[Gate-users] Materials not showing up on GATE simulation

David Leibold D.Leibold at tudelft.nl
Fri Aug 26 22:51:04 CEST 2022 

Dear Maggie,

I noticed that your phantom has a thickness of only 100 µm (if I’m not mistaken). With muscle tissue, you would see barely any attenuation; in fact, the attenuation is probably so low that you can’t see it in your projection images.

The alternative materials you mention (uranium, gold, platinum and tungsten) are high Z (high atomic number) materials, therefore their attenuation is considerably higher than body-like materials (check e.g. the NIST database<https://physics.nist.gov/PhysRefData/Xcom/html/xcom1.html> for X-ray attenuation of e.g. uranium and water).

I would advise you to increase the thickness of your phantom two a few centimetres, and then check whether you can see them in your projection images (note that a few centimetres of e.g. uranium would probably stop the X-ray beam completely). Let us know whether that works.

Best regards,
David



On 26 Aug2022, at 18:53, Margarete Kattau <margarete.kattau at icr.ac.uk<mailto:margarete.kattau at icr.ac.uk>> wrote:

Dear fellow GATE-users,

I am facing issues with a simulation. My geometry consists of a planar X-ray source (120 kVp) irradiating a simple phantom consisting of a large disc (muscle) and three smaller inserts (air, bone and adipose tissue). The detector is positioned behind the phantom (screenshot of geometry attached). The problem is that when I reconstruct the image based on the counts registered in the detector, I only see the source and no sign of the phantom (attached image.png). This is really odd, as I have previously run the same mac script but with different materials (uranium, gold, platinum, tungsten) and the image looked as expected (attached image2.png).

I tried many things, such as only using uranium as a higher absorbing material for the large disc and keeping the smaller inserts as air, adipose and bone, which then makes the large disc appear, but the smaller discs are translucent (image3.png). Finally, if I only use a bone disc without any inserts, I still see no disc, even though I should be able to see a difference in attenuation between bone and the surrounding air.
Please note that the images have different activity levels, but I don't expect that this to make such a big difference (~70e6 Bq for image.png and image2.png, ~7e6 Bq for image3.png, simulation time: 1 sec).

Has anyone ever experienced similar issues or knows how to solve this? Many thanks in advance!

Best,
Maggie

P.S.:
This is my mac script:

#==============================================================================================
# Visualization
#==============================================================================================

#/control/execute mac/visu.mac

#==============================================================================================
# Materials
#==============================================================================================

/gate/geometry/setMaterialDatabase data/GateMaterials.db

#==============================================================================================
# Geometry
#==============================================================================================

/gate/world/setMaterial       Air
/gate/world/geometry/setXLength     5 m
/gate/world/geometry/setYLength     5 m
/gate/world/geometry/setZLength     5 m

/gate/world/daughters/name              scanner
/gate/world/daughters/insert            box
/gate/scanner/geometry/setXLength         53. mm
/gate/scanner/geometry/setYLength         40. mm
/gate/scanner/geometry/setZLength         2. mm

/gate/scanner/daughters/name        detector
/gate/scanner/daughters/insert      box
/gate/detector/geometry/setXLength  0.220 mm
/gate/detector/geometry/setYLength  0.220 mm
/gate/detector/geometry/setZLength  1. mm
/gate/detector/setMaterial          CdTe
/gate/detector/repeaters/insert     cubicArray
/gate/detector/cubicArray/setRepeatNumberX      240
/gate/detector/cubicArray/setRepeatNumberY      180
/gate/detector/cubicArray/setRepeatVector 0.220 0.220 0. mm 
/gate/detector/vis/setVisible       1
/gate/detector/vis/setColor         yellow
/gate/detector/vis/forceSolid

/gate/world/daughters/name          musclePhantom
/gate/world/daughters/insert        cylinder
/gate/musclePhantom/geometry/setRmin      0. mm
/gate/musclePhantom/geometry/setRmax      15.84 mm
/gate/musclePhantom/geometry/setHeight    0.1 mm
/gate/musclePhantom/placement/setTranslation    0. 0. 5. cm
/gate/musclePhantom/setMaterial     Muscle
/gate/musclePhantom/vis/setVisible  1
/gate/musclePhantom/vis/setColor    red
/gate/musclePhantom/vis/forceWireframe

/gate/musclePhantom/daughters/name  airDisc
/gate/musclePhantom/daughters/insert      cylinder
/gate/airDisc/geometry/setRmin      0. mm
/gate/airDisc/geometry/setRmax      4. mm
/gate/airDisc/geometry/setHeight    0.1 mm
/gate/airDisc/placement/setTranslation    0. 10.42 0. mm
/gate/airDisc/setMaterial           Air
/gate/airDisc/vis/setVisible        1
/gate/airDisc/vis/setColor          cyan
/gate/airDisc/vis/forceSolid

/gate/musclePhantom/daughters/name  boneDisc
/gate/musclePhantom/daughters/insert      cylinder
/gate/boneDisc/geometry/setRmin     0. mm
/gate/boneDisc/geometry/setRmax     4. mm
/gate/boneDisc/geometry/setHeight   0.1 mm
/gate/boneDisc/placement/setTranslation   0. 0. 0. mm
/gate/boneDisc/setMaterial          Bone
/gate/boneDisc/vis/setVisible       1
/gate/boneDisc/vis/setColor         white
/gate/boneDisc/vis/forceSolid

/gate/musclePhantom/daughters/name  fatDisc
/gate/musclePhantom/daughters/insert      cylinder
/gate/fatDisc/geometry/setRmin      0. mm
/gate/fatDisc/geometry/setRmax      4. mm
/gate/fatDisc/geometry/setHeight    0.1 mm
/gate/fatDisc/placement/setTranslation    0. -10.42 0. mm
/gate/fatDisc/setMaterial           Adipose
/gate/fatDisc/vis/setVisible        1
/gate/fatDisc/vis/setColor          yellow
/gate/fatDisc/vis/forceSolid

#============================================================================================
# Physics
#============================================================================================

/gate/physics/addPhysicsList emstandard_opt4

#==============================================================================================
# Outputs & Actors
#==============================================================================================

/gate/systems/scanner/level1/attach detector
/gate/detector/attachCrystalSD

/gate/output/tree/enable
/gate/output/tree/addFileName             output/tree.root
/gate/output/tree/hits/enable

#==============================================================================================
# Initialisation
#==============================================================================================

/gate/run/initialize

#==============================================================================================
# Source
#==============================================================================================

# X-ray spectrum
/gate/source/addSource  interpolationSpectrum         gps
/gate/source/interpolationSpectrum/gps/particle gamma
/gate/source/interpolationSpectrum/gps/energytype     UserSpectrum
/gate/source/interpolationSpectrum/gps/setSpectrumFile ../Xray_spectrum120kVp_new_MeV.txt
/gate/source/interpolationSpectrum/gps/position 0. 0. 10. cm
/gate/source/interpolationSpectrum/gps/type           Plane
/gate/source/interpolationSpectrum/gps/shape          Circle
/gate/source/interpolationSpectrum/gps/radius         21.78 mm
/gate/source/interpolationSpectrum/setActivity  7.36e6 becquerel    

#==============================================================================================
# Main program
#==============================================================================================
/gate/random/setEngineSeed 523678

/gate/application/setTimeSlice      0.1 s
/gate/application/setTimeStart      0. s
/gate/application/setTimeStop 1. s
/gate/application/start





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