1 Gean4 Human Phantom advanced example: A Geant4 anthropomorphic model Dr. S. Guatelli Geant4...

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Gean4 Human Phantom advanced example: A Geant4 anthropomorphic model

Dr. S. GuatelliGeant4 Collaboration member,

Lecturer, Centre of Medical Radiation Physics, Engineering Physics Department, University of Wollongong, NSW, Australia

[email protected]

This application was developed by G. Guerrieri, S. Guatelli and M.G. Pia (INFN, Genova)

Geant4 School, 12-14 October 2009, Catania, Italy2

Outline

Context Anthropomorpic phantoms for medical physics Analytical vs voxelised phantoms Mix and Match model

Geant4 human phantom development User requirements Design Implementation details

Geometry component Physics component User Interface Visualisation

Summary and conclusions

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Context

Realistic software models of the human body are important for accurate

dosimetryi.e. radiation protection, radiotherapy,

etc.


Anthropomorpic phantoms

Analytical models The organs are described by means of

mathematical representations

Voxelised models The organs are approximated with voxels Usually they derive from CT or MRI scans


Mathematical phantoms Sizes and shapes of the human organs are

defined by means of analytical formulas

Several models available as for example W. S. Snyder et al, “MIRD Pamphlet No. 5 Revised, Estimates of

absorbed fractions for monoenergetic photon sources uniformly distributed in various organs of a heterogeneous phantom”, J. Nucl. Med. Suppl., no.3, pp.5-52, 1969

M. Cristy and K. F. Eckerman, “Specific absorbed fractions of energy at various ages from internal photon sources”, ORNL/TM-8381/V1, 1987


Voxelised phantoms Based on digital images recorded from scanning real

people, with CT or MRI

M. Caon, Voxel-based computational models of real human anatomy: a reviewRad. Env. Biophys. 42 (2004) 229–235

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Mathematical phantomsvs

voxelised phantoms

Which is the best approach?

Both approaches present advantages and drawbacks

It depends on the specific use case


Vision of the Geant4HumanPhantom

Development of a mix and match model Composite mathematical and voxelised anthropomorphic

phantom

Advantage: optimization of use of CPU and memory resources and accuracy of the simulation

This is possible thanks to the: OO technology Advanced Geant4 capability in geometry


G4 capability in geometry

G4 MaterialsG4 Materials Human tissues can be easily

implemented in Geant4 as compounds

G4 Solids used in G4 Solids used in G4HumanPhantom:G4HumanPhantom:

CSG (Constructed Solid Geometry) solids

G4Box, G4Tubs, G4Cons, G4Trd, G4Ellipse, G4Sphere

Boolean solids G4UnionSolid, G4SubtractionSolid, …

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for anthropomorphic phantoms


Software development of the

Geant4AnthropomorficPhantom

User requirements

Architecture of the software

Implementation details

Use of the

Geant4AnthropomorphicPhantom

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Main user requirements of the G4HumanPhantom

What should the software application do

Geometry component

Primary particle

Physics

User interface and visualisation


Geometry UR

The anthropomorphic model includes the body components:

Body regions: trunck, neck, head, legs, male genitalia

Skeletal system: leg bone, arm bone, pelvis, spine, cranium, facial skeleton, skull, rib cage, clavicles, scapulae

Internal organs (stomach, intestine, esophagus, heart, brain, adrenals, gall bladder, kidney, liver, lung, ovary pancreas, skin, spleen, testes, thymus, thyroid, bladder, uterus

Soft tissue, bone, lung material should be defined

The user shall be able to define mathematical organs

The user shall be able to define voxelised organs


Primary particle and physics UR

The user shall be able to define the radiation field Particle type, energy, primary vertex and momentum

The user shall be able to define the physics processes involved in the experimental set-up


Other UR Event:

The user shall be able to retrieve the position and material of the body traversed by tracks

The user shall be able to retrieve the energy deposition in body regions

User Interface: The user shall be able to select a phantom by sex, age and the

model The user shall be able to define a phantom using parts derived from

different models The user shall be able to create specific body regions corresponding

to subset of the phantom

Visualisation: The user shall be able to visualise the geometrical setup and the

particle tracks




User requirements



Use of the



Domain decomposition: Abstraction of the process of

building a phantom Builder: Separate the

construction of a complex object from its representation so that the same construction process can create different representations

Abstraction of the description of a phantom model

The abstract Factory pattern provides an interface for creating families of organs without specifying their concrete classes




