Status of GATE-related Projects at Helmholtz-Gemeinschaft
Helmholtz-Gemeinschaft's GATE-related projects involve research on PET-detector designs for BrainPET-insert, simulations of scintillation processes, and challenges with computing time for optical photon studies. Suggestions for improving efficiency are being discussed in the Steering Committee.
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Mitglied der Helmholtz-Gemeinschaft Part II Status of GATE-related projects (Clermont-Ferrand; May 2017) Mirjam Lenz Liliana Caldeira & Uwe Pietrzyk Institute of Neurosciences and Medicine (INM), Research Center Juelich, Germany School of Mathematics and Natural Sciences, University of Wuppertal, Germany
List of Activities FZ-J lich / Uni Wuppertal Mirjam Lenz, PhD - Candidate Extracting DOI-Information for Optical Photons Mitglied der Helmholtz-Gemeinschaft
List of Activities FZ-J lich / Uni Wuppertal Mirjam Lenz (PhD student, since Nov. 2015): Design of novel three-crystal-layer PET-detector as part of a new BrainPET-insert Studying sensitivity of different designs Simulation of scintillation process and tracking of optical photons in crystal arrays/lightguide Dedicated readout module for digitiser (work in progress, collaboration with C. Morel and M. Dupont, CPPM Marseille) Access to scintillation coordinates implemented (=DOI information) Stored in ROOT output: sourcePosX, sourcePosY, sourcePosZ, distinctive sourceID for optical photons, e.g. -5 No increase in computation time observed Flood maps of three-layer detector module calculated and studied Mitglied der Helmholtz-Gemeinschaft
Mirjam Lenz (PhD student): Open question: Future work on optical photons Idea: dedicated module for PET scanners (application and setup differ a lot from bioluminescence example!!) Problem: computing time increases kind of exponentially with crystal array size and especially number of layers! Obvious: GATE is not dedicated to these setups inefficient implementation? 6x7 22x23 23x24 24x24 Now: Simulating crystals instead of 7x8 8x8 Singles output only (Hit output not feasibile) on JURECA: >100000 core hours necessary for full size too expensive! Mitglied der Helmholtz-Gemeinschaft
Some General Suggestions TO be further discussed in the Steering Committee: Mitglied der Helmholtz-Gemeinschaft
Mailing list: template Problems: many emails about operating system, Gate, Geant4, root version, Small and not reproducible code snippets sent Mitglied der Helmholtz-Gemeinschaft
Extend it slightly... If you post to the mailing-list, please fill, copy and paste the following table to your email: Operating system: Gate version: Geant4 version: Root version: Mitglied der Helmholtz-Gemeinschaft and if possible attach a full minimal working example to your email, so that other users can reproduce the problem.
Problem with TrackerDetector under GATE-7.2 eMail from March 2, 2017 / Hancong Xu Hello. I encounted a problem when I tried to execute the example macro of Tracker Detector mode in GATE v7.2. The error information is explained below. To put it in a simple way, I think the GATE v7.2 can not terminate the simulation in the Detector mode and always tries to seek more files to open. So is there any easy approach to solve this problem for v7.2? Many thanks! GATE Version 7.2 GATE macro: example_TrackerDetector When executing the Tracker model, it pops the error when the program finishes: "WARNING - Attempt to delete the physical volume store while geometry closed ! WARNING - Attempt to delete the logical volume store while geometry closed ! WARNING - Attempt to delete the solid store while geometry closed ! WARNING - Attempt to delete the region store while geometry closed ! GateToRoot::RecordEndOfAcquisition(): Failed to access to 'total_nb_primaries' histogram to fill it !" When excuting the Detector model, the program goes to the endless loop. After interpreting the program, the error is : "GateSource::GeneratePrimaries End of Tracks Root file reached ... Seeking for more files to open. GateSource::GeneratePrimaries End of Tracks Root file reached ... Seeking for more files to open. Session terminated. -------- EEEE ------- G4Exception-START -------- EEEE ------- *** G4Exception : UI0001" The file created by Tracker mode is 234 Mb and for Detector mode is 322 Kb. But there is some useful simulated data in both files. So I think the simulation works for v7.2, but can not be terminated properly. If we execute the same script of Tracker mode on GATE Version 7.1, there is no error popped out like v7.2. And The Detector mode can be executed and terminated in the right way with a output of 322 Kb as well. However, there is till some error message. "GateSource::GeneratePrimaries End of Tracks Root file reached ... Seeking for more files to open. [Acquisition-0] Slice 1 from 1 to 1 s [slice=0 s], final stop at 1 s. <!> *** WARNING *** <!> Warning in GateApplicationMgr::GetTimeSlice, run=1 is greater than the list of slices. Do nothing Mitglied der Helmholtz-Gemeinschaft GateSource::GeneratePrimaries End of Tracks Root file reached ... Seeking for more files to open. [Acquisition-0] Slice 2 from 1 to 0 s [slice=0 s], final stop at 1 s. <!> *** WARNING *** <!> Warning in GateApplicationMgr::GetTimeSlice, run=2 is greater than the list of slices. Do nothing GateApplicationMgr.cc (l.218): Error in GateApplicationMgr::GetTimeSlice, run=2 WARNING - Attempt to delete the physical volume store while geometry closed ! WARNING - Attempt to delete the logical volume store while geometry closed ! WARNING - Attempt to delete the solid store while geometry closed ! WARNING - Attempt to delete the region store while geometry closed !" Thus we can see v7.1 and v7.2 have the similar simulation results. But both have some errors in the problem, which might need to be fixed.
The EduGATE Lecture Book Using GATE exposing Physics Introduction From Decay to Detection Sources the Origin of Particles and Radiation [*Spectro] Ion-Sources Radioactive Decay Gamma Sources, single or back to back Electrons and Positrons High Activity and Short simulation vs. Mitglied der Helmholtz-Gemeinschaft Low Activity and Long Simulation Sources Shapes, Materials, special: intrinsic radioactivity [* existing module]
The EduGATE Lecture Book Using GATE exposing Physics Physical Effects The Basis for Interaction and Detection [*Cerenkov, Attenuation, *MR_PET, *Spectrometry_Gamma] Photoelectric-Effect, Compton-Effect, Pair-Production Bremsstrahlung Ionization Cerenkov-Effect Basic Elements of a Radiation Detector From a single Channel to a full Imaging System [*Coin_Chan, *Gamma_Camera, *SPECT_to_Reco, Readout_Digitizer, Optical Photons] Mitglied der Helmholtz-Gemeinschaft Monte Carlo as a Method: Where are the Limits? A Critical Reflection [CPU vs. GPU] [* existing module]
Contact Prof. Dr. Uwe Pietrzyk Institute of Neuroscience and Medicine (INM-4) - Medical Imaging Physics - Forschungszentrum J lich GmbH U.Pietrzyk@fz-juelich.de http://www.fz-juelich.de and School of Mathematics and Natural Science - Medical Physics - Bergische Universit t Wuppertal Uwe.Pietrzyk@uni-wuppertal.de http://www.medizinphysik.uni-wuppertal.de Germany Mitglied der Helmholtz-Gemeinschaft
