=======================================================================
Geant4 - ICRP110_HumanPhantoms Example
=======================================================================
The ICRP110_HumanPhantoms example is developed and mantained by Susanna Guatelli, Matthew Large and Alessandra Malaroda,
Centre For Medical Radiation Physics (CMRP), University of Wollongong, NSW, Australia, and John Allison, Geant4 Associates International
and University of Manchester, UK.
Contacts:
- susanna@uow.edu.au
- mjl970@uowmail.edu.au
- malaroda@uow.edu.au
- John.Allison@g4ai.org
The example is based on the extended/medical/DICOM example
The authors acknowledge that this application of the ICRP110 human phantoms have been implemented in Geant4 with the kind permission of
the International Commission on Radiological Protection (ICRP).
----------------------------------------------------------------------------------------------------
--------------------------------------> Introduction <----------------------------------------------
----------------------------------------------------------------------------------------------------
This application models the ICRP110 reference computational human phantoms [1] in a Geant4 simulation and calculates
the dose in individual voxels and in entire organs.
The human male phantom, provided kindly by the ICRP, is created from a whole-body clinical CT image set of a 38yr old
individual with height 176 cm and mass approximately 70 kg. Similarly, the human female phantom was created from a set of
whole body CT images of a 43yr old individual with height 163 cm and weight 60 kg. The CT scans were acquired with both
individuals laying supine and with arms resting parallel alongside the body. Both sets of CT data were then scaled to
closely approximate the ICRP adult Reference Male and Reference Female, defined in previous ICRP publications [2, 3].
[1] HG Menzel, C Clement, and P DeLuca. ICRP publication 110. "Realistic reference phantoms:
an icrp/icru joint effort: A report of adult reference computational phantoms", Annals of the
ICRP, 39(2):1, 2009. URL: http://www.icrp.org/publication.asp?id=icrp%20publication%20110.
[2] Valetin J 2002 Basic anatomical and physiological data for use in radiological protection:
reference values: ICRP Publication 89 Ann. ICRP vol. 32 (Oxford: Elsevier) pp 1-277.
[3] Valetin J 2007 The 2007 recommendations of the international commission on radiological
protection Ann. ICRP vol 37 (Oxford: Elsevier) pp 1-133.
The table below summarises the key features of the male and female voxelised human phantoms.
PROPERTY AM AF
_____________________________________
Height (m) 1.76 1.63
Mass(Kg) 73.0 60.0
Slice Thickness(mm) 8.0 4.84
Voxel in-plane- 2.137 1.775
-resolution (mm)
Voxels along x 254 299
(i.e. columns)
Voxels along y 127 137
(i.e. rows)
Number of Slices 222 348
(i.e. along z)
______________________________________
----------------------------------------------------------------------------------------------------
------------------------------> Application Sub-Folder Structure <----------------------------------
----------------------------------------------------------------------------------------------------
- '/src': where the source .cc files are stored
- '/include': where header .hh files are stored
- '/ICRPdata': where the phantom data files (*.dat) and slice files are stored.
It is downloaded automatically from URL https://cern.ch/geant4-data/datasets/examples/advanced/ICRP110Phantoms/ICRPdata.tar.gz
during the configuration via cmake.
Phantom data files containing the voxelisation of each phantom, as well as files
containing the definitions of the phantom organs and materials used within geant4
code can be found in the folder /ICRPdata.
All data files used for this phantom were obtained from the ICRP's website on publication 110 under "Supplementary Data"
- https://www.icrp.org/publication.asp?id=ICRP%20Publication%20110.
----------------------------------------------------------------------------------------------------
----------------------------------> ICRP110Phantoms Data <------------------------------------------
----------------------------------------------------------------------------------------------------
Within the '/ICRPdata' directory, the following sub-directories are contained:
-> /ICRPdata/ : contains '*Data.dat' files which list the number of phantom slices to
simulate and the order in which to stack the phantom slices.
-> /ICRPdata/ICRP110_g4dat/AM/ : contains the individual male phantom slice files.
-> /ICRPdata/ICRP110_g4dat/AF/ : contains the individual female phantom slice files.
-> /ICRPdata/ICRP110_g4dat/P110_data_V1.2
The final directory contains the raw ICRP110 phantom data as obtained from the ICRP110 publication website [1];
5 files within folders for the AM and AF phantoms are given. These files are described as follows in the
supplementary data's included README file.
