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

Margarete Kattau margarete.kattau at icr.ac.uk
Fri Aug 26 18:53:55 CEST 2022 

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






The Institute of Cancer Research: Royal Cancer Hospital, a charitable Company Limited by Guarantee, Registered in England under Company No. 534147 with its Registered Office at 123 Old Brompton Road, London SW7 3RP.

This e-mail message is confidential and for use by the addressee only. If the message is received by anyone other than the addressee, please return the message to the sender by replying to it and then delete the message from your computer and network.
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.opengatecollaboration.org/pipermail/gate-users/attachments/20220826/e6a1b5e9/attachment-0001.html>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: geometry.png
Type: image/png
Size: 12452 bytes
Desc: geometry.png
URL: <http://lists.opengatecollaboration.org/pipermail/gate-users/attachments/20220826/e6a1b5e9/attachment-0004.png>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: image.png
Type: image/png
Size: 113218 bytes
Desc: image.png
URL: <http://lists.opengatecollaboration.org/pipermail/gate-users/attachments/20220826/e6a1b5e9/attachment-0005.png>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: image2.png
Type: image/png
Size: 111635 bytes
Desc: image2.png
URL: <http://lists.opengatecollaboration.org/pipermail/gate-users/attachments/20220826/e6a1b5e9/attachment-0006.png>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: image3.png
Type: image/png
Size: 151474 bytes
Desc: image3.png
URL: <http://lists.opengatecollaboration.org/pipermail/gate-users/attachments/20220826/e6a1b5e9/attachment-0007.png>

More information about the Gate-users mailing list