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Guatelli phantom INFN Powered By Docstoc
					       Gean4 Human Phantom advanced example:
                    A Geant4 anthropomorphic model



                                    Dr. S. Guatelli
                            Geant4 Collaboration member,
    Lecturer, Centre of Medical Radiation Physics, Engineering Physics Department,
                       University of Wollongong, NSW, Australia
                            susanna.guatelli@uow.edu.au



This application was developed by
G. Guerrieri, S. Guatelli and M.G. Pia (INFN, Genova)
                                                                                     1
                   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
                                                                            2
Geant4 School, 12-14 October 2009, Catania, Italy
Context
 Realistic software models of the human body
      are important for accurate dosimetry
  i.e. radiation protection, radiotherapy, etc.




                                                  3
                   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

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                   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



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               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 review
Geant4 School, 12-14 October 2009, Catania, Italy
                                                                              Rad. Env. Biophys. 42 (2004) 229–235 6
        Mathematical phantoms
                  vs
         voxelised phantoms


           Which is the best approach?
Both approaches present advantages and drawbacks
        It depends on the specific use case


                                               7
                    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


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                     G4 capability in geometry
                        for anthropomorphic phantoms


G4 Materials
    Human tissues can be easily implemented
     in Geant4 as compounds

G4 Solids used in G4HumanPhantom:
    CSG (Constructed Solid Geometry) solids
                  G4Box, G4Tubs, G4Cons, G4Trd,
                   G4Ellipse, G4Sphere

    Boolean solids
                  G4UnionSolid, G4SubtractionSolid, …    9
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                     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
                                          11
                   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
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                   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



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                   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                                                       14
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                     Software development of the
                     Geant4AnthropomorficPhantom

         User requirements

         Architecture of the software

         Implementation details

         Use of the Geant4AnthropomorphicPhantom


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    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



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                     Software development of the
                     Geant4AnthropomorficPhantom

         User requirements

         Architecture of the software

         Implementation details

         Use of the Geant4AnthropomorphicPhantom


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                   G4 HumanPhantom directory

     In geant4/example/advanced/human_phantom




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                   src directory




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                   include directory




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Implementation

  Geometry




                 21
                   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;
  }
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                   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);

   ………………



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                   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




                    25
                   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/




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                   Hard-coded organ
                   Example: 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));




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                   Hard-coded organ
                   Example: 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;
    }
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                   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


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     GDML
     webpage




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                   G4HumanPhantom
                    Implementation of organs with GDML
                     gdmlData/Female

                     gdmlData/Male




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                   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>


                                                                                               32
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                   GDML Breast (2)
                   gdmlData/Female/MIRDBreast.gdml

               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>
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                   GDML Breast (3)
                   gdmlData/Female/MIRDBreast.gdml

<solids>
 <ellipsoid aunit="cm" lunit="cm" name="OneBreast" ax="4.95" by="4.35" cz="4.15"
  zcut1="-4.15" zcut2="4.15" />
 <eltube aunit="cm" lunit="cm" name="Trunk" dx="17.25" dy="9.80" dz="31.55"/>
 <union name="BreastUnion">
 <first ref="OneBreast" />
 <second ref="OneBreast" />
 <positionref ref="BreastUnionRelativePos" />
 </union>
 <subtraction name="Breast">
 <first ref="BreastUnion" />
 <second ref="Trunk" />
 <positionref ref="BreastRelativePos" />
 <rotationref ref="BreastRotation" />
 </subtraction>
</solids>
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                   GDML Breast (4)
                   gdmlData/Female/MIRDBreast.gdml
                    <structure>
                     <volume name="BreastVolume" >
                      <materialref ref="SoftTissue" />
                      <solidref ref="Breast" />
                     </volume>
                    </structure>
                    <setup name="Default" version="1.0" >
                     <world ref="BreastVolume" />
                    </setup>
                    </gdml>


