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MESH-BASED HUMAN (XCAT) PHANTOMS FOR SIMULATION (mesh50_XCAT)

The Mesh-based XCAT phantom (mesh50_XCAT) is developed and maintained by Auer Benjamin from the Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA.

Contact: [email protected].

The mesh50_XCAT phantom is based on the 4D extended cardiac-torso digital anthropomorphic (XCAT) human phantom for a 50th percentile American male based on the PeopleSize anthropometric database.

The author acknowledge that the distribution free of charge of the mesh50_XCAT phantom is kindly permitted by the original developer team of the XCAT phantom.

Table of contents:

- 1. Objective and Background
- 2. Description
  - 2.1 STL-based phantoms (mesh50_XCAT)
  - 2.2 Voxelized version of the STL-based phantoms
- 3. Usage in GATE
  - 3.1 STL-based phantoms (mesh50_XCAT)
  - 3.2 Voxelized version of the STL-based phantoms 
- 4. Clinical Digital Activity Phantoms
  - 4.1 Brain Perfusion
  - 4.2 Brain DaT
  - 4.3 Thyroid
  - 4.4 Bone

1. Objective and Background

Objective

The mesh50_XCAT phantom provides realistic description of the human body for use in medical research, such as imaging, dosimetry, or radiation therapy. Simulation of such phantoms via adequate software capable of modelling mesh-based structures can emulate realistic medical data close to those obtained for actual patients.

Background

The Geant4 application for tomographic emission (GATE) remains one of the most commonly used simulation toolkits for medical research - GATE source page 1. GATE supports the simulation of Positron Emission Tomography (PET), Single Photon Emission Computed Tomography (SPECT), X-ray Computed Tomography (CT), optical, and Compton camera imaging, radiation therapy, and dosimetry in the same environment 2.

Most of the simulation software allows building system and phantom geometries based on the combination of simple idealized volumes (i.e. primitives). However, primitives are limited to model accurately complex geometries. Recent GATE releases (version 8 and 9) alleviate these limitations by allowing the users to import triangulated surface meshes as stereo-lithography (STL) file format, thus enabling improved accuracy of simulation of phantom geometries.

Taking advantage of such capability, we developed an STL-based version of the XCAT digitial anthropomorphic phantom34, named mesh50_XCAT, which provides an advanced anatomical description of the human body for simulation purposes.

In agreement with the original developer team of the XCAT phantom, we distribute below free of charge (see attached files) three versions of the mesh50_XCAT phantom with different lengths (Head only, Head-Torso-Abdominal only, and Whole Body). We provide below a detailled description of the usage in GATE of the phantoms. It is understandable that the mesh50_XCAT phantom can be used in any software capable of importing STL files (e.g. Geant4).

We refer readers interested on the generation, usage, and validation of the mesh50_XCAT phantom in the context of brain SPECT imaging to our previous publications. We kindly ask users to cite the following publications in their work,

  • Auer, B., Könik, A., Kalluri, K., De Beenhouwer, J., Furenlid, L. R., & King, M. A. (2018, November). Preliminary evaluation of surface mesh modeling of system geometry, anatomy phantom, and source activity for GATE simulations. In 2018 IEEE Nuclear Science Symposium and Medical Imaging Conference Proceedings (NSS/MIC) (pp. 1-3). IEEE.

An extended version of the mesh50_XCAT phantom was used in the following publications56.

2. Description

2.1 STL-based phantoms (mesh50_XCAT)

We provide 3 versions of the mesh50_XCAT phantom with different lengths (Whole Body, Head-Torso-Abdominal Only, and Head Only) as showed on the figure below.

Screen Shot 2022-06-02 at 4 41 26 PM

The 3 mesh50_XCAT phantom versions consist of the following structures,

  • Whole Body:
    Body, Brain, Skeleton, Liver, Lungs, Air Cavity and Bronchi Tree. Note, the Air Cavity volume was generated by merging part of the throat, nasal and oral cavities, and trachea. These volumes were embedded into a structure, named Body reflecting the outer surface of the phantom. Body was generated by unification of the head, ears, chest, arms, and legs into a single volume.

    Structures Size (cm x cm x cm) Volumes (cm3) # of Triangles STL file size (MB)
    Body 65.8 x 28.0 x 176.4 73,781.8 12,148 0.61
    Skeleton 64.0 x 25.4 x 175.0 6,539.1 73,832 3.7
    Air Cavity 5.9 x 14.0 x 26.7 141.3 3,830 0.19
    Brain 13.0 x 16.9 x 13.8 1,322.8 7,518 0.38
    Bronchi Tree 18.3 x 9.8 x 10.8 5.2 5,306 0.26
    Liver 18.9 x 19.1 x 18.7 1,798.7 3,698 0.18
    Lungs 24.1 x 18.0 x 22.1 2,804.7 5,354 0.27

    Screen Shot 2022-06-02 at 5 04 18 PM

  • Head-Torso-Abdominal Only:
    Brain, Liver, Lungs, Bronchi Tree, Air Cavity and Part of the Body and the Skeleton within the head, torso, and abdominal region.

    Structures Size (cm x cm x cm) Volumes (cm3) # of Triangles STL file size (MB)
    Body (Head-Torso-Abd) 65.8 x 28.0 x 95.6 53,869.5 15,502 0.77
    Skeleton (Head-Torso-Abd) 64.0 x 25.4 x 94.8 4,644.3 61,582 3.1
    Air Cavity 5.9 x 14.0 x 26.7 141.3 3,830 0.19
    Brain 13.0 x 16.9 x 13.8 1,322.8 7,518 0.38
    Bronchi Tree 18.3 x 9.8 x 10.8 5.2 5,306 0.26
    Liver 18.9 x 19.1 x 18.7 1,798.7 3,698 0.18
    Lungs 24.1 x 18.0 x 22.1 2,804.7 5,354 0.27

    Screen Shot 2022-06-02 at 5 05 29 PM

  • Head Only:
    Brain and Part of the Body, Skeleton, and Air Cavity within the head region.

