[Gate-users] 3-D image reconstruction using STIR from GATE Results
Claude Comtat
claude.comtat at cea.fr
Wed Apr 11 14:19:54 CEST 2007
Hi Guifen,
I just run your macro. First, your point source is not at the center
(x=0,y=0):
/gate/source/F18LineSource/gps/centre 10.0 0.0 0.0 cm
Anyhow, the resulting sinogram (MySinogramFile.S) just looks fine.
I do not see any particular problem. Maybe your problem is related to
the way you display the sinogram.
All the best,
Claude
Guifen Lin wrote:
> Hi
> simulate a point source (x=0,y=0) in the file PET_Ecat.mac.I
> reconstructe the image in two mwthod:
> 1.Method one
> <1>.
> cd /usr/local/gate/gate_v3.0.0/examples/my_example/PET
> source /usr/local/gate/gate_v3.0.0/env_gate.csh
> /usr/local/gate/g4work/bin/Linux-g++/Gate my_PET_Ecat.mac
> ......
>
> <2>.
> [root at localhost ~]# cd /usr/local/gate/STIR/my_test
> [root at localhost my_test]# /usr/local/gate/STIR/bin/ifheaders_for_ecat7
> MySinogramFile.S
> Attempt all data-sets (Y) or single data-set (N) [Y/N D:Y]:
> Data number ? [0,8 D:0]:
> WARNING: ECAT7 IO: Bin size from header.x_resolution (2.2471) does not
> agree with expected value 2.25
> for scanner ECAT 962. Using bin size from header...
>
> <3>.
> [root at localhost my_test]# /usr/local/gate/STIR/bin/display_projdata
> MySinogramFile_S_f1g1d0b0.hs
> The sinograms are shown in attachment.
> I'm looking forward to your help.
> Thank you in advance!
> guifen
>
> ------------------------------------------------------------------------
> Mp3疯狂搜-新歌热歌高速下
> <http://music.yahoo.com.cn/?source=mail_mailbox_footer>
>
>------------------------------------------------------------------------
>
># *********************************************************************
># * DISCLAIMER *
># * *
># * Neither the authors of this software system, nor their employing *
># * institutes, nor the agencies providing financial support for this *
># * work make any representation or warranty, express or implied, *
># * regarding this software system or assume any liability for its *
># * use. *
># * *
># * This code implementation is the intellectual property of the *
># * OpenGATE collaboration. *
># * By copying, distributing or modifying the Program (or any work *
># * based on the Program) you indicate your acceptance of this *
># * statement, and all its terms. *
># *********************************************************************
>#
># This macro has been prepared by:
># Sebastien JAN
>
>#-------------------oooooOOOOO00000OOOOOooooo---------------------#
># #
># P E T S C A N N E R G E O M E T R Y W I T H E C A T #
># S Y S T E M D E F I N I T I O N A N D E C A T 7 #
># F O R M A T O U T P U T #
># #
># Y O U N E E D T O I N S T A L L #
># T H E E C A T 7 L I B R A R Y #
># #
>#-------------------oooooOOOOO00000OOOOOooooo---------------------#
>
>###############################################################
># #
># #
># D E F I N E Y O U R P E T S C A N N E R A N D #
># #
># Y O U R C O M P L E T E G A T E S I M U L A T I O N #
># #
># #
>###############################################################
>
>
>#-------------------oooooOOOOO00000OOOOOooooo---------------------#
># #
># R U N T H E V I S U A L I S A T I O N A N D #
># C O N S T R U C T Y O U R E X P E R I M E N T A L A R E A #
># #
>#-------------------oooooOOOOO00000OOOOOooooo---------------------#
>
>
>
>
>#
># V I S U A L I S A T I O N
>#
>/vis/open OGLSX
>/vis/viewer/reset
>/vis/drawView 45 45
>/vis/viewer/zoom 4
>/vis/viewer/set/style surface
>/vis/drawVolume
>/tracking/storeTrajectory 1
>/vis/scene/endOfEventAction accumulate
>/vis/viewer/update
>/gate/geometry/enableAutoUpdate
>
># OR disable the visu
>#/vis/disable
>
>
>#
># W O R L D
>#
>/gate/world/geometry/setXLength 400. cm
>/gate/world/geometry/setYLength 400. cm
>/gate/world/geometry/setZLength 400. cm
>
>
>#-------------------oooooOOOOO00000OOOOOooooo---------------------#
># #
># D E F I N I T I O N A N D D E S C R I T I O N #
># O F Y O U R P E T D E V I C E #
># #
>#-------------------oooooOOOOO00000OOOOOooooo---------------------#
>
>
># E C A T
>/gate/world/daughters/name ecat
>/gate/world/daughters/insert cylinder
>/gate/ecat/setMaterial Air
>/gate/ecat/geometry/setRmax 50.0 cm
>/gate/ecat/geometry/setRmin 41.0 cm
>/gate/ecat/geometry/setHeight 15.5 cm
>/gate/ecat/vis/forceWireframe
>
>
># B L O C K
>/gate/ecat/daughters/name block
>/gate/ecat/daughters/insert box
>/gate/block/placement/setTranslation 413.5 0.0 0.0 mm
>/gate/block/geometry/setXLength 30.0 mm
>/gate/block/geometry/setYLength 35.8594 mm
>/gate/block/geometry/setZLength 38.7 mm
>/gate/block/setMaterial Air
>/gate/block/vis/forceWireframe
>
>
>
># C R Y S T A L
>/gate/block/daughters/name crystal
>/gate/block/daughters/insert box
>/gate/crystal/geometry/setXLength 30.0 mm
>/gate/crystal/geometry/setYLength 4.0 mm
>/gate/crystal/geometry/setZLength 4.1 mm
>/gate/crystal/setMaterial BGO
>/gate/crystal/vis/setColor yellow
>
>
>
>
># R E P E A T C R Y S T A L
>/gate/crystal/repeaters/insert cubicArray
>/gate/crystal/cubicArray/setRepeatNumberX 1
>/gate/crystal/cubicArray/setRepeatNumberY 8
>/gate/crystal/cubicArray/setRepeatNumberZ 8
>/gate/crystal/cubicArray/setRepeatVector 0. 4.4942 4.85 mm
>
>
># R E P E A T BLOCK
>/gate/block/repeaters/insert linear
>/gate/block/linear/setRepeatNumber 4
>/gate/block/linear/setRepeatVector 0. 0. 38.8 mm
>/gate/block/repeaters/insert ring
>/gate/block/ring/setRepeatNumber 72
>
>
># LEAD S H I E L D
>/gate/world/daughters/name carter
>/gate/world/daughters/insert cylinder
>/gate/carter/setMaterial Air
>/gate/carter/geometry/setRmax 44. cm
>/gate/carter/geometry/setRmin 28. cm
>/gate/carter/geometry/setHeight 3. cm
>/gate/carter/placement/setTranslation 0.0 0.0 7.8 cm
>/gate/carter/vis/setColor grey
>/gate/carter/vis/forceWireframe
>
>/gate/world/daughters/name carter
>/gate/world/daughters/insert cylinder
>/gate/carter/setMaterial Air
>/gate/carter/geometry/setRmax 44. cm
>/gate/carter/geometry/setRmin 28. cm
>/gate/carter/geometry/setHeight 3. cm
>/gate/carter/placement/setTranslation 0.0 0.0 -7.8 cm
>/gate/carter/vis/setColor grey
>/gate/carter/vis/forceWireframe
>
>
># A T T A C H S Y S T E M
>/gate/systems/ecat/block/attach block
>/gate/systems/ecat/crystal/attach crystal
>
># A T T A C H C R Y S T A L SD
>/gate/crystal/attachCrystalSD
>
>
>
>#-------------------oooooOOOOO00000OOOOOooooo---------------------#
># #
># D E F I N I T I O N A N D D E S C R I T I O N #
># O F Y O U R P H A N T O M #
># #
>#-------------------oooooOOOOO00000OOOOOooooo---------------------#
>
>
># P H A N T O M
>/gate/world/daughters/name phantom1
>/gate/world/daughters/insert cylinder
>/gate/phantom1/placement/setTranslation 10.0 0.0 0.0 cm
>/gate/phantom1/setMaterial SS304
>/gate/phantom1/vis/forceWireframe
>/gate/phantom1/vis/setColor green
>/gate/phantom1/geometry/setRmax 1.5 mm
>/gate/phantom1/geometry/setHeight 25.0 cm
>/gate/phantom1/attachPhantomSD
>
>/gate/phantom1/daughters/name phantom2
>/gate/phantom1/daughters/insert cylinder
>/gate/phantom2/placement/setTranslation 0.0 0.0 0.0 cm
>/gate/phantom2/geometry/setRmax 1.0 mm
>/gate/phantom2/geometry/setHeight 1.0 mm
