GATE application example using SuperComputer 국립암센터 박 세 준 연구원

GATE 란 GATE : G EANT4 A pplication for T omographic E mission Geant4 를 기반으로 하여 핵의학영상기기인 PET 과 SPECT 시뮬레이션을 위하여 2004 년 처음으로 release 됨 년 2 월에 release 된 GATE ver 부터 radiation therapy, hadron therapy 추가됨. ( Currently GATE ver. 6.1) GATE simulationSinogramReconstructed image

Main technical features GATE ▫ is based on Geant4 ▫ is written in C++ ▫ is user-friendly as simulations can be designed and controlled using macros, without any C++ writing ▫ is able to simulate SPECT, PET and CT scans and radiotherapy treatments ▫ is flexible enough to model almost any detector design ▫ explicitly models time, therefore make it possible to model detector motion, patient motion, radioactive decay, optical photon tracking, dead time, time of flight, tracer kinetecs ▫ can handle analytical or voxelized phantoms ▫ can run on a cluster architecture and on a grid

How it works Developer level ▫ Core and Application layer ▫ C++ programming User level ▫ Simulation parameters  Geometry  Sources  Time  Analysis  … ▫ Macro scripting only Structure of GATE

General Simulation Architecture 1.Scanner geometry 2.Phantom geometry 3.Physics processes 4.Initialization compute cross-section tables 5.Digitizer Description 6.Source Description 7.Output setup 8.Time management Materials ; Geometry ; Physical processes Post-initialization

Geometry scripting /gate/world/geometry/setXLength 100 cm /gate/world/geometry/setYLength 100 cm /gate/world/geometry/setZLength 100 cm world /gate/world/daughters/name SPECThead /gate/world/daughters/insert box scanner collimator crystal phantom /gate/SPECThead/repeaters/insert ring /gate/SPECThead/ring/setRepeatNumber 4 /gate/SPECThead/daughters/name collimator /gate/SPECThead/daughters/insert box /gate/SPECThead/daughters/name crystal /gate/SPECThead/daughters/insert box /gate/world/daughters/name Phantom /gate/world/daughters/insert cylinder

Geometry example PET camera Ocular brachytherapy treatment Radiotherapy OPET scanner

Material and Physics scripting /gate/geometry/setMaterialDatabase../../GateMaterials.db …… # P H Y S I C S ##### /gate/physics/addProcess PhotoElectric /gate/physics/addProcess LowEnergyCompton /gate/physics/addProcess LowEnergyRayleighScattering /gate/physics/addProcess ElectronIonisation /gate/physics/addProcess Bremsstrahlung /gate/physics/addProcess MultipleScattering e- /gate/physics/processList Enabled /gate/physics/processList Initialized /applic/applications/hep/Gate/gate_v6.1/GateMaterials.db

Sensitive volumes and digitization # S E N S I T I V E D E T E C T O R S # Crystal SD /gate/crystal/attachCrystalSD # 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 0.10 /gate/digitizer/Singles/blurring/setEnergyOfReference 140. keV /gate/digitizer/Singles/insert spblurring /gate/digitizer/Singles/spblurring/setSpresolution 2.0 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 w/o spblurring with spblurring

Source scripting Multiple sources ▫ Controlled by source manager ▫ Inserted via scripting ▫ Complex geometries: customized gps An example: dual isotope scan simulation ▫ F-18 and O-15 in PET ▫ Tc-99m and Tl-201 in SPECT /gate/source/addSource F18LineSource /gate/source/F18LineSource/setActivity Bq /gate/source/F18LineSource/gps/particle e+ /gate/source/F18LineSource/setForcedHalfLife s /gate/source/F18LineSource/gps/energytype Fluor18 /gate/source/addSource O15LineSource /gate/source/O15LineSource/setActivity Bq /gate/source/O15LineSource/gps/particle e+ /gate/source/O15LineSource/setForcedHalfLife s /gate/source/O15LineSource/gps/energytype Oxygen15

Output scripting #O U T P U T /gate/output/ascii/setOutFileHitsFlag 0 /gate/output/ascii/setOutFileSinglesFlag 0 /gate/output/ascii/setOutFileCoincidencesFlag 0 /gate/output/ascii/setOutFiledelayFlag 0 /gate/output/root/enable /gate/output/root/setFileName benchmarkPET /gate/output/root/setRootHitFlag 0 /gate/output/root/setRootSinglesFlag 0 /gate/output/root/setRootCoincidencesFlag 1 /gate/output/root/setRootdelayFlag 1

Timing scripting Simulation time ▫ A clock models the passing of time during experiments ▫ The user defines the experiment timing Time-dependent objects ▫ Updated when time changes ▫ Allows programming of movement, tracer kinetics.. /gate/application/setTimeSlice 37.5 s /gate/application/setTimeStart 0. s /gate/application/setTimeStop 600. s /gate/application/startDAQ 0. s150. s 300. s450. s

How to run GATE Interactive mode Batch mode Parameterized macro gate [G4] [G4] ************************************************************* [G4] Geant4 version Name: geant patch-03 (29-January-2010) [G4] Copyright : Geant4 Collaboration [G4] Reference : NIM A 506 (2003), [G4] WWW : [G4] ************************************************************* [G4] [Core-0] Initialization of geometry [Core-0] Initialization of physics [Core-0] Initialization of actors [Core-0] [Core-0] ********************************************************************* * [Core-0] GATE version name: gate_v6.0_p01 [Core-0] Copyright : OpenGATE Collaboration [Core-0] Reference : Phys. Med. Biol. 49 (2004) [Core-0] WWW : ; [Core-0] ********************************************************************* * [Core-0] Idle> /control/execute vis.mac Got standard cmap Window name: viewer-0 (OpenGLStoredX) /tracking/storeTrajectory 1 … Idle> gate benchSPECT.mac GATE 6.0 버젼 에서는 parameterized macro 실행 안됨. Bug!! 6.1. 버전에는 fix 되어 실행가능.

Submitting a job to SuperComputer #!/bin/bash #$ -V #$ -cwd #$ -N serial_job #$ -q normal #$ -R yes ##$ -wd /scratch/ /serialtest #$ -l h_rt=01:00:00 # To run Sequential, but multi-thread enabled program including Gaussian, # Users have to to set OMP_NUM_THREADS properly according to # job's inputfile's num_of_cpus or correspondent command line argument. # For example, Gaussian uses the parameter, %NProc or %NProcshared in input file. # Therefore, if %NProc=8 is defined in the input file, # users have to insert "export OMP_NUM_THREADS=8" into this job script. #$ -l OMP_NUM_THREADS=1 #$ -v OMP_NUM_THREADS=1 export OMP_NUM_THREADS=1 Gate benchSPECT.mac 주의 : 슈퍼컴에 submit 할 때는 macro 내에 # /control/execute vis.mac 반드시 주석 처리

scp 명령어로 output 파일 다운받기 scp 사용전 node 에서 잠시 나옴. ~]$ exit ~]$ scp –p 5211

감사합니다. ▫ GATE URL : ▫ GATE user mailing : gate- ▫ To install GATE: ▫ To use GATE: