp code,
Could that be the same problem you faced?or you suggest different things to check?
Below you can check the macrofiles I am using
#/control/execute verbose.mac
#/control/execute ../mac/visu.mac
#==============================
# GEOMETRY
#==============================
/gate/geometry/setMaterialDatabase ../data/GateMaterials.db
#----------------------
# World
#----------------------
/gate/world/geometry/setXLength 300 cm
/gate/world/geometry/setYLength 300 cm
/gate/world/geometry/setZLength 300 cm
/gate/world/setMaterial Air
/gate/world/vis/setVisible 0
# Body
/gate/world/daughters/name phantom
/gate/world/daughters/insert ImageNestedParametrisedVolume
/gate/phantom/geometry/setImage ../data/Segm.mhd
/gate/phantom/geometry/setRangeToMaterialFile ../data/range_geo.dat
#==============================
# PHYSICS
#==============================
#----------------------
# Physics List
#----------------------
/gate/physics/addPhysicsList emlivermore
#----------------------
# Cuts and Step limiters
#----------------------
/gate/physics/Electron/SetCutInRegion world 0.01 mm
/gate/physics/Gamma/SetCutInRegion world 0.01 mm
/gate/physics/Electron/SetCutInRegion phantom 0.001 mm
/gate/physics/Gamma/SetCutInRegion phantom 0.001 mm
/gate/physics/SetMaxStepSizeInRegion phantom 0.001 mm
/gate/physics/ActivateStepLimiter e-
/gate/physics/displayCuts
#########/gate/physics/addPhysicsList emlivermore
#########/gate/physics/Gamma/SetCutInRegion world 10.0 mm
##########/gate/physics/Electron/SetCutInRegion world 10.0 mm
##########/gate/physics/Positron/SetCutInRegion world 10.0 mm
##########/gate/physics/Gamma/SetCutInRegion phantom 0.1 mm
##########/gate/physics/Electron/SetCutInRegion phantom 0.1 mm
##########/gate/physics/Positron/SetCutInRegion phantom 0.1 mm
#==============================
# DETECTORS
#==============================
# It is possible to save a DoseActor as a 3D matrix.
/gate/actor/addActor DoseActor dose3D
/gate/actor/dose3D/attachTo phantom
/gate/actor/dose3D/stepHitType random
/gate/actor/dose3D/setResolution 1346 693 147
/gate/actor/dose3D/enableDose true
/gate/actor/dose3D/save ../output/output.mhd
/gate/actor/dose3D/inputDoseByRegions ../data/Segm.mhd
/gate/actor/dose3D/outputDoseByRegions ../output/DoseByRegions.txt
#==============================
# INITIALISATION
#==============================
/gate/run/initialize
#==============================
# BEAM
#==============================
# Source
/gate/source/addSource phantom voxel
# DECLARATION THAT THE VOXELIZED SOURCE WILL BE ENTERED USING IMAGE DATA
/gate/source/phantom/reader/insert image
/gate/source/phantom/imageReader/translator/insert range
/gate/source/phantom/imageReader/rangeTranslator/readTable ../data/ActivityRange.dat
/gate/source/phantom/imageReader/rangeTranslator/describe 1
# THE FOLLOWING LINE ALLOWS YOU TO INSERT THE IMAGE DATA USING THE APPROPRIATE EXTENSION FILE
/gate/source/phantom/imageReader/readFile ../data/Segm.mhd
# THE DEFAULT POSITION OF THE VOXELIZED SOURCE IS IN THE 1ST QUARTER
# SO THE VOXELIZED SOURCE HAS TO BE SHIFTED OVER HALF ITS DIMENSION IN THE NEGATIVE DIRECTION ON EACH AXIS
/gate/source/phantom/setPosition -673 -346.5 -73.5 mm
# THE FOLLOWING LINES CHARACTERIZE THE SIZE (NO DIFFERENCE WITH AN ANALYTICAL SOURCE)
/gate/source/phantom/gps/particle gamma
/gate/source/phantom/gps/energytype Mono
/gate/source/phantom/gps/monoenergy 0.1 MeV
/gate/source/phantom/gps/angtype iso
#==============================
#==============================
# START SIMULATION
#==============================
/gate/random/setEngineName MersenneTwister
/gate/random/setEngineSeed auto
/gate/application/setTotalNumberOfPrimaries 1000
/gate/application/start
==============================================================
#activity range file
1
135 135 1
Best Regards
Eng. Pharaon
===================
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________________________________
From: Gate-users <gate-users-bounces at lists.opengatecollaboration.org> on behalf of Matthew Strugari <matthew.strugari at dal.ca>
Sent: Tuesday, May 26, 2020 4:38:17 PM
To: gate-users at lists.opengatecollaboration.org <gate-users at lists.opengatecollaboration.org>
Subject: [Gate-users] Dose actor voxel precision issue
Hi all,
When using the dose actor with sub-mm voxels, I notice issues with the floating point precision of the Offset and ElementSpacing stored in the output mhd files:
Offset = -25.440999999999999 -25.440999999999999 -26.25
ElementSpacing = 0.49399998784065247 0.49399998784065247 1.5
Which are based on my settings:
/gate/actor/dose1/setSize 50.882 50.882 52.5 mm
/gate/actor/dose1/setVoxelSize 0.494 0.494 1.5 mm
I have been ignoring this and manually overwriting the header files since the difference is insignificant but it would be nice to avoid having to do that. Has anyone else experienced this issue?
Cheers,
Matthew
--
Matthew Strugari
Biomedical Translational Imaging Centre - BIOTIC,
5890 University Ave,
Halifax, NS, B3K 6R8
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