The array of organ identification numbers (in ASCII format); the file names are:
AM.dat
AF.dat
A list of individually segmented structures, their identification numbers, and assigned media (Appendix A in ICRP110); the file names are:
AM_organs.dat
AF_organs.dat
A list of the media, their elemental compositions and densities (Appendix B in ICRP110);
the file names are:
AM_media.dat
AF_media.dat
The mass ratios of bone constituents (trabecular bone, red and yellow bone marrow) in the spongiosa regions;
the file names are:
AM_spongiosa.dat
AF_spongiosa.dat
The mass ratios of blood in various body tissues; the file names are:
AM_blood.dat
AF_blood.dat
The primary data files AM.dat and AF.dat contain an array of organ identification numbers ranging from 0 to 141.
Each number respresents the organ associated with each voxel within the phantom. Within these files, the organ IDs
are listed slice by slice, within each slice row by row, within each row column by column. That means, the column
index changes fastest, then the row index, then the slice index - in other words, the phantom voxels first increase
along x, then along y and finally along z. Slice numbers increase from the toes up to the vertex of the body;
row numbers increase from front to back; and column numbers increase from right to left side.
For use in this application, the original AM.dat and AF.dat files containing the organ identification numbers of
all voxels of the phantom were sub-divided into many files with each representing a single phantom slice along z.
As such, each file represents a 2D phantom slice containing x,y voxel positions and organ identification numbers
of each voxel. This allows for subsections of the phantom to be simulated as required by the user, removing the
need to simulate the entire phantom every time when this may not nessecrily be needed by the user. This also will
allow for reductions in the simulation time depending on what portion of the total phantom is simulated by the user.
This feature was achieved via a code developed by Dr Alessandra Malaroda, University of Wollongong, Australia in 2017.
The AM human phantom is voxelised in x,y,z with 254 x 127 x 222 voxels with dimensions 2.137 x 2.137 x 8 mm.
The AF human phantom is voxelised in x,y,z with 299 x 137 x 348 voxels with dimensions 1.775 x 1.775 x 4.84 mm.
----------------------------------------------------------------------------------------------------
---------------------------------------> How to compile and run <-----------------------------------
----------------------------------------------------------------------------------------------------
- Create a build folder for the phantom run
% mkdir build/
- Navigate to inside the build folder and initialise Geant4
% cmake ../
The ICRP110 phantom data will be automatically downloaded from https://cern.ch/geant4-data/datasets/examples/advanced/ICRP110Phantoms/ICRPdata.tar.gz
- Compile and link to generate the executable (in your CMAKE build directory):
% make
This should make two executables - ICRP110phantoms and ICRP110standalone.
- Execute the application in 'interactive' mode with visualization:
% ./ICRP110phantoms
- Execute the "standalone" application in 'interactive' mode with visualization:
% ./ICRP110standalone
This allows you to visualise the phantom without the overhead of the run manager and initialising all the physics tables.
Of course, you cannot run or visualise trajectories.
- Execute the application in 'batch' mode from macro files:
% ./ICRP110phantoms female_head.in
-----------------------------
AVAILABLE MACRO FILES
-----------------------------
For the users convenience, macro files have been created which are designed to construct partial head
and trunk phantoms for both the male and female models. These macro files can be called upon in batch
mode when executing the application as specified above. If the user wishes to construct a completed/full
male or female phantom, the macros male.in and female.in can be called upon, respectively.
- male_head.in/female_head.in : Creates a partial head phantom for the male and female, respectively.
- male_trunk.in/female_trunk.in : Creates a partial trunk phantom for the male and female, respectively.
- male.in : Creates full male ICRP110 phantom. This can be modified along with 'ICRPdata/MaleData.dat'
if the user wishes to create their own custom partial phantom section.
- female.in : Creates full female ICRP110 phantom. This can be modified along with
'ICRPdata/FemaleData.dat' if the user wishes to create their own custom partial phantom section.
- openGLVis.mac : macro for visualisation with openGL.
- vis.mac (default) : Executed by default when the simulation is run in 'interactive' mode.
- primary.mac : Contains the definition of the primary radiation field.
At the very top of the various '.in' macro files (pre-initialization), there are a series of commands
which define the sex and section of the phantom to create. These commands are listed below:
o /phantom/setPhantomSex