User requirements



Use of the



G4 HumanPhantom directory

In geant4/example/advanced/human_phantom


src directory


include directory

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Implementation

Geometry


Definition of materials: G4HumanPhantomMaterial.cc

G4HumanPhantomMaterial::G4HumanPhantomMaterial(): soft(0), skeleton(0),lung(0), adipose(0), glandular(0), adipose_glandular(0) {;}

G4HumanPhantomMaterial::~G4HumanPhantomMaterial() {;}

void G4HumanPhantomMaterial::DefineMaterials(){ // Define required materials}

G4Material* G4HumanPhantomMaterial::GetMaterial(G4String material){ // Returns a material G4Material* pttoMaterial = G4Material::GetMaterial(material); return pttoMaterial; }


Define the elements

G4Element* elH = new G4Element ("Hydrogen","H“, Z = 1.,A=1.01*g/mole);

G4Element* elC = new G4Element("Carbon","C",Z = 6.,A = 12.011*g/mole);

G4Element* elN = new G4Element("Nitrogen","N",Z = 7.,A = 14.01*g/mole);

G4Element* elO = new G4Element("Oxygen","O",Z = 8.,A = 16.00*g/mole);

G4Element* elNa = new G4Element("Sodium","Na",Z = 11.,A = 22.99*g/mole);

G4Element* elMg = new G4Element("Magnesium","Mg",Z = 12.,A

=24.305*g/mole);

G4Element* elP = new G4Element("Phosphorus","P",Z = 15.,A = 30.974*g/mole);

………………


Example: definition of bone

density = 1.4862*g/cm3;

skeleton = new G4Material("skeleton",density,15); skeleton -> AddElement(elH,0.0704); skeleton -> AddElement(elC,0.2279); skeleton -> AddElement(elN,0.0387); skeleton -> AddElement(elO,0.4856); skeleton -> AddElement(elNa,0.0032); skeleton -> AddElement(elMg,0.0011); skeleton -> AddElement(elP,0.0694); skeleton -> AddElement(elS,0.0017); skeleton -> AddElement(elCl,0.0014); skeleton -> AddElement(elK,0.0015); skeleton -> AddElement(elCa,0.0991); skeleton -> AddElement(elFe,0.00008); skeleton -> AddElement(elZn,0.000048); skeleton -> AddElement(elSr,0.000032); skeleton -> AddElement(elPb,0.000011);

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Analytical organs


Modelling analytical organs

Two alternative methods

Hard-coded implementation of the organs and body parts

Geometry Description Markup Language (GDML) http://gdml.web.cern.ch/GDML/


Hard-coded organExample: right breast G4MIRDRightBreast.cc (1)

G4VPhysicalVolume* G4MIRDRightBreast::Construct(const G4String& volumeName,G4VPhysicalVolume* mother, const G4String& colourName, G4bool wireFrame, G4bool sensitivity)

{G4double ax= 4.95* cm; G4double by= 4.35* cm; G4double cz= 4.15*cm;G4Ellipsoid* oneRightBreast = new G4Ellipsoid("OneRightBreast”, ax, by, cz);

G4double dx= 20.* cm; G4double dy= 10.* cm; G4double dz= 35.* cm;G4EllipticalTube* Trunk = new G4EllipticalTube("Trunk",dx, dy, dz );

G4RotationMatrix* rm_relative = new G4RotationMatrix(); rm_relative -> rotateX(90. * degree);

G4SubtractionSolid* breast = new G4SubtractionSolid("RightBreast“, oneRightBreast, Trunk,rm_relative,

G4ThreeVector(10.*cm, 0.0*cm, -8.66*cm));


Hard-coded organExample: right breast G4MIRDRightBreast.cc (2)

G4HumanPhantomMaterial* material = new G4HumanPhantomMaterial(); G4Material* soft = material -> GetMaterial("soft_tissue");

G4LogicalVolume* logicRightBreast = new G4LogicalVolume(breast, soft,"logical" + volumeName, 0, 0,0);

G4VPhysicalVolume* physRightBreast = new G4PVPlacement(0, G4ThreeVector(-10.*cm, 52.* cm,- 8.66 *cm),

"physicalRightBreast", logicRightBreast, mother,false, 0, true);