    Structures Size (cm x cm x cm) Volumes (cm3) # of Triangles STL file size (MB)
    Body (Head) 34.1 x 24.8 x 25.6 5,476.5 2,004 0.10
    Skeleton (Head) 21.8 x 20.2 x 24.9 1,000.7 13,156 0.66
    Air Cavity (Head) 5.1 x 9.6 x 12.4 103.1 1,736 0.19
    Brain 13.0 x 16.9 x 13.8 1,322.8 7,518 0.38

    Screen Shot 2022-06-02 at 5 06 06 PM

2.2 Voxelized version of the STL-based phantoms

We also provide voxelized versions in interfile format (16-bit unsigned integer, *.i33 for raw data and *.h33 for the header files) of the 3 STL-based (mesh50_XCAT) phantoms described above. The voxelized phantoms can be used in attenuation correction for SPECT or PET reconstruction or as attenuation media or activity sources for GATE simulation.

Screen Shot 2022-06-05 at 2 51 39 PM

The Body, Air Cavity, Brain, Bronchi Tree, Liver, Lungs, and Skeleton regions were set of values from 1 to 7 by increment of 1.

The STL-based (mesh50_XCAT) phantoms were converted into voxelized phantoms following an approach similar to the one described in this paper7.

The voxelized attenuation phantoms were generated for a voxel size of 1 mm3. The Whole Body voxelized phantom is of 658x280x1764 mm3 (size of 650 MB). The Head-Torso-Abdominal Only phantom is of 658x280x956 mm3 (size of 352 MB). The Head Only phantom is of 338x248x256 mm3 (size of 43 MB).

3. Usage in GATE

3.1 STL-based phantoms (mesh50_XCAT)

We provide a macro 'GateSTLPhantoms.mac' to load and simulate in GATE the STL-based (mesh50_XCAT) attenuation phantoms along with the voxelized source defined above.

We desribe the GATE command lines to import the whole-body mesh50_XCAT phantom. Importation process is similar for the Head and Head-Torso-Abdominal mesh50_XCAT phantoms. All the mesh50_XCAT internal structures (Skeleton, Liver, Lungs, Bronchi Tree, Brain, and Air Cavity) are part of the Body volume. The Body volume can be set as a sub-volume of the world or SPECTHead, or any other volumes emcompassing its size. Examples of biological material composition from the ICRP and the ICRU of the STL-based human structures are provided below (Geant4 ICRP110_HumanPhantoms Example, GATE Example).

/gate/SPECThead/daughters/name Body
/gate/SPECThead/daughters/insert tessellated
/gate/Body/geometry/setPathToSTLFile PATH_TO/WholeBody_Body.stl
/gate/Body/placement/setTranslation 0.0   0.0   0.0  cm
/gate/Body/setMaterial Water
/gate/Body/vis/setColor blue
/gate/Body/vis/forceSolid
/gate/Body/attachPhantomSD

/gate/Body/daughters/name Lung
/gate/Body/daughters/insert tessellated
/gate/Lung/geometry/setPathToSTLFile PATH_TO/WholeBody_Lungs.stl
/gate/Lung/placement/setTranslation 0.0   0.0   0.0  cm
/gate/Lung/setMaterial Lung
/gate/Lung/vis/setColor blue
/gate/Lung/vis/forceSolid
/gate/Lung/attachPhantomSD

/gate/Body/daughters/name Skeleton
/gate/Body/daughters/insert tessellated
/gate/Skeleton/geometry/setPathToSTLFile PATH_TO/WholeBody_Skeleton.stl
/gate/Skeleton/placement/setTranslation 0.0   0.0   0.0  cm
/gate/Skeleton/setMaterial SpineBone
/gate/Skeleton/vis/setColor cyan
/gate/Skeleton/vis/forceSolid
/gate/Skeleton/attachPhantomSD

/gate/Body/daughters/name Brain
/gate/Body/daughters/insert tessellated
/gate/Brain/geometry/setPathToSTLFile PATH_TO/WholeBody_Brain.stl
/gate/Brain/placement/setTranslation 0.0   0.0   0.0  cm
/gate/Brain/setMaterial Brain
/gate/Brain/vis/setColor cyan
/gate/Brain/vis/forceSolid
/gate/Brain/attachPhantomSD

/gate/Body/daughters/name Liver
/gate/Body/daughters/insert tessellated
/gate/Liver/geometry/setPathToSTLFile PATH_TO/WholeBody_Liver.stl
/gate/Liver/placement/setTranslation 0.0   0.0   0.0  cm
/gate/Liver/setMaterial Liver
/gate/Liver/vis/setColor cyan
/gate/Liver/vis/forceSolid
/gate/Liver/attachPhantomSD

/gate/Body/daughters/name AirCavity
/gate/Body/daughters/insert tessellated
/gate/AirCavity/geometry/setPathToSTLFile PATH_TO/WholeBody_AirCavity.stl
/gate/AirCavity/placement/setTranslation 0.0   0.0   0.0  cm
/gate/AirCavity/setMaterial Air
/gate/AirCavity/vis/setColor cyan
/gate/AirCavity/vis/forceSolid
/gate/AirCavity/attachPhantomSD

The Bronchi Tree is a subvolume of the Lung volume,

/gate/Lung/daughters/name BronchiTree
/gate/Lung/daughters/insert tessellated
/gate/BronchiTree/geometry/setPathToSTLFile PATH_TO/WholeBody_BronchiTree.stl
/gate/BronchiTree/placement/setTranslation 0.0   0.0   0.0  cm
/gate/BronchiTree/setMaterial Water
/gate/BronchiTree/vis/setColor blue
/gate/BronchiTree/vis/forceSolid
/gate/BronchiTree/attachPhantomSD

