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1 =======================================================================
2 Geant4 - ICRP110_HumanPhantoms Example
3 =======================================================================
4
5 The ICRP110_HumanPhantoms example is developed and mantained by Susanna Guatelli, Matthew Large and Alessandra Malaroda,
6 Centre For Medical Radiation Physics (CMRP), University of Wollongong, NSW, Australia, and John Allison, Geant4 Associates International
7 and University of Manchester, UK.
8
9 Contacts:
10 - susanna@uow.edu.au
11 - mjl970@uowmail.edu.au
12 - malaroda@uow.edu.au
13 - John.Allison@g4ai.org
14
15 The example is based on the extended/medical/DICOM example
16
17 The authors acknowledge that this application of the ICRP110 human phantoms have been implemented in Geant4 with the kind permission of
18 the International Commission on Radiological Protection (ICRP).
19
20 ----------------------------------------------------------------------------------------------------
21 --------------------------------------> Introduction <----------------------------------------------
22 ----------------------------------------------------------------------------------------------------
23
24 This application models the ICRP110 reference computational human phantoms [1] in a Geant4 simulation and calculates
25 the dose in individual voxels and in entire organs.
26
27 The human male phantom, provided kindly by the ICRP, is created from a whole-body clinical CT image set of a 38yr old
28 individual with height 176 cm and mass approximately 70 kg. Similarly, the human female phantom was created from a set of
29 whole body CT images of a 43yr old individual with height 163 cm and weight 60 kg. The CT scans were acquired with both
30 individuals laying supine and with arms resting parallel alongside the body. Both sets of CT data were then scaled to
31 closely approximate the ICRP adult Reference Male and Reference Female, defined in previous ICRP publications [2, 3].
32
33 [1] HG Menzel, C Clement, and P DeLuca. ICRP publication 110. "Realistic reference phantoms:
34 an icrp/icru joint effort: A report of adult reference computational phantoms", Annals of the
35 ICRP, 39(2):1, 2009. URL: http://www.icrp.org/publication.asp?id=icrp%20publication%20110.
36
37 [2] Valetin J 2002 Basic anatomical and physiological data for use in radiological protection:
38 reference values: ICRP Publication 89 Ann. ICRP vol. 32 (Oxford: Elsevier) pp 1-277.
39
40 [3] Valetin J 2007 The 2007 recommendations of the international commission on radiological
41 protection Ann. ICRP vol 37 (Oxford: Elsevier) pp 1-133.
42
43 The table below summarises the key features of the male and female voxelised human phantoms.
44
45 PROPERTY AM AF
46 _____________________________________
47 Height (m) 1.76 1.63
48
49 Mass(Kg) 73.0 60.0
50
51 Slice Thickness(mm) 8.0 4.84
52
53 Voxel in-plane- 2.137 1.775
54 -resolution (mm)
55
56 Voxels along x 254 299
57 (i.e. columns)
58
59 Voxels along y 127 137
60 (i.e. rows)
61
62 Number of Slices 222 348
63 (i.e. along z)
64 ______________________________________
65
66 ----------------------------------------------------------------------------------------------------
67 ------------------------------> Application Sub-Folder Structure <----------------------------------
68 ----------------------------------------------------------------------------------------------------
69
70 - '/src': where the source .cc files are stored
71
72 - '/include': where header .hh files are stored
73
74 - '/ICRPdata': where the phantom data files (*.dat) and slice files are stored.
75 It is downloaded automatically from URL https://cern.ch/geant4-data/datasets/examples/advanced/ICRP110Phantoms/ICRPdata.tar.gz
76 during the configuration via cmake.
77
78 Phantom data files containing the voxelisation of each phantom, as well as files
79 containing the definitions of the phantom organs and materials used within geant4
80 code can be found in the folder /ICRPdata.
81
82 All data files used for this phantom were obtained from the ICRP's website on publication 110 under "Supplementary Data"
83 - https://www.icrp.org/publication.asp?id=ICRP%20Publication%20110.
84
85 ----------------------------------------------------------------------------------------------------
86 ----------------------------------> ICRP110Phantoms Data <------------------------------------------
87 ----------------------------------------------------------------------------------------------------
88
89 Within the '/ICRPdata' directory, the following sub-directories are contained:
90
91 -> /ICRPdata/ : contains '*Data.dat' files which list the number of phantom slices to
92 simulate and the order in which to stack the phantom slices.
93
94 -> /ICRPdata/ICRP110_g4dat/AM/ : contains the individual male phantom slice files.
95
96 -> /ICRPdata/ICRP110_g4dat/AF/ : contains the individual female phantom slice files.
97
98 -> /ICRPdata/ICRP110_g4dat/P110_data_V1.2
99
100 The final directory contains the raw ICRP110 phantom data as obtained from the ICRP110 publication website [1];
101 5 files within folders for the AM and AF phantoms are given. These files are described as follows in the
102 supplementary data's included README file.