>/gate/phantom2/setMaterial Water
>/gate/phantom2/vis/setColor blue
>/gate/phantom2/vis/forceWireframe
>/gate/phantom2/attachPhantomSD
>
>
>
>#-------------------oooooOOOOO00000OOOOOooooo---------------------#
># #
># S E C O N D P A R T O F Y O U R #
># P E T S I M U L A T I O N #
># #
>#-------------------oooooOOOOO00000OOOOOooooo---------------------#
>
>
>
>#-------------------oooooOOOOO00000OOOOOooooo---------------------#
># #
># D E F I N I T I O N A N D D E S C R I T I O N #
># O F Y O U R P H Y S I C S #
># #
>#-------------------oooooOOOOO00000OOOOOooooo---------------------#
>
># EM P R O C E S S
>/gate/physics/gamma/selectRayleigh lowenergy
>/gate/physics/gamma/selectPhotoelectric standard
>/gate/physics/gamma/selectCompton standard
>
># I N A C T I V E S E C O N D A R Y E L E C T R O N S
>/gate/physics/setElectronCut 1. m
>
># I N A C T I V E X - R A Y S
>/gate/physics/setXRayCut 1. GeV
>/gate/physics/setDeltaRayCut 1. GeV
>
>
>
>#-------------------oooooOOOOO00000OOOOOooooo---------------------#
># #
># I N I T I A L I Z A T I O N O F Y O U R #
># S I M U L A T I O N #
># #
>#-------------------oooooOOOOO00000OOOOOooooo---------------------#
>
>
>/gate/geometry/enableAutoUpdate
>/run/initialize
>
>
>
>
>#-------------------oooooOOOOO00000OOOOOooooo---------------------#
># #
># D E F I N I T I O N O F Y O U R A C Q U I S I T I O N #
># D I G I T I Z E R & C O I N C I D E N C E S H O R T E R #
># #
>#-------------------oooooOOOOO00000OOOOOooooo---------------------#
>
># A D D E R
>/gate/digitizer/Singles/insert adder
>
>
># R E A D O U T
>/gate/digitizer/Singles/insert readout
>/gate/digitizer/Singles/readout/setDepth 1
>
>
># E N E R G Y B L U R R I N G
>/gate/digitizer/Singles/insert blurring
>/gate/digitizer/Singles/blurring/setResolution 0.26
>/gate/digitizer/Singles/blurring/setEnergyOfReference 511. keV
>
>
># E N E R G Y C U T
>/gate/digitizer/Singles/insert thresholder
>/gate/digitizer/Singles/thresholder/setThreshold 350. keV
>/gate/digitizer/Singles/insert upholder
>/gate/digitizer/Singles/upholder/setUphold 650. keV
>
>
># D E A D T I M E
>/gate/digitizer/Singles/insert deadtime
>/gate/digitizer/Singles/deadtime/setDeadTime 3000000. ps
>/gate/digitizer/Singles/deadtime/setMode paralysable
>/gate/digitizer/Singles/deadtime/chooseDTVolume block
>
>
># C O I N C I S O R T E R
>/gate/digitizer/Coincidences/setWindow 12. ns
>/gate/digitizer/Coincidences/setOffset 0. ns
>/gate/digitizer/Coincidences/describe
>
>/gate/digitizer/name delay
>/gate/digitizer/insert coincidenceSorter
>/gate/digitizer/delay/setWindow 10. ns
>/gate/digitizer/delay/setOffset 500. ns
>/gate/digitizer/delay/describe
>
>
>/gate/digitizer/name finalCoinc
>/gate/digitizer/insert coincidenceChain
>/gate/digitizer/finalCoinc/addInputName delay
>/gate/digitizer/finalCoinc/addInputName Coincidences
>/gate/digitizer/finalCoinc/usePriority true
>/gate/digitizer/finalCoinc/describe
>
>
>
>#-------------------oooooOOOOO00000OOOOOooooo---------------------#
># #
># D E F I N I T I O N O F #
># Y O U R O U T P U T F I L E #
># #
>#-------------------oooooOOOOO00000OOOOOooooo---------------------#
>
># C H A N G E T H E S E E D (1) O R N O T (0)
>/gate/output/root/setSaveRndmFlag 1
>
># S E T U P - R O O T _ F I L E
>/gate/output/root/setFileName Your_PET_Simu
>/gate/output/root/setRootSinglesAdderFlag 0
>/gate/output/root/setRootSinglesReadoutFlag 0
>/gate/output/root/setRootHitFlag 0
>/gate/output/root/setRootSinglesFlag 0
>/gate/output/root/setRootNtupleFlag 0
>/gate/output/root/setRootCoincidencesFlag 1
>