3.2 Voxelized version of the STL-based phantoms

The voxelized phantoms (interfile format) can be loaded in GATE via the following command lines, where 'VoxSource' is the source volume name,

/gate/source/addSource                                            VoxSource voxel
/gate/source/VoxSource/reader/insert                              image
/gate/source/VoxSource/imageReader/translator/insert              linear
/gate/source/VoxSource/imageReader/linearTranslator/setScale      0.001 Bq
/gate/source/VoxSource/imageReader/readFile PATH_TO/VoxWholeBody_658x280x1764.h33 
# OR Head_Assembled_338x248x256 OR HeadTorsoAbd_Assembled_658x280x956
/gate/source/VoxSource/imageReader/verbose 1
/gate/source/VoxSource/gps/particle gamma
/gate/source/VoxSource/gps/angtype iso
/gate/source/VoxSource/gps/energy 140.5 keV # For Tc-99m

The default position of the voxelized source is in the 1st quarter, so the voxelized source has to be shifted over half its dimension in the negative direction on each axis. As the voxel size is 1 mm3, dimensions of the image (provided in the file name) need to be divided by two along X, Y, Z dimensions.

This results in the addition of the following two lines,

/gate/source/VoxSource/setPosition -329.0 -140.0 -882.0 mm
/gate/source/list

The voxelized phantoms can also be used as attenuation map in GATE via the following command lines. Note, the voxelized phantom should A) not collide with any other system components and B) be contained entirely within its 'mother' volume. The voxelized phantom can be a sub-volume of the SPECThead volume as shown below,

/gate/SPECThead/daughters/name VoxAttn
/gate/SPECThead/daughters/insert ImageRegularParametrisedVolume
/gate/VoxAttn/geometry/setImage PATH_TO/VoxWholeBody_658x280x1764.h33
/gate/VoxAttn/geometry/setRangeToMaterialFile AttnRange.dat
/gate/VoxAttn/placement/setTranslation  0. 0. 0. mm
/gate/VoxAttn/setSkipEqualMaterials 1
/gate/VoxAttn/attachPhantomSD

Indices in the voxelized image are translated into biological materials via the parameters defined in the 'AttnRange.dat' file. For example, we recommend the following indices to materials conversion,

Image Indices Human Structures Biological materials
0 Volume surrounding the body region of the phantom Air
1 Body Water
2 Air Cavity Air
3 Brain Brain
4 Bronchi Tree Air
5 Liver Liver
6 Lungs Lung
7 Skeleton SpineBone

Note, the biological materials are defined in the 'GateMaterials.db' file available for download (GATE_macros.zip).

3. Clinical Digital Activity Phantoms

We provide multiple activity phantoms to simulate clinical distribution for brain perfusion, brain DaT, bone and thyroid imaging. The phantoms can be downloaded via the Digital_Activity_Phantoms.zip file.

3.1. Brain Perfusion

3.1.1 Description

We provide the voxelized brain perfusion activity phantom in interfile format (16-bit unsigned integer, *.i33 for raw data and *.h33 for the header files). The brain perfusion phantom can emulate a clinical 99mTc ECD/HMPAO or 123I-IMP brain perfusion distribution as imaged 1h post injection. It can be used in combination of the voxelized or STL attenuation Head-Torso-Abdominal mesh50_XCAT phantoms described in the previous section. The brain perfusion activity phantom is co-registered with these attenuation phantom, thus no translation in GATE for simulation is needed to align the activity and attenuation phantoms.

For additional information, please see below references,

  • Auer, Benjamin, Navid Zeraatkar, Justin C. Goding, Arda Könik, Timothy J. Fromme, Kesava S. Kalluri, Lars R. Furenlid, Phillip H. Kuo, and Michael A. King. "Inclusion of quasi-vertex views in a brain-dedicated multi-pinhole SPECT system for improved imaging performance." Physics in Medicine & Biology 66, no. 3 (2021): 035007

Screen Shot 2023-06-21 at 1 16 13 AM

The brain perfusion activity phantom can be simulated (VoxHeadTorsoAbd_BrainPerfusion_Source_658x280x956.i33) as being filled with uniform tracer activity in striatum:grey matter:white matter : lungs : liver : background with concentration ratio of 10.1:9.3:2.3:6.0:11.4:1. It consists of 658x280x956 voxels of 1.0x1.0x1.0 mm3 (size of 352.3 MB).

3.2.2 Usage in GATE

The voxelized phantoms (interfile format) can be loaded in GATE via the following command lines for a 99mTc or 123I sources, where 'VoxSource' is the source volume name,

/gate/source/addSource VoxSource voxel
/gate/source/VoxSource/reader/insert image
/gate/source/VoxSource/imageReader/translator/insert linear
/gate/source/VoxSource/imageReader/linearTranslator/setScale 0.03 Bq
/gate/source/VoxSource/imageReader/readFile PATH_TO/VoxHeadTorsoAbd_BrainPerfusion_Source_658x280x956.h33
/gate/source/VoxSource/imageReader/verbose 1
/gate/source/VoxSource/gps/particle gamma
/gate/source/VoxSource/gps/ang/type iso
/gate/source/VoxSource/gps/ang/mintheta 0.0 deg
/gate/source/VoxSource/gps/ang/maxtheta 180.0 deg
/gate/source/VoxSource/gps/ang/minphi 0.0  deg
/gate/source/VoxSource/gps/ang/maxphi 360.0 deg
/gate/source/VoxSource/gps/energytype Mono
/gate/source/VoxSource/gps/ene/mono 140.5 keV # For Tc-99m
/gate/source/VoxSource/gps/ene/mono 159.0 keV # For I-123 primary emission
/gate/source/VoxSource/setIntensity 1
/gate/source/VoxSource/setPosition -329.0 -140.0 -478.0 mm
/gate/source/VoxSource/dump 1

The default position of the voxelized source is in the 1st quarter, so the voxelized source has to be shifted over half its dimension in the negative direction on each axis. As the voxel size is 1 mm3, dimensions of the image (provided in the file name) need to be divided by two along X, Y, Z dimensions.

