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<p class="MsoNormal"><span lang="EN-US">Dear GATE users,<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">We are trying to run a GATE simulation with voxelized phantom on our GPU. Installation of CUDA inside GATE seems successful but when we run our script, we get the following error:<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">GateGPUEmisTomo.cc (l.359): pelvis_phantom is not a GateRegularParameterized.<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">=======================================================================<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">====== Radioactive Decay Physics Parameters ========<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">=======================================================================<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">Max life time 1e+15 ps<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">Internal e- conversion flag true<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">Stored internal conversion coefficients false<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">Enable correlated gamma emission false<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">Max 2J for sampling of angular correlations 10<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">Atomic de-excitation enabled true<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">Auger electron emission enabled false<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">Auger cascade enabled false<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">Check EM cuts disabled for atomic de-excitation false<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">Use Bearden atomic level energies false<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">=======================================================================<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">GateGPUEmisTomoMessenger Update<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">WARNING - Attempt to delete the physical volume store while geometry closed !<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">WARNING - Attempt to delete the logical volume store while geometry closed !<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">WARNING - Attempt to delete the solid store while geometry closed !<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">WARNING - Attempt to delete the region store while geometry closed !<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">and the simulation seems to freeze. This is a bit strange as we have defined our phantom as a ImageRegularParametrisedVolume, see below:<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">--------------------------------------------------------------<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">Contents voxelized_pelvis_phantom.mac:<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">#<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">#<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"># P E L V I S S C A N V O X E L I Z E D P H A N T O M<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">/gate/world/daughters/name pelvis_phantom<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">/gate/world/daughters/insert ImageRegularParametrisedVolume<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">/gate/pelvis_phantom/geometry/setImage pelvis_phantom.mhd<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">/gate/pelvis_phantom/geometry/setRangeToMaterialFile range_atten_pelvis_phantom.dat<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">/gate/pelvis_phantom/placement/setTranslation 0.0 0.0 0.0 mm<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">/gate/pelvis_phantom/placement/setRotationAxis 1 0 0<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">/gate/pelvis_phantom/placement/setRotationAngle 0 deg<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">/gate/pelvis_phantom/attachPhantomSD<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">--------------------------------------------------------------<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">Contents range_atten_pelvis_phantom.dat:<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">3<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">0 9 Air true 1.0 0.0 0.0 0.2<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">10 19 Water false 0.0 1.0 0.0 0.2<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">20 29 SpineBone true 0.0 0.0 1.0 0.2<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">--------------------------------------------------------------<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">Contents voxelized_pelvis_phantom_source.mac:<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"># DECLARATION OF THE FACT THAT A VOXELIZED SOURCE WILL BE USED<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"># Always use the keyword voxel to declare the type<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">/gate/source/addSource pelvis_phantom_source GPUEmisTomo<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">/gate/source/pelvis_phantom_source/attachPhantomTo pelvis_phantom<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">/gate/source/pelvis_phantom_source/setGPUBufferSize 1000000<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">/gate/source/pelvis_phantom_source/setGPUDeviceID 1<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"># DECLARATION THAT THE VOXELIZED SOURCE WILL BE ENTERED USING IMAGE DATA<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">/gate/source/pelvis_phantom_source/reader/insert