GATE tutorial - SUNICung.in.ua/upload/user_files/N4U/gate/IntroductionLM.pdf2012 EPIKH Training...

2012 EPIKH Training Course on GATE and Grid Computing Lydia Maigne, Yann Perrot 9th – 12th April 2012, Algeria 1

Lydia MAIGNE, maigne@clermont.in2p3.fr

Yann PERROT, perrot@clermont.in2p3.fr

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...