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Using GATE Quick tour & Highlights !

GATE Training, INSTN-Saclay, February 2012

Sébastien JANSHFJ - CEA

Orsay - France

Didier BENOITIMNC - CNRSOrsay - France

Simon StuteSHFJ - CEA

Orsay - France

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�� GATE conceptGATE concept

�� Application fieldsApplication fields

OutlineOutlineOutline

�� GATE quick tour !GATE quick tour !

�� Next releaseNext release

GATE status – Available features

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�� GATE concept GATE concept






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Geant4� Developments: CERN collaboration (> 10 years)� Toolkit for particle/mater interactions modelling� OO C++ architecture� HEP ; Spatial ; Medical …

Geant4Distributed by the CERN

GATE : A Geant4 application

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Geant4

Tool class Tool class

User

User class User class

Simulationprogram

� What’s Geant4 ?Geant4 is a toolkit, not a program

� Using Geant4?Users write their own Geant4-based programs (C++)

Geant4: the toolkit concept

GATEGATE

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User scripts

Application classes

Framework

Geant4

## C R Y S T A LC R Y S T A L/gate/block/daughters/name crystal/gate/block/daughters/name crystal/gate/block/daughters/insert box/gate/block/daughters/insert box/gate/crystal/placement//gate/crystal/placement/setTranslationsetTranslation 0.0 0.0 0.00.0 0.00.0 cmcm/gate/crystal/geometry//gate/crystal/geometry/setXLengthsetXLength 3.0 cm3.0 cm/gate/crystal/geometry//gate/crystal/geometry/setYLengthsetYLength 3.0 mm3.0 mm/gate/crystal/geometry//gate/crystal/geometry/setZLengthsetZLength 3.8 mm3.8 mm/gate/crystal//gate/crystal/setMaterialsetMaterial AirAir/gate/crystal//gate/crystal/vis/setVisiblevis/setVisible 00

C++ level

needed to code

GATE core

Geant4

GATE

PET/SPECT/CT/Radiotherapy developments

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A complete Simulation: 8 steps with GATE

1 – Scanner Description2 – Phantom Description3 – Physics Description

4 – Initialization : Compute cross-section tables

5 – Source Description6 – Digitizer Description7 – Output setup 8 – Time management

Materials ; geometry ; Materials ; geometry ; Physical processesPhysical processes

PostPost --InitializationInitialization

Geometry

Physics

Sources

Runs

Initialisation

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The geometry tree: Geant4 concept

world

Source

Body Head

Scanner

Block detector

Crystal

LSO BGO

Experimental AreaExperimental Area

YourYour PETPET ororSPECTSPECT ScannerScanner

Your Your PhantomPhantom

Russian Dolls approachRussian Dolls approach

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Description of scanner @ the User level

A block detectorA block detector

# BLOCK/gate/module/daughters/name block/gate/module/daughters/insert box

# C R Y S T A L/gate/block/daughters/name crystal/gate/block/daughters/insert box/gate/crystal/placement/setTranslation 0.0 0.0 0.0 cm/gate/crystal/geometry/setXLength 3.0 cm/gate/crystal/geometry/setYLength 3.0 mm/gate/crystal/geometry/setZLength 3.8 mm/gate/crystal/setMaterial Air/gate/crystal/vis/setVisible 0

# 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 5/gate/crystal/cubicArray/setRepeatNumberZ 5/gate/crystal/cubicArray/setRepeatVector 0.0 3.2 4.0 mm

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A scanner moduleA scanner module

# R E P E A T BLOCK/gate/block/repeaters/insert cubicArray/gate/block/cubicArray/setRepeatNumberX 1/gate/block/cubicArray/setRepeatNumberY 8/gate/block/cubicArray/setRepeatNumberZ 12/gate/block/cubicArray/setRepeatVector 0.0 1.6 2.0 cm


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A complete A complete tomographtomograph

# R E P E A T MODULE/gate/module/repeaters/insert ring/gate/module/ring/setRepeatNumber 8


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Geant4Geant4From the sources./Configure -build

CLHEPCLHEPBinary files or from the sources./Configuregmake

ROOTROOTBinaries or sources

LMFLMFFrom the sources

ECAT7ECAT7From the sources

GATEGATECompilation from the sources-Set GATEHOME variable-Set G4VERSION-Adapt the env_gate.csh file-Source this file: >source env_gate.csh-Type make or gmake

The baseThe baseThe output formatsThe output formats

GATE platformGATE platform

-- One day for a complete installationOne day for a complete installation-- Installation guideInstallation guide-- Installation verifications:Installation verifications:

SPECT + PET benchmarksSPECT + PET benchmarks

GATE installation

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�� GATE concept & Release news GATE concept & Release news






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Acquisition modellingAcquisition modelling

GE - Advance Siemens - ECAT EXACT HR+

Philips - Allegro

Siemens - HRRT

microPETFOCUS 220

Detector prototype

- Scanner description (geometry)- Material description (properties)- Detector modelling (scintillation, light collection…)- Electronic treatments (front end, coincidences…)- Dead time and data transfer

Prototype and commercial scanners

Courtesy by OpenGATE collaboration

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Numerical phantoms & Detector design

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The Digitizer : How to model your detector response ?

