<html> <head> <meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1"> </head> <body bgcolor="#FFFFFF"> <div class="moz-cite-prefix">Hi Deborah, in case you have not found the problem yet: There is just a tiny mistake in your macro: Instead of the line /run/initialize you have to use the line /gate/run/initialize for the physics initialization. Then you should see data in your output files. Best regards, Michaela On 11/22/2013 01:40 PM, Débora Salvado wrote: </div> <blockquote type="cite"> <div dir="ltr"> <div> <div>Hi all, </div> I'm trying to simulate a simple pinhole collimator for a SPECT system. For simplicity, I defined a large aperture, and a point source with only a few counts. </div> I managed to run the simulation without any errors, but when I open any of the output files, there's nothing in there. No counts at all. Any suggestions about what might be wrong? You can check the code below. Thanks. <div> <div> <div> <div>Cheers Debora Salvado </div> <div>PhD student, UCL Institute of Nuclear Medicine -- ############################################# # V I S U A L I S A T I O N /vis/disable ################################################# # M A T E R I A L S # Mandatory load of materials file /gate/geometry/setMaterialDatabase GateMaterials.db ################################################# # W O R L D # Define the world dimensions /gate/world/geometry/setXLength 1000.0 mm /gate/world/geometry/setYLength 1000.0 mm /gate/world/geometry/setZLength 1000.0 mm ################################################# # S C A N N E R H E A D # Create a new box representing the main # head-volume SPECThead is the name of the # predefined SPECT system Create the SPECT # system, which will yield an Interfile output # of projection data /gate/world/daughters/name SPECThead /gate/world/daughters/insert box # Define the dimensions of the main volume /gate/SPECThead/geometry/setXLength 300. mm /gate/SPECThead/geometry/setYLength 300. mm /gate/SPECThead/geometry/setZLength 300. mm # Define the position of the main volume # Move the head x cm away from the Z axis, # which is the rotation axis and the # replication axis /gate/SPECThead/placement/setTranslation 350. 0. 0. mm /gate/SPECThead/repeaters/insert ring /gate/SPECThead/ring/setRepeatNumber 4 # Set the material associated with the main volume /gate/SPECThead/setMaterial Air /gate/SPECThead/attachPhantomSD # Define some visualisation options /gate/SPECThead/vis/forceWireframe # Shielding # Create the shielding volume /gate/SPECThead/daughters/name shielding /gate/SPECThead/daughters/insert box # Define the dimensions of the shielding volume /gate/shielding/geometry/setXLength 300. mm /gate/shielding/geometry/setYLength 300. mm /gate/shielding/geometry/setZLength 300. mm # Define the position of the shielding volume /gate/shielding/placement/setTranslation 0. 0. 0. mm # Set the material corresponding to the # shielding volume /gate/shielding/setMaterial Lead # Define some visualisation options /gate/shielding/vis/setColor red /gate/shielding/vis/forceWireframe # Attach phantom SD to record Compton # interactions in the shielding volume # Needed to discriminate between scattered # and unscattered photons /gate/shielding/attachPhantomSD ################################################# # C O L L I M A T O R # Create a full volume defining the shape # of the collimator /gate/SPECThead/daughters/name collimator /gate/SPECThead/daughters/insert box /gate/collimator/geometry/setXLength 20. mm /gate/collimator/geometry/setYLength 300. mm /gate/collimator/geometry/setZLength 300. mm /gate/collimator/setMaterial Lead /gate/collimator/placement/setTranslation -140. 0. 0. mm /gate/collimator/vis/forceWireframe /gate/collimator/vis/setColor red # Attach PhantomSD to record Compton # interactions in the collimator volume /gate/collimator/attachPhantomSD ################################################# # P I N H O L E # Insert the pinhole in the collimator /gate/collimator/daughters/name hole /gate/collimator/daughters/insert cylinder /gate/hole/geometry/setHeight 20. mm /gate/hole/geometry/setRmax 10. mm /gate/hole/placement/alignToX /gate/hole/setMaterial Air /gate/hole/vis/forceSolid /gate/collimator/daughters/name cone1 /gate/collimator/daughters/insert cone /gate/cone1/geometry/setHeight 10. mm /gate/cone1/geometry/setRmin1 0. mm /gate/cone1/geometry/setRmax1 30. mm /gate/cone1/geometry/setRmin2 0. mm /gate/cone1/geometry/setRmax2 10. mm /gate/cone1/placement/setTranslation -5. 0. 0. mm /gate/cone1/placement/alignToX /gate/cone1/setMaterial Air /gate/cone1/vis/forceSolid /gate/collimator/daughters/name cone2 /gate/collimator/daughters/insert cone /gate/cone2/geometry/setHeight 10. mm /gate/cone2/geometry/setRmin1 0. mm /gate/cone2/geometry/setRmax1 10. mm /gate/cone2/geometry/setRmin2 0. mm /gate/cone2/geometry/setRmax2 30. mm /gate/cone2/placement/setTranslation 5. 0. 