image<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"># INSERT THE TRANSLATOR THAT WILL CONVERT THE IMAGE FROM DIGITAL VALUES TO ACTIVITY VALUES<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"># Example for a linear translator: this scales all image values directly into activities<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">/gate/source/pelvis_phantom_source/imageReader/translator/insert linear<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">/gate/source/pelvis_phantom_source/imageReader/linearTranslator/setScale 1. Bq<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"># THE FOLLOWING LINE ALLOWS YOU TO INSERT THE IMAGE DATA USING THE APPROPRIATE EXTENSION FILE<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">/gate/source/pelvis_phantom_source/imageReader/readFile pelvis_phantom_source.mhd<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">/gate/source/pelvis_phantom_source/imageReader/verbose 1<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"># THE DEFAULT POSITION OF THE VOXELIZED SOURCE IS IN THE 1ST QUARTER<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"># SO THE VOXELIZED SOURCE HAS TO BE SHIFTED OVER HALF ITS DIMENSION IN THE NEGATIVE DIRECTION ON EACH AXIS<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">/gate/source/pelvis_phantom_source/setPosition -65.165 -65.165 16.216 mm<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">#/gate/source/pelvis_phantom_source/dump 1<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"># THE FOLLOWING LINES CHARACTERIZE THE SIZE (NO DIFFERENCE WITH AN ANALYTICAL SOURCE)<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"># The source emits pairs of particles back-to-back<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">/gate/source/pelvis_phantom_source/setType backtoback<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"># The particles emitted by the source are gammas<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">/gate/source/pelvis_phantom_source/gps/particle gamma<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"># The gammas have an energy of 511 keV<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">/gate/source/pelvis_phantom_source/gps/energytype Mono<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">/gate/source/pelvis_phantom_source/gps/monoenergy 0.511 MeV<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"># The angular distribution of emission angles is isotropic<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">/gate/source/pelvis_phantom_source/gps/confine NULL<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">/gate/source/pelvis_phantom_source/gps/angtype iso<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"># The parameters below mean that the source emits at all angles along the z axis<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">/gate/source/pelvis_phantom_source/gps/mintheta 0. deg<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">/gate/source/pelvis_phantom_source/gps/maxtheta 180. deg<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"># The parameters below mean that the source emits at all angles in the transverse (XY) directions<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">/gate/source/pelvis_phantom_source/gps/minphi 0. deg<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">/gate/source/pelvis_phantom_source/gps/maxphi 360. deg<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">--------------------------------------------------------------<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">The above scripts work fine when defining the source as voxel (so without GPU). Does anybody have a similar experience and know how to solve this problem?<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal">Best regards,<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Woutjan Branderhorst<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal"><b><span style="font-family:"Segoe UI",sans-serif;color:#00539F;mso-fareast-language:NL">Woutjan Branderhorst<o:p></o:p></span></b></p>
<p class="MsoNormal"><b><span style="font-size:8.0pt;font-family:"Segoe UI",sans-serif;color:#00539F;mso-fareast-language:NL"><o:p> </o:p></span></b></p>
<p class="MsoNormal"><span style="color:#1F497D;mso-fareast-language:NL"><img width="155" height="60" style="width:1.6145in;height:.625in" id="Afbeelding_x0020_1" src="cid:image001.jpg@01D695AD.BD00DEC0" alt="Beschrijving: Beschrijving: Beschrijving: cid:EEA90C32-0871-49FB-AB50-67779C278527@ds.umcutrecht.nl"></span><b><span style="font-size:10.0pt;font-family:"Arial",sans-serif;color:#0070C0;mso-fareast-language:NL"><o:p></o:p></span></b></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:9.0pt;font-family:"Segoe UI",sans-serif;color:#1F497D;mso-fareast-language:NL">Woutjan Branderhorst, PhD | Post-doctoral researcher | University Medical Center Utrecht<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:9.0pt;font-family:"Segoe UI",sans-serif;color:#1F497D;mso-fareast-language:NL">Division Imaging & Oncology | Department of Radiology and Nuclear Medicine | Room number E.02.3.15<o:p></o:p></span></p>
<p class="MsoNormal" style="text-autospace:none"><span style="font-size:9.0pt;font-family:"Segoe UI",sans-serif;color:#1F497D;mso-fareast-language:NL"><a href="mailto:w.j.branderhorst@umcutrecht.nl"><span lang="EN-US" style="color:blue">w.j.branderhorst@umcutrecht.nl</span></a></span><span lang="EN-US" style="font-size:9.0pt;font-family:"Segoe UI",sans-serif;color:#1F497D;mso-fareast-language:NL">
| T +31 (0) 88 75 50580 | M +31 (0) 642130614<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
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