The following example shows how to define a source of 123I gammas. The gamma emission data is from the IAEA database: https://www-nds.iaea.org/relnsd/vcharthtml/VChartHTML.html. Note that this example shows the gamma emissions only, so the simulation output will be missing the X-ray peaks seen in true 123I spectra.

`VS_gamma` is the name of the voxelised gamma source 
# Set verbosity (2 = every event)
# Good to set to 2 initially to check output is as expected
/gate/source/VS_gamma/gps/verbose 0

/gate/source/addSource VS_gamma voxel
/gate/source/VS_gamma/reader/insert image
/gate/source/VS_gamma/imageReader/translator/insert linear
/gate/source/VS_gamma/imageReader/linearTranslator/setScale 0.05 Bq
/gate/source/VS_gamma/imageReader/readFile PATH_TO/VoxHeadTorsoAbd_BrainPerfusion_Source_658x280x956.h33
/gate/source/VS_gamma/imageReader/verbose 1
/gate/source/VS_gamma/gps/particle gamma
/gate/source/VS_gamma/gps/ang/type iso
/gate/source/VS_gamma/setPosition -329.0 -140.0 -478.0 mm

# Force unstable
/gate/source/VS_gamma/setForcedUnstableFlag  true
/gate/source/VS_gamma/setForcedHalfLife 47602.8 s

/gate/source/VS_gamma/gps/particle    gamma
/gate/source/VS_gamma/gps/ene/type  User
/gate/source/VS_gamma/gps/hist/type    energy

/gate/source/VS_gamma/gps/ene/min  0.150 MeV
/gate/source/VS_gamma/gps/ene/max  1.037 MeV

# ------------------hist of emissions----------------------------- #
/gate/source/VS_gamma/gps/hist/point 0.1589999 0.0
/gate/source/VS_gamma/gps/hist/point 0.159 83.6
/gate/source/VS_gamma/gps/hist/point 0.1590001 0.0

/gate/source/VS_gamma/gps/hist/point 0.17419999 0.0
/gate/source/VS_gamma/gps/hist/point 0.1742 0.0008
/gate/source/VS_gamma/gps/hist/point 0.1742001 0.0

/gate/source/VS_gamma/gps/hist/point 0.18261999 0.0
/gate/source/VS_gamma/gps/hist/point 0.18262 0.013
/gate/source/VS_gamma/gps/hist/point 0.18262001 0.0

/gate/source/VS_gamma/gps/hist/point 0.19069999 0.0
/gate/source/VS_gamma/gps/hist/point 0.1907 0.0005
/gate/source/VS_gamma/gps/hist/point 0.19070001 0.0

/gate/source/VS_gamma/gps/hist/point 0.19217999 0.0
/gate/source/VS_gamma/gps/hist/point 0.19218 0.0177
/gate/source/VS_gamma/gps/hist/point 0.19218001 0.0

/gate/source/VS_gamma/gps/hist/point 0.1972299 0.0
/gate/source/VS_gamma/gps/hist/point 0.19723 0.00033
/gate/source/VS_gamma/gps/hist/point 0.19723001 0.0

/gate/source/VS_gamma/gps/hist/point 0.19822999 0.0
/gate/source/VS_gamma/gps/hist/point 0.19823 0.0033
/gate/source/VS_gamma/gps/hist/point 0.19823001 0.0

/gate/source/VS_gamma/gps/hist/point 0.206799 0.0
/gate/source/VS_gamma/gps/hist/point 0.2068 0.0033
/gate/source/VS_gamma/gps/hist/point 0.2068001 0.0

/gate/source/VS_gamma/gps/hist/point 0.20779999 0.0
/gate/source/VS_gamma/gps/hist/point 0.2078 0.0011
/gate/source/VS_gamma/gps/hist/point 0.2078001 0.0

/gate/source/VS_gamma/gps/hist/point 0.247969999 0.0
/gate/source/VS_gamma/gps/hist/point 0.24797 0.0693
/gate/source/VS_gamma/gps/hist/point 0.247970001 0.0

/gate/source/VS_gamma/gps/hist/point 0.25750999 0.0
/gate/source/VS_gamma/gps/hist/point 0.25751 0.0015
/gate/source/VS_gamma/gps/hist/point 0.257510001 0.0

/gate/source/VS_gamma/gps/hist/point 0.2589999 0.0
/gate/source/VS_gamma/gps/hist/point 0.259 0.0009
/gate/source/VS_gamma/gps/hist/point 0.2590001 0.0

/gate/source/VS_gamma/gps/hist/point 0.27835999 0.0
/gate/source/VS_gamma/gps/hist/point 0.27836 0.0023
/gate/source/VS_gamma/gps/hist/point 0.2783001 0.0

/gate/source/VS_gamma/gps/hist/point 0.28102999 0.0
/gate/source/VS_gamma/gps/hist/point 0.28103 0.072
/gate/source/VS_gamma/gps/hist/point 0.28103001 0.0

/gate/source/VS_gamma/gps/hist/point 0.28531999 0.0
/gate/source/VS_gamma/gps/hist/point 0.28532 0.0043
/gate/source/VS_gamma/gps/hist/point 0.28533001 0.0