103
104 The array of organ identification numbers (in ASCII format); the file names are:
105 AM.dat
106 AF.dat
107
108 A list of individually segmented structures, their identification numbers, and assigned media (Appendix A in ICRP110); the file names are:
109 AM_organs.dat
110 AF_organs.dat
111
112 A list of the media, their elemental compositions and densities (Appendix B in ICRP110);
113 the file names are:
114 AM_media.dat
115 AF_media.dat
116
117 The mass ratios of bone constituents (trabecular bone, red and yellow bone marrow) in the spongiosa regions;
118 the file names are:
119 AM_spongiosa.dat
120 AF_spongiosa.dat
121
122 The mass ratios of blood in various body tissues; the file names are:
123 AM_blood.dat
124 AF_blood.dat
125
126 The primary data files AM.dat and AF.dat contain an array of organ identification numbers ranging from 0 to 141.
127 Each number respresents the organ associated with each voxel within the phantom. Within these files, the organ IDs
128 are listed slice by slice, within each slice row by row, within each row column by column. That means, the column
129 index changes fastest, then the row index, then the slice index - in other words, the phantom voxels first increase
130 along x, then along y and finally along z. Slice numbers increase from the toes up to the vertex of the body;
131 row numbers increase from front to back; and column numbers increase from right to left side.
132
133 For use in this application, the original AM.dat and AF.dat files containing the organ identification numbers of
134 all voxels of the phantom were sub-divided into many files with each representing a single phantom slice along z.
135 As such, each file represents a 2D phantom slice containing x,y voxel positions and organ identification numbers
136 of each voxel. This allows for subsections of the phantom to be simulated as required by the user, removing the
137 need to simulate the entire phantom every time when this may not nessecrily be needed by the user. This also will
138 allow for reductions in the simulation time depending on what portion of the total phantom is simulated by the user.
139 This feature was achieved via a code developed by Dr Alessandra Malaroda, University of Wollongong, Australia in 2017.
140
141 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.
142 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.
143
144 ----------------------------------------------------------------------------------------------------
145 ---------------------------------------> How to compile and run <-----------------------------------
146 ----------------------------------------------------------------------------------------------------
147
148 - Create a build folder for the phantom run
149 % mkdir build/
150
151 - Navigate to inside the build folder and initialise Geant4
152 % cmake ../
153
154 The ICRP110 phantom data will be automatically downloaded from https://cern.ch/geant4-data/datasets/examples/advanced/ICRP110Phantoms/ICRPdata.tar.gz
155
156 - Compile and link to generate the executable (in your CMAKE build directory):
157 % make
158 This should make two executables - ICRP110phantoms and ICRP110standalone.
159
160 - Execute the application in 'interactive' mode with visualization:
161 % ./ICRP110phantoms
162
163 - Execute the "standalone" application in 'interactive' mode with visualization:
164 % ./ICRP110standalone
165 This allows you to visualise the phantom without the overhead of the run manager and initialising all the physics tables.
166 Of course, you cannot run or visualise trajectories.
167
168 - Execute the application in 'batch' mode from macro files:
169 % ./ICRP110phantoms female_head.in
170
171 -----------------------------
172 AVAILABLE MACRO FILES
173 -----------------------------
174 For the users convenience, macro files have been created which are designed to construct partial head
175 and trunk phantoms for both the male and female models. These macro files can be called upon in batch
176 mode when executing the application as specified above. If the user wishes to construct a completed/full
177 male or female phantom, the macros male.in and female.in can be called upon, respectively.
178
179 - male_head.in/female_head.in : Creates a partial head phantom for the male and female, respectively.
180 - male_trunk.in/female_trunk.in : Creates a partial trunk phantom for the male and female, respectively.
181 - male.in : Creates full male ICRP110 phantom. This can be modified along with 'ICRPdata/MaleData.dat'
182 if the user wishes to create their own custom partial phantom section.
183 - female.in : Creates full female ICRP110 phantom. This can be modified along with
184 'ICRPdata/FemaleData.dat' if the user wishes to create their own custom partial phantom section.
185 - openGLVis.mac : macro for visualisation with openGL.
186 - vis.mac (default) : Executed by default when the simulation is run in 'interactive' mode.
187 - primary.mac : Contains the definition of the primary radiation field.
188
189 At the very top of the various '.in' macro files (pre-initialization), there are a series of commands
190 which define the sex and section of the phantom to create. These commands are listed below:
191
192 o /phantom/setPhantomSex <option> : Passes sex of phantom to Detector Construction
193 o /phantom/setScoreWriterSex <option> : Passes sex of phantom to User Score Writer
194
195 o /phantom/setPhantomSection <option> : Passes section of phantom to Detector Construction
196 o /phantom/setScoreWriterSection <option> Passes section of phantom to User Score Writer
197
198 Available options for the first 2 commands are: male or female.
199 Avalable options for the last 2 commands are: head, trunk or full.
200
201 In the event that the macro called upon by the user when executing the application in 'batch' mode
202 does not contain these commands (default case), the application sets phantom sex to female and the section as the head.