// Sensitive Body Part if (sensitivity==true) { G4SDManager* SDman = G4SDManager::GetSDMpointer(); logicRightBreast->SetSensitiveDetector( SDman->FindSensitiveDetector("BodyPartSD") ); } // Visualization Attributes // Define the visualisation attributes of the organ

return physRightBreast;}


GDML organ

What is GDML? Geometry Description Markup Language

GDML can be used as the primary geometry implementation language

GDML is an application-indepedent geometry description format based on XML


GDML webpage


G4HumanPhantom

Implementation of organs with GDML

gdmlData/Female gdmlData/Male


GDML Breast (1) gdmlData/Female/MIRDBreast.gdml

<?xml version="1.0" encoding="UTF-8" ?>

<gdml xmlns:gdml="http://cern.ch/2001/Schemas/GDML" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:noNamespaceSchemaLocation="http://service-spi.web.cern.ch/service-spi/app/releases/GDML/schema/gdml.xsd" >

<define> <constant name="PI" value="1.*pi" /> <constant name="TWOPI" value="2.*pi"/> <constant name="HALFPI" value="0.5*pi"/> <position name="BreastUnionRelativePos" unit="cm" x="17.26" y="0" z="0" /> <position name="BreastRelativePos" unit="cm" x="8.63" y="0.0" z="-8.4854" /> <rotation name="BreastRotation" unit="degree" x="90" y="0" z="0" /> <position name="BreastPos" unit="cm" x="-8.63" y="46.87" z="8.4854" /> <rotation name="BreastRot" unit="degree" x="0" y="0" z="0" /> <position name="TrunkPos" unit="cm" x="0" y="31.55" z="0" /> <rotation name="TrunkRot" unit="degree" x="90" y="0" z="0" /> </define>


Definition of elements and materials<materials> <material name="sH" formula=" " Z="1."> <D value="0.00009" /> <atom value="1.008"/>…. etc </material><material formula=" " name="SoftTissue"> <D value="1.04" /> <fraction n="0.10454" ref="sH" /> <fraction n="0.22663" ref="sC" /> <fraction n="0.02490" ref="sN" /> <fraction n="0.63525" ref="sO" />… etc</material> </materials>



How to build GDML organG4VPhysicalVolume* G4ORNLFemaleBodyFactory::CreateOrgan(const G4String&

gdmlFile, G4VPhysicalVolume* motherVolume,const G4String& colourName, G4bool visAttribute, G4bool sensitivity)

{ G4GDMLParser parser; G4String filename = "gdmlData/Female/ORNL"+ gdmlFile + ".gdml"; parser.Read(filename); G4String logicalVolumeName = gdmlFile + "Volume";

G4LogicalVolume* logicOrgan = parser.GetVolume(logicalVolumeName);

G4ThreeVector position = parser.GetPosition("OrganPos"); G4ThreeVector rot = parser.GetRotation("OrganRot"); G4RotationMatrix* rm = new G4RotationMatrix(); rm -> rotateX(rot.x()); rm->rotateY(rot.y()); rm->rotateZ(rot.z());

G4VPhysicalVolume* physOrgan = new G4PVPlacement(rm,position, "physicalOrgan",logicOrgan, motherVolume, false, 0,

true);…….}

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Voxelised organ


Voxelised organ

Define the RO geometry The ReadOut geometry is a

virtual, parallel geometry to describe the read-out configuration of the detector

Retrieve the energy deposition in each voxel

From talk: S. Guatelli et al., “Geant4 Anthropomorphic Phantoms”, IEEE NSS 2006, San Diego, November 2006.S. Guatelli, B. Mascialino, M.G. Pia, W. Pokorski, “Geant4 anthropomorphic phantoms”, Nuclear Science Symposium Conference Record, 2006, vol. 3, pp. 1359-1362


Radiation field and physics list

The user has to define the radiation field in theG4HumanPhantomPrimaryParticle class

The user has to define the physics processes in G4HumanPhantomPhysicsList class

Geant4 School, 12-14 October 2009, Catania, Italy

How to visualise organs1) Initialise visualisation mamanger in the main:

int main(int argc,char** argv)

{

......