0. mm /gate/cone2/placement/alignToX /gate/cone2/setMaterial Air /gate/cone2/vis/forceSolid ################################################# # C A M H E A D A I R # insert air behind the collimator /gate/SPECThead/daughters/name aircomp /gate/SPECThead/daughters/insert box /gate/aircomp/geometry/setXLength 70. mm /gate/aircomp/geometry/setYLength 260. mm /gate/aircomp/geometry/setZLength 260. mm /gate/aircomp/placement/setTranslation -95. 0. 0. mm /gate/aircomp/vis/forceWireframe /gate/aircomp/setMaterial Air ################################################# # C R Y S T A L # Create the crystal volume /gate/SPECThead/daughters/name crystal /gate/SPECThead/daughters/insert box # Define the dimensions of the crystal volume /gate/crystal/geometry/setXLength 26. mm /gate/crystal/geometry/setYLength 260. mm /gate/crystal/geometry/setZLength 260. mm # Define the position of the crystal volume /gate/crystal/placement/setTranslation -47. 0. 0. mm # Set the material associated with the crystal # volume /gate/crystal/setMaterial NaI # Define some visualisation options /gate/crystal/vis/setColor yellow # The crystal SD makes it possible to # record hits in a sensitive volume /gate/crystal/attachCrystalSD ################################################# # B A C K - C O M P A R T M E N T # Create the back-compartment volume /gate/SPECThead/daughters/name compartment /gate/SPECThead/daughters/insert box # Define the dimensions of the back-compartment volume /gate/compartment/geometry/setXLength 40. mm /gate/compartment/geometry/setYLength 260. mm /gate/compartment/geometry/setZLength 260. mm # Define the position of the back-compartment volume /gate/compartment/placement/setTranslation -14. 0. 0. mm # Set the material of the back-compartment volume /gate/compartment/setMaterial Glass # Define some visualisation options /gate/compartment/vis/setColor grey # Attach PhantomSD to record Compton # interactions in the back-compartment volume /gate/compartment/attachPhantomSD ################################################# # P H A N T O M # Create the phantom volume /gate/world/daughters/name Phantom /gate/world/daughters/insert sphere # Define the dimensions of the phantom # volume /gate/Phantom/geometry/setRmax 0.01 cm /gate/Phantom/geometry/setRmin 0. mm /gate/Phantom/placement/setTranslation 0. 0. 0. mm # Set the material corresponding to the # phantom volume /gate/Phantom/setMaterial Water # Define some visualisation options /gate/Phantom/vis/setColor blue /gate/Phantom/vis/forceWireframe # Attach PhantomSD to record Compton # interactions in the phantom volume # This can provide information # for result analysis to discriminate between # scattered and unscattered photons. /gate/Phantom/attachPhantomSD ################################################# # SENSITIVE DETECTORS # GATE provides two sensitive detectors, # which have two different functions # Using them properly is very important # for getting accurate results. ################################################# # S Y S T E M # The system acts as an interpretor between # the GATE geometry and data outputs for # reconstruction in our case, the Interfile # writer. A system must know which components # of the geometry are parts of the scanner, # and what their role are. For the moment, # there is only a system SPECThead, which # was built when the SPECThead volume was # inserted. # The SPECThead system is made of three # levels: base (for the head), crystal (for # the crystal and crystal matrix) and pixel # (for individual crystals for pixellated # gamma camera) For now, only the base of # the system is attached to a volume: the # volume SPECThead. For the system to get # information about your crystal, the level # crystal must be attached to the volume that # has been defined for the scintillating # crystal (crystal) /gate/systems/SPECThead/crystal/attach crystal # Look at the system /gate/systems/SPECThead/describe ################################################# # P H Y S I C S /gate/physics/addProcess PhotoElectric /gate/physics/processes/PhotoElectric/setModel StandardModel /gate/physics/addProcess Compton /gate/physics/processes/Compton/setModel PenelopeModel /gate/physics/addProcess RayleighScattering /gate/physics/processes/RayleighScattering/setModel PenelopeModel /gate/physics/addProcess ElectronIonisation /gate/physics/processes/ElectronIonisation/setModel StandardModel e- /gate/physics/addProcess Bremsstrahlung /gate/physics/processes/Bremsstrahlung/setModel StandardModel e- /gate/physics/addProcess MultipleScattering e- /gate/physics/processList Enabled /gate/physics/processList Initialized ################################################# # C U T S # Cuts for particle in WORLD /gate/physics/Gamma/SetCutInRegion SPECThead 0.1 cm /gate/physics/Electron/SetCutInRegion SPECThead 1.0 cm # Physics initialization /run/initialize ################################################# # S O U R C E # Setting up the source /gate/source/addSource SourceConfinement # Define the shape of the source /gate/source/SourceConfinement/gps/type Volume /gate/source/SourceConfinement/gps/shape Sphere # Define the dimensions of the source /gate/source/SourceConfinement/gps/radius 0.01 cm # Define the placement of the source /gate/source/SourceConfinement/gps/centre 0. 