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              How to build GDML organ
G4VPhysicalVolume* 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);
…….}                                                                                                         36
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Voxelised organ




                  37
                   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                      From talk: S. Guatelli et al., “Geant4 Anthropomorphic
                                                    Phantoms”, IEEE NSS 2006, San Diego, November 2006.

           deposition in each voxel
                                                    S. Guatelli, B. Mascialino, M.G. Pia, W. Pokorski, “Geant4
                                                    anthropomorphic phantoms”, Nuclear Science Symposium
                                                    Conference Record, 2006, vol. 3, pp. 1359-1362



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                   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




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                   How to visualise organs
   1) 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




                                                                              41
                   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);
   ………..
   }
   …….
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                   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                           AdultMixFemale.mac
                  /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
                  #
                  ……                                                                                    43
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                     How to run the
                     G4HantropomorphicPhantom example

                 Install Geant4
                 Install GDML
                 Run the executable
                 Execute the macro initializing the model of
                  G4Anthropomorphic phantom




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        Components in G4PhantomBuilder
                                             Skull
                                        Thyroid      Spine

                                         Lungs          Esophagus

                                       Breasts                Arm Bones
                                                              Spleen
                                         Heart                 Pancreas
                                           Liver               Stomach
                                                               Kidneys
                           Upper Large                         Pelvis
                           Intestine
                                                               Ovaries
                                         Uterus
                                                           Lower Large Intestine
                                         Urinary
                                         Bladder       Leg Bones


                                                      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
                      Not visible:                    Conference Record, 2006, vol. 3, pp.
                                                      1359-1362                                  45
                      Brain (inside the skull)
Geant4 School, 12-14 October 2009, Catania, Italy
   Female ORNL Anthropomorphic Phantom




                                                    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   46
Geant4 School, 12-14 October 2009, Catania, Italy   Science Symposium Conference Record, 2006, vol. 3, pp. 1359-1362
                   Dosimetry
                                                            Anatomical components can be defined as
                                                            Geant4 SensitiveDetectors
                                                            Energy deposit collected in Geant4 Hits




                                                    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         47
Geant4 School, 12-14 October 2009, Catania, Italy
                                                                                     From talk: S. Guatelli et al., “Geant4 Anthropomorphic Phantoms”, IEEE NSS 2006, San Diego,




                   Mix & Match
                                                                                     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




                   Mathematical phantom with one voxel breast

                                                       MIRD
                                                    mathematical
                                                       breast




                                                    Dance & Hunt
                                                       voxel
                                                       breast
                                                D. R. Dance and R. A. Hunt, REPORT
                                                          RMTPC 02/1005                                                                                                       48
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                                                                                                                              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



                             Dosimetry
                                                                                                                              Science Symposium Conference Record, 2006, vol. 3, pp. 1359-1362




                             in mixed mathematical-voxel phantom
                                                                                                                                              Dose in each
                                                                                                                                              breast voxel
                                       35




                                       30
                                                         Dose in
                                       25
                                                    analytical organs
          Energy deposit




                                       20




                                       15




                                       10




                                        5




                                        0
                                            1   2   3   4   5   6     7      8      9   10   11         12       13      14      15    16    17    18    19     20
                                                  Kidney
                                      Breast


                                                    Heart




                                                                                             Pancreas
                                                    Head




                                                                                                                                               Uterus
                                       Brain




                                                                                                                                              Bladder
                                                                                    Spine




                                                                                                                 Skull
                                                                Intestine



                                                                                    Ovary


                                                                                                        Pelvis


                                                                                                                           Spleen
                                                                    Liver
                           Arm bone




                                                                            Lungs
                                                Leg bone




                                                                                                                         Stomach
                                                                                                                          Thyroid




                                                                                                                                                                                                                       49
Geant4 School, 12-14 October 2009, Catania, Italy
           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


                                                                                   50
Thank you !

              Questions?




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