G4VisManager* visManager = new G4VisExecutive;

visManager -> Initialize();

.....}

2) Define the visualisation attributes of the logical volumes of the body parts

G4VisAttributes* RightBreastVisAtt = new G4VisAttributes(G4Colour(1.0,0.41,0.71));

RightBreastVisAtt -> SetForceSolid(wireFrame);

LogicRightBreast -> SetVisAttributes(RightBreastVisAtt);

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User Interface

Definition of

A messenger to “build” the human phantom (entire model or just a

body part)

Macro files to be executed during the simulation


G4HumanPhantomMessenger

……….G4HumanPhantomMessenger::G4HumanPhantomMessenger(G4HumanPhantomConstruction* myUsrPhtm):myUserPhantom(myUsrPhtm),bps(false){ phantomDir = new G4UIdirectory("/phantom/"); phantomDir->SetGuidance("Set Your Phantom."); bpDir = new G4UIdirectory("/bodypart/"); bpDir->SetGuidance("Add Body Part to Phantom");

modelCmd = new G4UIcmdWithAString("/phantom/setPhantomModel",this); modelCmd->SetGuidance("Set sex of Phantom: MIRD, ORNLFemale, ORNLMale, MIX, MIRDHead, ORNLHead."); modelCmd->SetParameterName("phantomModel",true); modelCmd->SetDefaultValue("MIRD"); modelCmd->SetCandidates("MIRD ORNLFemale ORNLMale MIX MIRDHead ORNLHead"); modelCmd->AvailableForStates(G4State_PreInit,G4State_Idle);

sexCmd = new G4UIcmdWithAString("/phantom/setPhantomSex",this); sexCmd->SetGuidance("Set sex of Phantom: Male or Female."); sexCmd->SetParameterName("phantomSex",true); sexCmd->SetDefaultValue("Female"); sexCmd->SetCandidates("Male Female"); sexCmd->AvailableForStates(G4State_PreInit,G4State_Idle); bodypartCmd = new G4UIcmdWithAString("/bodypart/addBodyPart",this); bodypartCmd->SetGuidance("Add a Body Part to Phantom"); bodypartCmd->SetParameterName("bpName",true); bodypartCmd->AvailableForStates(G4State_PreInit,G4State_Idle);……….. }…….


Macro files to initialize the phantom interactively

# Initialize New Phantom# Choose model: ORNLFemale, ORNLMale, MIRD, MIX, MIRDHead, ORNLHead/phantom/setPhantomModel MIX/phantom/setPhantomSex Female# Insert Body Part and their Sensitivity# The energy deposit is calculated in the organs declared sensitive/bodypart/addBodyPart Head yes/bodypart/addBodyPart Trunk yes/bodypart/addBodyPart LeftLeg yes/bodypart/addBodyPart RightLeg yes# Skeleton System/bodypart/addBodyPart LeftLegBone yes/bodypart/addBodyPart RightLegBone yes/bodypart/addBodyPart LeftArmBone yes/bodypart/addBodyPart RightArmBone yes……# Organs/bodypart/addBodyPart LeftBreast yes/bodypart/addBodyPart RightBreast yes/bodypart/addBodyPart LeftLung yes/bodypart/addBodyPart RightLung yes/bodypart/addBodyPart Brain yes/bodypart/addBodyPart Heart no…….# Genitalia/bodypart/addBodyPart LeftOvary yes/bodypart/addBodyPart RightOvary yes/bodypart/addBodyPart Uterus yes# Construct your Phantom/phantom/buildNewPhantom/run/initialize#……

AdultMixFemale.mac


How to run the G4HantropomorphicPhantom example

Install Geant4 Install GDML Run the executable Execute the macro initializing the model

of G4Anthropomorphic phantom


Thyroid

Skull

Lungs Arm Bones

Spine

Esophagus

Spleen

StomachKidneysPelvis

Ovaries

Lower Large Intestine

Leg BonesUrinary Bladder

Uterus

Upper Large Intestine

Liver

Breasts

Heart

Not visible: Brain (inside the skull)

Pancreas

Components in G4PhantomBuilder



Female ORNL Anthropomorphic Phantom



Anatomical components can be defined as Geant4 SensitiveDetectorsEnergy deposit collected in Geant4 Hits

Dosimetry



Mix & MatchMathematical phantom with one voxel breast

MIRD mathematical

breast

Dance & Hunt voxel breast

D. R. Dance and R. A. Hunt, REPORT RMTPC 02/1005



Dosimetry in mixed mathematical-voxel phantom

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Dose in Dose in

analytical organsanalytical organs

Dose in each Dose in each breast voxelbreast voxel


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Summary: G4AnthropomorphicPhantom

Application mixing and matching analytical and voxelised models

Flexibility and extensibility of the Geant4 application thanks to the design

It is possible to integrate G4AnthropomorphicPhantom with DICOM interface

Use of G4Parameterised volumes

DICOM interface: geant4/examples/extended/medical/DICOM

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Thank you !

Questions?

1 Gean4 Human Phantom advanced example: A Geant4 anthropomorphic model Dr. S. Guatelli Geant4...

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