/gate/source/VS_gamma/gps/hist/point 0.29518999 0.0
/gate/source/VS_gamma/gps/hist/point 0.29519 0.001588
/gate/source/VS_gamma/gps/hist/point 0.29519001 0.0

/gate/source/VS_gamma/gps/hist/point 0.3293799 0.0
/gate/source/VS_gamma/gps/hist/point 0.32938 0.0026
/gate/source/VS_gamma/gps/hist/point 0.32938001 0.0

/gate/source/VS_gamma/gps/hist/point 0.33069999 0.0
/gate/source/VS_gamma/gps/hist/point 0.3307 0.0116
/gate/source/VS_gamma/gps/hist/point 0.3307001 0.0

/gate/source/VS_gamma/gps/hist/point 0.34372999 0.0
/gate/source/VS_gamma/gps/hist/point 0.34373 0.0043
/gate/source/VS_gamma/gps/hist/point 0.34373001 0.0

/gate/source/VS_gamma/gps/hist/point 0.34635999 0.0
/gate/source/VS_gamma/gps/hist/point 0.34636 0.12
/gate/source/VS_gamma/gps/hist/point 0.34636001 0.0

/gate/source/VS_gamma/gps/hist/point 0.40501999 0.0
/gate/source/VS_gamma/gps/hist/point 0.40502 0.0027
/gate/source/VS_gamma/gps/hist/point 0.40502001 0.0

/gate/source/VS_gamma/gps/hist/point 0.43749999 0.0
/gate/source/VS_gamma/gps/hist/point 0.4375 0.0008
/gate/source/VS_gamma/gps/hist/point 0.43750001 0.0

/gate/source/VS_gamma/gps/hist/point 0.44001999 0.0
/gate/source/VS_gamma/gps/hist/point 0.44002 0.388
/gate/source/VS_gamma/gps/hist/point 0.44002001 0.0

/gate/source/VS_gamma/gps/hist/point 0.45475999 0.0
/gate/source/VS_gamma/gps/hist/point 0.45476 0.0034
/gate/source/VS_gamma/gps/hist/point 0.45476001 0.0

/gate/source/VS_gamma/gps/hist/point 0.50532999 0.0
/gate/source/VS_gamma/gps/hist/point 0.50533 0.288
/gate/source/VS_gamma/gps/hist/point 0.50533001 0.0

/gate/source/VS_gamma/gps/hist/point 0.52896999 0.0
/gate/source/VS_gamma/gps/hist/point 0.52897 1.27
/gate/source/VS_gamma/gps/hist/point 0.52897001 0.0

/gate/source/VS_gamma/gps/hist/point 0.53853999 0.0
/gate/source/VS_gamma/gps/hist/point 0.53854 0.31
/gate/source/VS_gamma/gps/hist/point 0.53854001 0.0

/gate/source/VS_gamma/gps/hist/point 0.55604999 0.0
/gate/source/VS_gamma/gps/hist/point 0.55605 0.0025
/gate/source/VS_gamma/gps/hist/point 0.55605001 0.0

/gate/source/VS_gamma/gps/hist/point 0.56278999 0.0
/gate/source/VS_gamma/gps/hist/point 0.56279 0.0009
/gate/source/VS_gamma/gps/hist/point 0.56279001 0.0

/gate/source/VS_gamma/gps/hist/point 0.57399 0.0
/gate/source/VS_gamma/gps/hist/point 0.574 0.005852
/gate/source/VS_gamma/gps/hist/point 0.57401 0.0

/gate/source/VS_gamma/gps/hist/point 0.57825999 0.0
/gate/source/VS_gamma/gps/hist/point 0.57826 0.0016
/gate/source/VS_gamma/gps/hist/point 0.57826001 0.0

/gate/source/VS_gamma/gps/hist/point 0.59968999 0.0
/gate/source/VS_gamma/gps/hist/point 0.59969 0.0026
/gate/source/VS_gamma/gps/hist/point 0.59969001 0.0

/gate/source/VS_gamma/gps/hist/point 0.61004999 0.0
/gate/source/VS_gamma/gps/hist/point 0.61005 0.0011
/gate/source/VS_gamma/gps/hist/point 0.61005001 0.0

/gate/source/VS_gamma/gps/hist/point 0.62457999 0.0
/gate/source/VS_gamma/gps/hist/point 0.62458 0.078
/gate/source/VS_gamma/gps/hist/point 0.62458001 0.0

/gate/source/VS_gamma/gps/hist/point 0.62825999 0.0
/gate/source/VS_gamma/gps/hist/point 0.62826 0.0016
/gate/source/VS_gamma/gps/hist/point 0.62826001 0.0

/gate/source/VS_gamma/gps/hist/point 0.68793999 0.0
/gate/source/VS_gamma/gps/hist/point 0.68794 0.0268
/gate/source/VS_gamma/gps/hist/point 0.68794001 0.0

/gate/source/VS_gamma/gps/hist/point 0.73586999 0.0
/gate/source/VS_gamma/gps/hist/point 0.73587 0.047
/gate/source/VS_gamma/gps/hist/point 0.73587001 0.0

/gate/source/VS_gamma/gps/hist/point 0.76084999 0.0
/gate/source/VS_gamma/gps/hist/point 0.76085 0.00063
/gate/source/VS_gamma/gps/hist/point 0.76085001 0.0

/gate/source/VS_gamma/gps/hist/point 0.78359999 0.0
/gate/source/VS_gamma/gps/hist/point 0.7836 0.053
/gate/source/VS_gamma/gps/hist/point 0.7836001 0.0

/gate/source/VS_gamma/gps/hist/point 0.83709999 0.0
/gate/source/VS_gamma/gps/hist/point 0.8371 0.00047
/gate/source/VS_gamma/gps/hist/point 0.8371001 0.0

