gate tutorial - sunicung.in.ua/upload/user_files/n4u/gate/introductionlm.pdf2012 epikh training...
TRANSCRIPT
2012 EPIKH Training Course on GATE and Grid Computing Lydia Maigne, Yann Perrot 9th – 12th April 2012, Algeria 1
Lydia MAIGNE, [email protected]
Yann PERROT, [email protected]
LPC, PCSV team, CNRS-IN2P3
FRANCE
GATE tutorial Introduction
http://www.opengatecollaboration.org/
2012 EPIKH Training Course on GATE and Grid Computing Lydia Maigne, Yann Perrot 9th – 12th April 2012, Algeria 2
Medical physics simulations
PET camera
Ocular brachytherapy treatment
Radiotherapy
OpenGATE collaboration
http://www.opengatecollaboration.org
2012 EPIKH Training Course on GATE and Grid Computing Lydia Maigne, Yann Perrot 9th – 12th April 2012, Algeria 3
GATE web site
2012 EPIKH Training Course on GATE and Grid Computing Lydia Maigne, Yann Perrot 9th – 12th April 2012, Algeria 4
The genesis of GATE July 2001
Concept proposed by C. Morel at the « Monte Carlo in nuclear medicine workshop » organised by I.Buvat in Paris
Autumn 2001
First specification documents
Initiation of developments
December 2001
First collaboration meeting
Participants : University of Lausanne, University of Geneva, LPC Clermont-Ferrand IN2P3
May 2002
OpenGATE public meeting
May 2004: First Gate release
May 2009: Gate version 4.0.0 dedicated to nuclear medicine
June 2009: GATE version 5.0.0 for nuclear medicine and radiotherapy
June 2010: GATE version 6.0.0 with improved RT features and CT imaging
March 2011: GATE version 6.1.0
2012 EPIKH Training Course on GATE and Grid Computing Lydia Maigne, Yann Perrot 9th – 12th April 2012, Algeria 5
Today: GATE collaboration status
All members contribute
According to their interest and know-how
OpenGATE meetings
2/3 per year
New focus: cluster/grid computation and dosimetry
Coordination
Irène BUVAT, IMNC, spokesman
Sébastien JAN, SHFJ CEA Orsay, technical coordinator
Current status
19 groups
Fields: SPECT, PET, µPET, radiotherapy-brachytherapy
2012 EPIKH Training Course on GATE and Grid Computing Lydia Maigne, Yann Perrot 9th – 12th April 2012, Algeria 6
Imaging in nuclear medicine
PromeTEP - Lyon
Gamma camera Philips Marconi
PET:
Biological molecules tagged with radioactive isotopes with
short life-time (FDG 18: 108 min,15O:T1/2~2 min, 11C:20 min)
Resolution down to a few mm3
SPECT:
Longer decay times (99mTc:6 h, 123I:13 h ,133Xe:5 d)
Poorer sensitivity (and resolution)
2012 EPIKH Training Course on GATE and Grid Computing Lydia Maigne, Yann Perrot 9th – 12th April 2012, Algeria 7
From ET systems to cancer treatments
Radiation oncology:
• CT simulation with
patient in treatment
position with
immobilisation
• Patient marked
isocentrically
PET:
• Patient preparation with
isotope injection
• Patient scanned with
immobilisation in treatment
therapy position
• Reconstruction of PET
images with attenuation
correction
+
=
SmartSim CT Simulation software on Pinnacle
2012 EPIKH Training Course on GATE and Grid Computing Lydia Maigne, Yann Perrot 9th – 12th April 2012, Algeria 8
Radiation therapy Using photons and electrons
Dedicated tools for dosimetry applications : phase space approach, optimized navigation in voxelized structures, reduction variance techniques…
Using hadrons
Particle processes extended to hadrons
Dynamic
simulations Brems. Splitting Region oriented CT image representation
The HICAT carbon gantry
Protontherapy <= PSI =>Seoul
2012 EPIKH Training Course on GATE and Grid Computing Lydia Maigne, Yann Perrot 9th – 12th April 2012, Algeria 9
Medical physics simulations requirements
Modelling ET experiments
Realistic sources (human/animal body or brain)
Detectors (PET, SPECT, probes.)