�For each event � The Crystal-SD creates

hits,� … which are grouped

into a hit-collection,� … which is processed

by the digitizer,� … which returns a

single event collection

hithit hit

hit hit hit

Digitizer to model the detector response

Single Event

Coincidence Event

SPECTSPECTCTCTDosimetryDosimetry

PETPET

Coincidence processing

γ

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Delayedwindow

Promptswindow One

processor unit for

Coincidence

Singles

Histogram curves

Head curves

• Energy blurring• Spatial blurring• Dead time model• Optical crosstalk

� Short list of digitizer modules

• Coincidence sorter• Delayed coincidences• Pill-up• Background noise…

� Example: Coincidence processing

The Digitizer : How to model your detector response ?

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For radiotherapy and dosimetryapplications

Data output management

List mode oriented

Image oriented

�ROOT (most general output) ; ASCII

�LMF (cylindricalPET system)

�Interfile projection (SPECT system)

�ECAT 7 (PET system)�RAW sinogram (PET system)

“Actors” + Filters based on G4 scorers and G4Filters� 3D dose scorer (dose map – Analyze format)� Simulation statistic� Track killer� …..

Courtesy of the O

penGA

TE

collaboration

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•• GATE cluster tools for a parallel implementation GATE cluster tools for a parallel implementation •• New particle navigator New particle navigator •• Variance Reduction Techniques Variance Reduction Techniques •• ……future approach: GPU & hybrid implementationsfuture approach: GPU & hybrid implementations

From the light architecturesFrom the light architectures ……..

- Analytical code

...to the cluster architectures...to the cluster architectures ……

Computing efficiency

Speed Up

Realistic Data

Analytical code

Full MC code

Monte Carlo approach- For a real exam : from 109 to 5009 particles generated- From 0.1 µsec to 500 µsec / event

- Fast and dedicated Monte Carlo (SORTEO ; SIMSET…)

- Generalist Monte Carlo (MCNP ; Geant4 ; GATE…)

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�� GATE concept & Release news GATE concept & Release news






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Molecular and pre-clinical imaging

CT scan: attenuation Full numerical phantom

GATE simulation

[18F]FDG scan simulation- microPET FOCUS 220 system- Injected dose: 200 µCi- Start acquisition: 45 min. after injection- Acquisition time: 15’

Simulation result

[ Jan et al - 2005 ]

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4D MOBY phantom

[ A. Bonissentet al - 2009 ]

GATE simulation

CT scan simulation- PIXSCAN-XPAD3 developed in CPPM, Marseille

- X ray beam 17 keV- Coupled with prototype PET scan- Cluster of 10 CPUs & CPU time : 24h

Simulation result

Molecular and pre-clinical imaging

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Neurodegenerative diseasesNeurodegenerative diseases

Monte Carlo data basesMonte Carlo data baseso Realistic

o Full scanner & tracer compatible

Quantification analysis & disease understanding

Brain simulation: Metabolic & Receptor imaging

1818FF--FDGFDG1111CC--RacloprideRaclopride

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Oncology: Simulation of a whole body PET exam

Tumor volume22 ml

- Start acqui. : 264 MBq- 7 bed positions- 7’ per bed position

GATE Simulation Simulation set-up

Simulation result

+

From 2006 to 2009

SpeedSpeed--up factor of up factor of 10 to 2010 to 20

Courtesy of the O

penGA

TE

collaboration

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Radiotherapy and dosimetry

Conventional radiotherapy• Precise – Elekta system

[ L. Grevillot et al – Submitted ]

• Collimator motion• Photon dose validations• Realistic protocols

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Proton beam interactions (Spread Out Bragg Peak)

Example of physics for proton beams (Geant4 9.1.p02):•Low Energy Electromagnetic Physics•Precompound + GEMEvaporation•G4LElastic

[ Romanoet al – 2008 ]

Hadrontherapy• Active Geant4 team for physics dev. & validations• Important merging version in the Hadronic package

for next G4 release (december 09)

Proton beam interactions (Pure Bragg Peak)


27[ Pshenichnovet al – 2005 ]

Example of physics for ions beams :• Geant4 7.0• 12C and 18O against GSI & RIKEN data


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Hadron-PET : Feasibility test with Gate

Monitoring of the deposited dose using PET imaging for a 12C treatment

Principle

Fragmentation: 12C 15O β+ emitting radionuclide

11C

Hounsfield number

• Phantom: CT scan• Tumor Head ø 2 cm - segmentation• 1 beam - 9.108 12C

• PET scan simulation – 20 min post-irradiation acquisition – commercial scanner

Simulation Set-Up

• Phantom: CT scan 4D including complete breathing cycle• Real Tumor • 3 beams - 108 12C / beam

Hounsfield number


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13 Gy

0

12C deposited dose

Depth – pixel unit

Map of 11C with Ekin = 0

11C PET scan


a.u.



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12C deposited dose 11C PET scan 15O PET scan

Bq/cc


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…Including respiratory motion in our simulation

….4D 12C deposited dose


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