/gate/source/VS_gamma/gps/hist/point 0.87751999 0.0
/gate/source/VS_gamma/gps/hist/point 0.87752 0.00072
/gate/source/VS_gamma/gps/hist/point 0.87752001 0.0

/gate/source/VS_gamma/gps/hist/point 0.89479999 0.0
/gate/source/VS_gamma/gps/hist/point 0.8948 0.0007
/gate/source/VS_gamma/gps/hist/point 0.89480001 0.0

/gate/source/VS_gamma/gps/hist/point 0.89819999 0.0
/gate/source/VS_gamma/gps/hist/point 0.8982 0.0006
/gate/source/VS_gamma/gps/hist/point 0.8982001 0.0

/gate/source/VS_gamma/gps/hist/point 0.90911999 0.0
/gate/source/VS_gamma/gps/hist/point 0.90912 0.0013
/gate/source/VS_gamma/gps/hist/point 0.909120001 0.0

/gate/source/VS_gamma/gps/hist/point 1.03662999 0.0
/gate/source/VS_gamma/gps/hist/point 1.03663 0.00077
/gate/source/VS_gamma/gps/hist/point 1.03663001 0.0
###################################################

/gate/source/list
/gate/source/VS_gamma/dump 1

4.2 Brain Dopamine DaT

4.2.1 Description

We provide the voxelized brain DaT activity phantom in interfile format (16-bit unsigned integer, *.i33 for raw data and *.h33 for the header files). The brain DaT phantom can emulate a clinical 123I-Ioflupane brain dopamine distribution as imaged 4h post injection. It can be used in combination of the voxelized or STL attenuation Head-Torso-Abdominal mesh50_XCAT phantoms described in the previous section. The brain perfusion activity phantom is co-registered with these attenuation phantom, thus no translation in GATE for simulation is needed to align the activity and attenuation phantoms.

For additional information, please see below references,

  • Auer, Benjamin, Navid Zeraatkar, Justin C. Goding, Arda Könik, Timothy J. Fromme, Kesava S. Kalluri, Lars R. Furenlid, Phillip H. Kuo, and Michael A. King. "Inclusion of quasi-vertex views in a brain-dedicated multi-pinhole SPECT system for improved imaging performance." Physics in Medicine & Biology 66, no. 3 (2021): 035007

Screen Shot 2023-06-21 at 12 44 30 AM

The brain DaT activity phantom can be simulated (VoxHeadTorsoAbd_DaT_Source_658x280x956.i33) as being filled with uniform tracer activity in striatum : salivary glands : lungs : liver : background with concentration ratio of 8:4:1.8:6.2:1, respectively. It consists of 658x280x956 voxels of 1.0x1.0x1.0 mm3 (size of 352.3 MB).

4.2.2 Usage in GATE

The voxelized phantoms (interfile format) can be loaded in GATE via the following command lines for a 123I source, where 'VoxSource' is the source volume name,

/gate/source/addSource VoxSource voxel
/gate/source/VoxSource/reader/insert image
/gate/source/VoxSource/imageReader/translator/insert linear
/gate/source/VoxSource/imageReader/linearTranslator/setScale 0.03 Bq
/gate/source/VoxSource/imageReader/readFile PATH_TO/VoxHeadTorsoAbd_DaT_Source_658x280x956.h33
/gate/source/VoxSource/imageReader/verbose 1
/gate/source/VoxSource/gps/particle gamma
/gate/source/VoxSource/gps/ang/type iso
/gate/source/VoxSource/gps/ang/mintheta 0.0 deg
/gate/source/VoxSource/gps/ang/maxtheta 180.0 deg
/gate/source/VoxSource/gps/ang/minphi 0.0  deg
/gate/source/VoxSource/gps/ang/maxphi 360.0 deg
/gate/source/VoxSource/gps/energytype Mono
/gate/source/VoxSource/gps/ene/mono 159.0 keV # For I-123 primary emission
/gate/source/VoxSource/setIntensity 1
/gate/source/VoxSource/setPosition -329.0 -140.0 -478.0 mm
/gate/source/VoxSource/dump 1

An example of a complete source of 123I gammas consisting of all the gammas emissions can be found in the previous section.

4.3 Thyroid

4.3.1 Description

We provide the voxelized thyroid activity phantoms in interfile format (16-bit unsigned integer, *.i33 for raw data and *.h33 for the header files). The thyroid phantoms can emulate a clinical 123I or 131I thyroid distribution with and without background activity. It can be used in combination of the voxelized or STL attenuation Head-Torso-Abdominal mesh50_XCAT phantoms described in the previous section. The brain perfusion activity phantom is co-registered with these attenuation phantom, thus no translation in GATE for simulation is needed to align the activity and attenuation phantoms.

Screen Shot 2023-06-21 at 1 25 53 AM

The thyroid activity phantom can be simulated (VoxHeadTorsoAbd_Thyroid_Source_658x280x956.i33) as being filled with uniform tracer activity in thyroid : salivary glands : background with concentration ratios of 8:5:1, respectively. We provide as well the thyroid phantom without background activity (VoxHeadTorsoAbd_Thyroid_NoBkg_Source_658x280x956.i33). Both phantom consist of 658x280x956 voxels of 1.0x1.0x1.0 mm3 (size of 352.3 MB).