0. 0. mm # Define the source as a gamma source /gate/source/SourceConfinement/gps/particle gamma # Define the gamma energy /gate/source/SourceConfinement/gps/energy 140. keV # Set the activity of the source /gate/source/SourceConfinement/setActivity 8000. Bq # Define the emission direction (4 str) /gate/source/SourceConfinement/gps/angtype iso ################################################# # D I G I T I Z E R # The digitizer tracks what happens in the # detection system and in the electronics # Build a digitizer that first computes the # centroid of interactions /gate/digitizer/Singles/insert adder /gate/digitizer/Singles/insert blurring /gate/digitizer/Singles/blurring/setResolution 0.15 /gate/digitizer/Singles/blurring/setEnergyOfReference 140. keV /gate/digitizer/Singles/insert spblurring /gate/digitizer/Singles/spblurring/setSpresolution 10.0 mm /gate/digitizer/Singles/spblurring/verbose 0 /gate/digitizer/Singles/insert thresholder /gate/digitizer/Singles/thresholder/setThreshold 20. keV /gate/digitizer/Singles/insert upholder /gate/digitizer/Singles/upholder/setUphold 190. keV ################################################# # O U T P U T # Select the options of the data output # As there are several modules, settings have # to be defined for each module, especially in # SPECT, where there are a lots of hits for # only a few counts, so it's better to limit # the amount of data produced Here the # SingleDigi output can be used if you have # your own program to process the data /gate/output/root/enable /gate/output/root/setFileName pinholeSPECT /gate/output/root/setRootHitFlag 1 /gate/output/root/setRootSinglesAdderFlag 1 /gate/output/root/setRootSinglesBlurringFlag 1 /gate/output/root/setRootSinglesSpblurringFlag 1 /gate/output/root/setRootSinglesThresholderFlag 1 /gate/output/root/setRootSinglesUpholderFlag 1 /gate/output/ascii/enable /gate/output/ascii/setFileName test /gate/output/ascii/setOutFileHitsFlag 1 /gate/output/ascii/setOutFileSinglesFlag 1 /gate/output/ascii/setOutFileSinglesAdderFlag 0 /gate/output/ascii/setOutFileSinglesSpblurringFlag 0 /gate/output/ascii/setOutFileSinglesBlurringFlag 0 /gate/output/ascii/setOutFileSinglesThresholderFlag 0 /gate/output/ascii/setOutFileSinglesUpholderFlag 0 ################################################# # R A N D O M # Change the root of the random module to run different simulations /gate/random/setEngineName Ranlux64 /gate/random/setEngineSeed 123456789 /gate/random/verbose 1 ################################################# # P R O J E C T I O N # Makes a set of projections from the crystal # hits Define the binning the projection module # to be used /gate/output/projection/enable /gate/output/projection/setFileName gate /gate/output/projection/pixelSizeX 2.03125 mm /gate/output/projection/pixelSizeY 2.03125 mm /gate/output/projection/pixelNumberX 128 /gate/output/projection/pixelNumberY 128 # Specify the projection plane (XY, YZ or ZX) /gate/output/projection/projectionPlane YZ ################################################# # E X P E R I M E N T # Define the parameters of the experiment # (start time, stop time and time slice) # The number of projections depends on the # number of time slice, the rotation speed of # the system and the number of heads /gate/application/setTimeSlice 240. s /gate/application/setTimeStart 0. s /gate/application/setTimeStop 240. s ################################################# # V E R B O S I T Y /control/verbose 0 /run/verbose 0 /event/verbose 0 /tracking/verbose 0 ################################################# # L E T ' S R U N T H E S I M U L A T I O N ! /gate/application/startDAQ </div> </div> </div> </div> </div> <fieldset class="mimeAttachmentHeader"></fieldset> <pre>_______________________________________________ Gate-users mailing list <a class="moz-txt-link-abbreviated" href="mailto:Gate-users@lists.opengatecollaboration.org">Gate-users@lists.opengatecollaboration.org</a> <a class="moz-txt-link-freetext" href="http://lists.opengatecollaboration.org/mailman/listinfo/gate-users">http://lists.opengatecollaboration.org/mailman/listinfo/gate-users</a></pre> </blockquote> ------------------------------------------------------------------------------------------------ ------------------------------------------------------------------------------------------------ Forschungszentrum Juelich GmbH 52425 Juelich Sitz der Gesellschaft: Juelich Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. 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