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Dear Gate users,
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<p>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. <b>However, after my
simulation my root file is empty.<br>
</b>I checked the forum and followed the few inputs I found
but I really don't understand the reason of my problem.<b> </b>Hereafter
are a few details.<b><br>
</b></p>
<p>I hope one of you already faced this issue and will remember
what needs to be changed/added.<b><br>
</b></p>
<p><b><br>
</b></p>
<p>I am using:<br>
Gate 9.0<br>
geant4-10-06-patch-02<br>
root 6.22/02<br>
Ubuntu 20.04.4<br>
</p>
<p>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.<br>
I would like to save only the singles in the output file.<br>
</p>
<p>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.<br>
</p>
<p><img src="cid:part1.yQ7lZu5f.d0rcCj23@phys.ethz.ch" alt=""
class="" width="835" height="308"></p>
<p>Source verbose:<br>
</p>
<p>[GateSourceVoxellized::GeneratePrimaries] Centre: 4.87951
4.50845 7.91909 cm <br>
NumberOfParticlesToBeGenerated: 2<br>
Particle name: gamma<br>
Energy: 0.511<br>
Position: (48.9512,25.5379,79.5088)<br>
Direction: (-0.619851,0.684191,0.384275)<br>
Particle name: gamma<br>
Energy: 0.511<br>
Position: (48.9512,25.5379,79.5088)<br>
Direction: (-0.495773,-0.863156,-0.0957614)<br>
Primary Vertex generated !<br>
GetNumberOfPrimaryVertex : 1<br>
GetNumberOfParticle : 2<br>
GateVSource::GetNextTime : Initial activity (becq) : 589.609<br>
At time (s) 0.657133 activity
(becq) 589.568<br>
GateVSource::GetNextTime : next time (s) 0.00132811<br>
GateSourceVoxellized::GetNextTime : firstTime (s) 0.00132811<br>
</p>
<p><br>
</p>
<p><b>A few settings:</b><br>
<b>* The digitizer is set like that:</b><br>
/gate/digitizer/Singles/insert adder<br>
/gate/digitizer/Singles/insert readout<br>
/gate/digitizer/Singles/readout/setDepth 4</p>
<p><b>* The physic list is set like that:</b><br>
/gate/physics/addPhysicsList emstandard_opt3<br>
/gate/physics/addProcess RadioactiveDecay<br>
/gate/physics/addProcess Decay<br>
</p>
<p><b>* For the output file the settings are these:</b><br>
/gate/output/root/enable<br>
/gate/output/root/setFileName
refFullBrain_root<br>
/gate/output/root/setRootHitFlag 0<br>
/gate/output/root/setRootSinglesFlag 1<br>
/gate/output/root/setRootCoincidencesFlag 0<br>
/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 <br>
</p>
<p><b>* the voxelized phantom is set as followed:</b><br>
/gate/patientVolume/daughters/name
phantom_brain<br>
/gate/patientVolume/daughters/insert
ImageNestedParametrisedVolume<br>
<br>
/gate/geometry/setMaterialDatabase
gate_stuff/HUmaterials.db<br>
/gate/phantom_brain/geometry/setHUToMaterialFile
gate_stuff/HU2mat.mac<br>
/gate/phantom_brain/geometry/setImage
data/rawData.mhd<br>
<br>
/gate/phantom_brain/vis/setVisible 1<br>
/gate/phantom_brain/vis/forceWireframe<br>
/gate/phantom_brain/placement/setTranslation
{phantom_x} {phantom_y} {phantom_z} mm<br>
/gate/phantom_brain/attachPhantomSD<br>
</p>
<p><b>*the voxelized source is set as followed:</b><br>
/gate/source/addSource
voxel_brain voxel<br>
/gate/source/voxel_brain/attachTo
phantom_brain<br>
/gate/source/voxel_brain/reader/insert
image<br>
<br>
/gate/source/voxel_brain/imageReader/translator/insert
linear<br>
/gate/source/voxel_brain/imageReader/linearTranslator/setScale
60000000 Bq<br>
/gate/source/voxel_brain/imageReader/readFile
data/rawPT.mhd<br>
/gate/source/voxel_brain/setPosition
{source_x} {source_y} {source_z} mm<br>
<br>
/gate/source/voxel_brain/setType
backtoback<br>
/gate/source/voxel_brain/gps/particle
gamma<br>
/gate/source/voxel_brain/gps/ene/type
Mono<br>
/gate/source/voxel_brain/setForcedUnstableFlag true<br>
/gate/source/voxel_brain/setForcedHalfLife
6586.2 s<br>
/gate/source/voxel_brain/gps/ene/mono 511.
keV<br>
/gate/source/voxel_brain/gps/ang/type iso<br>
<br>
/gate/source/voxel_brain/dump 1<br>
/gate/source/list<br>
</p>
<p><br>
</p>
<p>Conclusions of what I tried for debugging:<br>
</p>
<p> </p>
<p>- 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.</p>
<p>- If I save the Hits, Singles and Coincidences in an ascii
output file but nothing is saved.</p>
<p><br>
</p>
<p>Any insight would be greatly appreciated.<br>
Don't hesitate if something is not clear or if you need more
details. Thanks you very much in advance.<br>
</p>
<p>Best regards,</p>
<p>Marina<br>
</p>
<p><br>
</p>
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