4.3.2 Usage in GATE

The voxelized phantoms (interfile format) can be loaded in GATE via the following command lines for a 99mTc source, where 'VoxSource' is the source volume name,

/gate/source/addSource VoxSource voxel
/gate/source/VoxSource/reader/insert image
/gate/source/VoxSource/imageReader/translator/insert linear
/gate/source/VoxSource/imageReader/linearTranslator/setScale 0.03 Bq
/gate/source/VoxSource/imageReader/readFile PATH_TO/VoxHeadTorsoAbd_Thyroid_Source_658x280x956.h33
#/gate/source/VoxSource/imageReader/readFile PATH_TO/VoxHeadTorsoAbd_Thyroid_NoBkg_Source_658x280x956.h33 # No Background Activity
/gate/source/VoxSource/imageReader/verbose 1
/gate/source/VoxSource/gps/particle gamma
/gate/source/VoxSource/gps/ang/type iso
/gate/source/VoxSource/gps/ang/mintheta 0.0 deg
/gate/source/VoxSource/gps/ang/maxtheta 180.0 deg
/gate/source/VoxSource/gps/ang/minphi 0.0  deg
/gate/source/VoxSource/gps/ang/maxphi 360.0 deg
/gate/source/VoxSource/gps/energytype Mono
/gate/source/VoxSource/gps/ene/mono 159.0 keV # For I-123 primary emission
/gate/source/VoxSource/gps/ene/mono 364.0 keV # For I-131 primary emission
/gate/source/VoxSource/setIntensity 1
/gate/source/VoxSource/setPosition -329.0 -140.0 -478.0 mm
/gate/source/VoxSource/dump 1

An example of a complete source of 123I gammas consisting of all the gammas emissions can be found in the brain perfusion section. The following example shows how to define a source of 131I gammas. The gamma emission data is from the IAEA database: https://www-nds.iaea.org/relnsd/vcharthtml/VChartHTML.html. Note that this example shows the gamma emissions only, so the simulation output will be missing the X-ray peaks or beta emissions seen in true 131I energy spectra.

VS_gamma is the name of the voxelised gamma source

# Set verbosity (2 = every event)
# Good to set to 2 initially to check output is as expected
/gate/source/VS_gamma/gps/verbose 0

/gate/source/addSource VS_gamma voxel
/gate/source/VS_gamma/reader/insert image
/gate/source/VS_gamma/imageReader/translator/insert linear
/gate/source/VS_gamma/imageReader/linearTranslator/setScale 0.05 Bq
/gate/source/VoxSource/imageReader/readFile PATH_TO/VoxHeadTorsoAbd_Thyroid_Source_658x280x956.h33
#/gate/source/VoxSource/imageReader/readFile PATH_TO/VoxHeadTorsoAbd_Thyroid_NoBkg_Source_658x280x956.h33 # No Background Activity
/gate/source/VS_gamma/imageReader/verbose 1
/gate/source/VS_gamma/gps/particle gamma
/gate/source/VS_gamma/gps/ang/type iso
/gate/source/VoxSource/setPosition -329.0 -140.0 -478.0 mm

# Force unstable
/gate/source/VS_gamma/setForcedUnstableFlag  true
/gate/source/VS_gamma/setForcedHalfLife 692988 s

/gate/source/VS_gamma/gps/particle    gamma
/gate/source/VS_gamma/gps/ene/type  User
/gate/source/VS_gamma/gps/hist/type    energy

/gate/source/VS_gamma/gps/ene/min    0.08 MeV
/gate/source/VS_gamma/gps/ene/max    0.636989 MeV

 # ---------------------------------------------------- #
/gate/source/VS_gamma/gps/hist/point 0.080175 0.0
/gate/source/VS_gamma/gps/hist/point 0.080185 2.61615
/gate/source/VS_gamma/gps/hist/point 0.080195 0.0

/gate/source/VS_gamma/gps/hist/point 0.08589 0.0
/gate/source/VS_gamma/gps/hist/point 0.0859 8.965e-05
/gate/source/VS_gamma/gps/hist/point 0.08591 0.0

/gate/source/VS_gamma/gps/hist/point 0.16392 0.0
/gate/source/VS_gamma/gps/hist/point 0.16393 0.0211085
/gate/source/VS_gamma/gps/hist/point 0.16394 0.0

/gate/source/VS_gamma/gps/hist/point 0.177204 0.0
/gate/source/VS_gamma/gps/hist/point 0.177214 0.26895
/gate/source/VS_gamma/gps/hist/point 0.177224 0.0

/gate/source/VS_gamma/gps/hist/point 0.23217 0.0
/gate/source/VS_gamma/gps/hist/point 0.23218 0.0031785
/gate/source/VS_gamma/gps/hist/point 0.23219 0.0

/gate/source/VS_gamma/gps/hist/point 0.272488 0.0
/gate/source/VS_gamma/gps/hist/point 0.272498 0.0576205
/gate/source/VS_gamma/gps/hist/point 0.272508 0.0

/gate/source/VS_gamma/gps/hist/point 0.284295 0.0
/gate/source/VS_gamma/gps/hist/point 0.284305 6.12065
/gate/source/VS_gamma/gps/hist/point 0.284315 0.0

/gate/source/VS_gamma/gps/hist/point 0.29579 0.0
/gate/source/VS_gamma/gps/hist/point 0.2958 0.001793
/gate/source/VS_gamma/gps/hist/point 0.29581 0.0

/gate/source/VS_gamma/gps/hist/point 0.30239 0.0
/gate/source/VS_gamma/gps/hist/point 0.3024 0.004727
/gate/source/VS_gamma/gps/hist/point 0.30241 0.0

/gate/source/VS_gamma/gps/hist/point 0.318078 0.0
/gate/source/VS_gamma/gps/hist/point 0.318088 0.077425
/gate/source/VS_gamma/gps/hist/point 0.318098 0.0

/gate/source/VS_gamma/gps/hist/point 0.324641 0.0
/gate/source/VS_gamma/gps/hist/point 0.324651 0.02119
/gate/source/VS_gamma/gps/hist/point 0.324661 0.0