Movement (subject, detector, breathing.)
Decay and biological kinetics
Detector and electronics
Adapted to ET needs
Multiple types of data output
Fast: 1-100 M events in 1 hour - 1 day
Ease-of-use
Long term availability and support
2012 EPIKH Training Course on GATE and Grid Computing Lydia Maigne, Yann Perrot 9th – 12th April 2012, Algeria 10
The GATE platform
2012 EPIKH Training Course on GATE and Grid Computing Lydia Maigne, Yann Perrot 9th – 12th April 2012, Algeria 11
How it works
Geant4
Core layer
Application layer
User interface
Based on Geant4: version 4.9.3 and 9.4
C++ object oriented langage
Reliable cross sections
GATE development: C++ classes
derived from the core layer classes
Ease of use
Command scripts to define all the parameters
of the simulation (geometry construction,
specification of physical processes, sources)
Core layer: C++ classes close to the G4 kernel
modelisation of detectors, sources,
patient
movement (detector, patient)
time-dependent processes (radioactive
decay, movement management, biological
kinetics)
2012 EPIKH Training Course on GATE and Grid Computing Lydia Maigne, Yann Perrot 9th – 12th April 2012, Algeria 12
About the framework
Geant4
Source mgr Geometry mgr
Analysis mgr
Time mgr I/O mgr
Specific
Volume
Specific
source
type
Specific I/O Specific
analysis
Specific
readout
Geometry
scripting
Source
scripting
Time
scripting
Analysis
scripting I/O choice
scripting
More than 200 classes
User interface
2012 EPIKH Training Course on GATE and Grid Computing Lydia Maigne, Yann Perrot 9th – 12th April 2012, Algeria 13
The installation of GATE Install CLHEP libraries
clhep-2.1.0.1.tar.gz
Install ROOT software
root-5.14.tar.gz to last version
Install GEANT4
geant4-9.4.tar.gz
Install GEANT4 data
G4EMLOW6.19.tar.gz
G4NDL.0.2.tar.gz
PhotonEvaporation-2.1.tar.gz
G4RadioactiveDecay-3.3.tar.gz
G4ABLA.3.0.tar.gz
G4NEUTRONXS.1.0.tar.gz
G4PII.1.2.tar.gz
RealSurface.1.0.tar.gz
Install GATE 6.1
gate_v6.1.0.tar.gz
Install CLHEP: ./configure -- prefix
/home/toto/clhep
make
make install
Install ROOT: ./configure
make
export $ROOTSYS=/home/toto/root
make install
Install GEANT4: ./configure –build
Remarks:
Geant4 headers
Shared and static libraries
G4VIS_USE_OPENGLX_DRIVER
Install GATE: gmake
2012 EPIKH Training Course on GATE and Grid Computing Lydia Maigne, Yann Perrot 9th – 12th April 2012, Algeria 14
GATE code architecture Repositories
gate_v6.1.0/
general/
GNUmakefile
include/
src/
geometry/
GNUmakefile
include/
src/
physics/
GNUmakefile
include/
src/
digits_hits/
GNUmakefile
include/
src/
GateClock,GateHounsfield,GateIDFilter,
GateParticleFilter,GatePrimaryGeneratorAction,
GateRunManager....
GateBox, GateCone, GateCylinder,
GateGeometryVoxel, GateHexagone, GateSphere,
GatePolyhedra, GateImageNestedParametrisation,
GateImageRegionalizedVolume,
GateCPETSystem.cc, GateCylindricalPETSystem.cc,
GatePETScannerSystem.cc, GateScannerSystem.cc,
GateSPECTHeadSystem.cc
GateBremsstrahlung, GateElectronionisation,
GateHadron..., GateCompton...,
GatePhotoelectric..., GateRayleigh,
GatePositron....
GateActor, GateCrystalHit, GateCrystalSD,
GateDoseActor, GateKillActor, GateToAscii,
GateToRoot, GateToInterfile, GateToSinogram...