[Gate-users] Empty output file with voxelized source/phantom and ring PET scanner

Marina Beguin mbeguin at phys.ethz.ch
Mon Aug 22 12:11:32 CEST 2022

Dear Gate users,

I am having difficulties obtaining an output from my simulation. The 
simulation run as it should be (long enough), smoothly and there is no 
error messages. *However, after my simulation my root file is empty.
*I checked the forum and followed the few inputs I found but I really 
don't understand the reason of my problem.**Hereafter are a few details.*

I hope one of you already faced this issue and will remember what needs 
to be changed/added.*


I am using:
Gate 9.0
root 6.22/02
Ubuntu 20.04.4

I am simulating a brain scan from real CT/PT data and centered in a ring 
PET scanner. Both my source and my phantom are voxelized. I am using 
back-to-back gamma radiations with the emstandard_opt3 physics list and 
the RadioactiveDecay process.
I would like to save only the singles in the output file.

The sourceMap below shows that the simulation is running correctly. 
Furthermore, below the image is a part of the verbose from source. It 
also proves that particles are generated.

Source verbose:

[GateSourceVoxellized::GeneratePrimaries] Centre: 4.87951 4.50845 
7.91909 cm
  NumberOfParticlesToBeGenerated: 2
Particle name: gamma
        Energy: 0.511
      Position: (48.9512,25.5379,79.5088)
     Direction: (-0.619851,0.684191,0.384275)
Particle name: gamma
        Energy: 0.511
      Position: (48.9512,25.5379,79.5088)
     Direction: (-0.495773,-0.863156,-0.0957614)
  Primary Vertex generated !
GetNumberOfPrimaryVertex : 1
GetNumberOfParticle      : 2
GateVSource::GetNextTime : Initial activity (becq) : 589.609
                             At time (s) 0.657133 activity (becq) 589.568
GateVSource::GetNextTime : next time (s) 0.00132811
GateSourceVoxellized::GetNextTime : firstTime (s) 0.00132811

*A few settings:*
** The digitizer is set like that:*
/gate/digitizer/Singles/insert                     adder
/gate/digitizer/Singles/insert                     readout
/gate/digitizer/Singles/readout/setDepth  4

** The physic list is set like that:*
/gate/physics/addPhysicsList           emstandard_opt3
/gate/physics/addProcess                RadioactiveDecay
/gate/physics/addProcess                Decay

** For the output file the settings are these:*
/gate/output/root/setFileName refFullBrain_root
/gate/output/root/setRootHitFlag                     0
/gate/output/root/setRootSinglesFlag              1
/gate/output/root/setRootCoincidencesFlag    0
/gate/output/ascii/setSingleMask                    1 1 1 0 0 0 1 1 1 1 
1 1 1 0 0 0 0 0 0 0 0

** the voxelized phantom is set as followed:*
/gate/patientVolume/daughters/name phantom_brain
/gate/patientVolume/daughters/insert ImageNestedParametrisedVolume

/gate/geometry/setMaterialDatabase gate_stuff/HUmaterials.db
/gate/phantom_brain/geometry/setHUToMaterialFile gate_stuff/HU2mat.mac
/gate/phantom_brain/geometry/setImage data/rawData.mhd

/gate/phantom_brain/vis/setVisible                              1
/gate/phantom_brain/placement/setTranslation {phantom_x} {phantom_y} 
{phantom_z} mm

**the voxelized source is set as followed:*
/gate/source/addSource           voxel_brain voxel
/gate/source/voxel_brain/attachTo phantom_brain
/gate/source/voxel_brain/reader/insert    image

/gate/source/voxel_brain/imageReader/translator/insert linear
/gate/source/voxel_brain/imageReader/linearTranslator/setScale 60000000 Bq
/gate/source/voxel_brain/imageReader/readFile      data/rawPT.mhd
/gate/source/voxel_brain/setPosition                          {source_x} 
{source_y} {source_z} mm

/gate/source/voxel_brain/setType backtoback
/gate/source/voxel_brain/gps/particle gamma
/gate/source/voxel_brain/gps/ene/type Mono
/gate/source/voxel_brain/setForcedUnstableFlag       true
/gate/source/voxel_brain/setForcedHalfLife 6586.2 s
/gate/source/voxel_brain/gps/ene/mono                    511. keV
/gate/source/voxel_brain/gps/ang/type                      iso

/gate/source/voxel_brain/dump         1

Conclusions of what I tried for debugging:

- If I use the exact same code with a sphere phantom (not voxelized), 
the simulation runs and the singles are  correctly saved in the output 
root file.

- If I save the Hits, Singles and Coincidences in an ascii output file 
but nothing is saved.

Any insight would be greatly appreciated.
Don't hesitate if something is not clear or if you need more details. 
Thanks you very much in advance.

Best regards,


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