># S E T U P - A S C I I _ F I L E
>/gate/output/ascii/setOutFileSinglesAdderFlag 0
>/gate/output/ascii/setOutFileSinglesReadoutFlag 0
>/gate/output/ascii/setOutFileSinglesThresholderFlag 0
>/gate/output/ascii/setOutFileSinglesUpholderFlag 0
>/gate/output/ascii/setOutFileSinglesFlag 0
>/gate/output/ascii/setOutFileHitsFlag 0
>/gate/output/ascii/setOutFileCoincidencesFlag 0
>
>###################################################
># E C A T 7 O U T P U T
>#
># W I T H N E W F U N C T I O N A L I T I E S
># *-*-* according to the coincidence sorter *-*-*
>#
># 01 J U N E 2 0 0 6
>###################################################
>/gate/output/sinogram/enable
>/gate/output/sinogram/setTangCrystalBlurring 1.8 mm
>/gate/output/sinogram/setAxialCrystalBlurring 1.8 mm
>/gate/output/sinogram/verbose 2
>/gate/output/sinogram/RawOutputEnable false
>/gate/output/sinogram/setFileName MySinogramFile
>/gate/output/sinogram/StoreDelayeds
>/gate/output/sinogram/StoreScatters
>/gate/output/sinogram/setInputDataName finalCoinc
>/gate/output/sinogram/describe
>
>/gate/output/ecat7/enable
>/gate/output/ecat7/verbose 2
>/gate/output/ecat7/setFileName MySinogramFile
>/gate/output/ecat7/describe
>/gate/output/ecat7/mashing 1
>/gate/output/ecat7/span 3
>/gate/output/ecat7/maxringdiff 22
>/gate/output/ecat7/system 962
>/gate/output/ecat7/IsotopeCode F-18
>/gate/output/ecat7/IsotopeHalflife 6586.2 second
>/gate/output/ecat7/IsotopeBranchingFraction 1.0
>
>
>#-------------------oooooOOOOO00000OOOOOooooo---------------------#
># #
># D E F I N I T I O N O F #
># Y O U R V E R B O S I T Y L E V E L #
># #
>#-------------------oooooOOOOO00000OOOOOooooo---------------------#
>
>/control/verbose 0
>/grdm/verbose 0
>/run/verbose 0
>/event/verbose 0
>/tracking/verbose 0
>/gate/application/verbose 0
>/gate/generator/verbose 0
>/gate/stacking/verbose 0
>/gate/event/verbose 0
>/gate/source/verbose 0
>
>
>#-------------------oooooOOOOO00000OOOOOooooo---------------------#
># #
># D E F I N I T I O N O F #
># Y O U R S O U R C E S #
># #
>#-------------------oooooOOOOO00000OOOOOooooo---------------------#
>
>
>/gate/source/addSource F18LineSource
>/gate/source/F18LineSource/setActivity 50000. becquerel
>
>/gate/source/F18LineSource/gps/particle e+
>/gate/source/F18LineSource/setForcedUnstableFlag true
>/gate/source/F18LineSource/setForcedHalfLife 6586.2 s
>/gate/source/F18LineSource/gps/energytype Fluor18
>/gate/source/F18LineSource/gps/type Volume
>/gate/source/F18LineSource/gps/shape Cylinder
>/gate/source/F18LineSource/gps/radius 1.0 mm
>/gate/source/F18LineSource/gps/halfz 1.0 mm
>/gate/source/F18LineSource/gps/angtype iso
>/gate/source/F18LineSource/gps/centre 10.0 0.0 0.0 cm
>/gate/source/F18LineSource/gps/confine NULL
>/gate/source/list
>
>
>#-------------------oooooOOOOO00000OOOOOooooo---------------------#
># #
># S T A R T A C Q U I S I T I O N #
># T I M E P A R A M E T E R S #
># #
>#-------------------oooooOOOOO00000OOOOOooooo---------------------#
>
>#
># EXPERIMENT
>#
>/gate/application/setTimeSlice 20. s
>/gate/application/setTimeStart 0. s
>/gate/application/setTimeStop 20. s
>
>#
># LET'S RUN THE SIMULATION!
>#
>/gate/application/startDAQ
>
>
>
>
>
>
>
>
> ------------------------------------------------------------------------
>
>
>------------------------------------------------------------------------
>
>_______________________________________________
>Gate-users mailing list
>Gate-users at lists.healthgrid.org
>http://lists.healthgrid.org/mailman/listinfo/gate-users
>
>
More information about the Gate-users
mailing list