/gate/source/VS_gamma/gps/hist/point 0.325779 0.0
/gate/source/VS_gamma/gps/hist/point 0.325789 0.273025
/gate/source/VS_gamma/gps/hist/point 0.325799 0.0

/gate/source/VS_gamma/gps/hist/point 0.35839 0.0
/gate/source/VS_gamma/gps/hist/point 0.3584 0.0163
/gate/source/VS_gamma/gps/hist/point 0.35841 0.0

/gate/source/VS_gamma/gps/hist/point 0.364479 0.0
/gate/source/VS_gamma/gps/hist/point 0.364489 81.5
/gate/source/VS_gamma/gps/hist/point 0.364499 0.0

/gate/source/VS_gamma/gps/hist/point 0.404804 0.0
/gate/source/VS_gamma/gps/hist/point 0.404814 0.054605
/gate/source/VS_gamma/gps/hist/point 0.404824 0.0

/gate/source/VS_gamma/gps/hist/point 0.44959 0.0
/gate/source/VS_gamma/gps/hist/point 0.4496 0.007335
/gate/source/VS_gamma/gps/hist/point 0.44961 0.0

/gate/source/VS_gamma/gps/hist/point 0.502994 0.0
/gate/source/VS_gamma/gps/hist/point 0.503004 0.359415
/gate/source/VS_gamma/gps/hist/point 0.503014 0.0

/gate/source/VS_gamma/gps/hist/point 0.636979 0.0
/gate/source/VS_gamma/gps/hist/point 0.636989 7.1557
/gate/source/VS_gamma/gps/hist/point 0.636999 0.0
###################################################

/gate/source/list
/gate/source/VS_gamma/dump 1

4.4 Bone

4.4.1 Description

We provide the voxelized bone activity phantom in interfile format (16-bit unsigned integer, *.i33 for raw data and *.h33 for the header files). The bone phantom can emulate a clinical 99mTc bone distribution. It can be used in combination of the voxelized or STL attenuation whole-body mesh50_XCAT phantoms described in the above. The bone activity phantom is co-registered with these attenuation phantom, thus no translation in GATE for simulation is needed to align the activity and attenuation phantoms.

Screen Shot 2023-06-21 at 1 23 38 AM

The bone activity phantom can be simulated (VoxWholeBody_Bone_Source_658x280x1764.i33) as being filled with uniform tracer activity in bone : background with concentration ratios of 8:1, respectively. It consists of 1764 voxels of 1.0x1.0x1.0 mm3 (size of 650 MB).

4.4.2 Usage in GATE

The voxelized phantoms (interfile format) can be loaded in GATE via the following command lines for a 99mTc source, where 'VoxSource' is the source volume name,

/gate/source/addSource VoxSource voxel
/gate/source/VoxSource/reader/insert image
/gate/source/VoxSource/imageReader/translator/insert linear
/gate/source/VoxSource/imageReader/linearTranslator/setScale 0.03 Bq
/gate/source/VoxSource/imageReader/readFile PATH_TO/VoxWholeBody_Bone_Source_658x280x1764.h33
/gate/source/VoxSource/imageReader/verbose 1
/gate/source/VoxSource/gps/particle gamma
/gate/source/VoxSource/gps/ang/type iso
/gate/source/VoxSource/gps/ang/mintheta 0.0 deg
/gate/source/VoxSource/gps/ang/maxtheta 180.0 deg
/gate/source/VoxSource/gps/ang/minphi 0.0  deg
/gate/source/VoxSource/gps/ang/maxphi 360.0 deg
/gate/source/VoxSource/gps/energytype Mono
/gate/source/VoxSource/gps/ene/mono 140.5 keV # For Tc-99m primary emission
/gate/source/VoxSource/setIntensity 1
/gate/source/VoxSource/setPosition -329.0 -140.0 -882.0 mm
/gate/source/VoxSource/dump 1

Footnotes

  1. Jan, S., Santin, G., Strul, D., Staelens, S., Assié, K., Autret, D., ... & Morel, C. (2004). GATE: a simulation toolkit for PET and SPECT. Physics in Medicine & Biology, 49(19), 4543. ↩

  2. Sarrut, D., Bardiès, M., Boussion, N., Freud, N., Jan, S., Létang, J. M., ... & Buvat, I. (2014). A review of the use and potential of the GATE Monte Carlo simulation code for radiation therapy and dosimetry applications. Medical physics, 41(6Part1), 064301. ↩

  3. Segars, W. P., Sturgeon, G., Mendonca, S., Grimes, J., & Tsui, B. M. (2010). 4D XCAT phantom for multimodality imaging research. Medical physics, 37(9), 4902-4915. ↩

  4. Segars, W. P., & Tsui, B. M. (2009). MCAT to XCAT: The evolution of 4-D computerized phantoms for imaging research. Proceedings of the IEEE, 97(12), 1954-1968. ↩

  5. Auer, B., Zeraatkar, N., Goding, J. C., Könik, A., Fromme, T. J., Kalluri, K. S., ... & King, M. A. (2021). Inclusion of quasi-vertex views in a brain-dedicated multi-pinhole SPECT system for improved imaging performance. Physics in Medicine & Biology, 66(3), 035007. ↩

  6. Könik, A., Auer, B., De Beenhouwer, J., Kalluri, K., Zeraatkar, N., Furenlid, L. R., & King, M. A. (2019). Primary, scatter, and penetration characterizations of parallel-hole and pinhole collimators for I-123 SPECT. Physics in Medicine & Biology, 64(24), 245001. ↩

  7. Patil, S. and Ravi, B. (2005) ‘Voxel-based representation, display and thickness analysis of intricate shapes’, in Ninth International Conference on Computer Aided Design and Computer Graphics (CAD-CG’05). IEEE, pp. 6-pp. ↩

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