203
204 WARNING: the phantom model can be chosen only in the initialization phase of the simulation!!!
205 It cannot be changed during the run session. This feature will be implemented in the next future.
206
207 ----------------------------------------------------------------------------------------------------
208 ----------------------------------> Creating a Custom Phantom <------------------------------------
209 ----------------------------------------------------------------------------------------------------
210
211 If the user wishes to construct a customised section of the phantom (i.e. a single slice, the legs, etc),
212 he/she has to create a specific macro or edit the ones provided. The recommended method for a custom male
213 phantom is outlined as follows.
214
215 The user should edit the macro 'male.in' and the data file
216 'MaleData.dat'. Firstly, in 'FemaleData.dat', there are 2 simple ways in which the user can
217 select a custom range of phantom slices to simulate:
218
219 1. The very first entry of each Data.dat indicates how many slices to simulate.
220 Changing this number will determine the number of slices to construct.
221
222 2. Further down in the Data.dat files (beginning at line 61) is the name of the first slice to simulate, followed
223 by successive slices. Changing the slice file orders here will allow various subsections of the human
224 phantom to be simulated. As an indication the following phantom subsections have been identified for the
225 male phantom below.
226
227 --> AM_Slice1.g4dat to AM_Slice20.g4dat: Feet to ankles
228
229 --> AM_Slice21.g4dat to AM_Slice121.g4dat: Ankles to hips
230
231 --> AM_Slice169.g4dat: Single chest slice with good visualisation
232 of lungs, ribs, heart.
233
234 --> AM_Slice182.g4dat to AM_Slice222.g4dat: Neck and Head
235
236 NOTE: o Always order phantom slices beginning with the lowest number and increasing
237 in slice number going down the .dat files.
238 o Always use consecutive/adjacent slices when simulating multiple slices.
239 o The default number of slices for both male and female phantoms is set to 10
240 and starts at the feet of each phantom.
241
242 Once the user customises the MaleData.dat/FemaleData.dat (for example starting from the full phantoms macros),
243 he/she has also to fix appropriately the scoring mesh in male.in/female.in.
244
245 ----------------------------------------------------------------------------------------------------
246 ------------------------------> Scoring Mesh and the User Score Writer <----------------------------
247 ----------------------------------------------------------------------------------------------------
248
249 The macro primary.mac defines the radiation beam type, energy, direction and geometry. The UI commands of the
250 General Particle Source should be used to change the radiation field. The macros male.in and female.in contain
251 the /run/beamOn command and can call upon the radiation beam definition through the UI command
252 '/control/execute primary.mac'.
253
254 Within male.in and female.in, a scoring mesh is defined which records the dose deposition within each individual
255 phantom voxel. The size of the scoring mesh is defined in line 54 of the male.in/female.in files, and must be defined
256 to match the constructed phantom dimensions (whole or partial) defined in the according '/ICRPdata/*Data.dat' file.
257
258 The mesh dimensions are defined as half-dimensions in x,y,z - meaning a defined scoring mesh x-dimension of 100mm will construct
259 a scoring mesh spanning from -100mm to +100mm in the geometrical world in which the phantom lies. Furthermore, for the completed
260 male phantom which has dimensions along x,y,z of 542.798 x 271.399 x 1776 mm, the scoring mesh half-dimensions should be defined
261 as 271.399 x 135.6995 x 888. mm. The number of bins or divisions to segment the mesh into is then defined in line 51. These
262 should match the number of phantom voxels in x,y,z which are defined in the MaleData.dat and FemaleData.dat files in the '/ICRPdata'
263 directory.
264
265 If the user edits the MaleData.dat or FemaleData.dat files to change the number of z-slices simulated in a run, they must also edit
266 the scoring mesh dimensions and number of bins to ensure it correctly scores their defined phantom. To do so, the user will typically
267 only have to edit lines 54 and 55 of the male.in or female.in macro files.
268
269 After completion of a simulation run, the phantom mesh records the deposited dose in each phantom voxel and outputs the data to a text file named
270 "PhantomMesh_Dose.txt". This text file lists the x,y,z positional number of the voxel in the phantom and the dose recorded within that voxel (in Gy).
271
272 The output PhantomMesh_Dose.txt file is created by the User Score Writer class defined in the source code ICRP110UserScoreWriter.cc. In the same class the dose
273 in the voxels is analysed and associated to organs.
274
275 A final output file "ICRP.out" is then created which contains the total dose delivered to each organ.
276
277 ----------------------------------------------------------------------------------------------------
278 ----------------------------------------> Further Info <--------------------------------------------
279 ----------------------------------------------------------------------------------------------------
280
281 -------> ColourMap.dat <--------
282
283 This file located in the build directory assigns G4colours to the 53 phantom materials.
284 The user may edit these as they wish for visualistion purposes.
285
286 ----------> Physics <-----------
287
288 The QGSP_BIC_HP Physics List is adopted. The user may want to change the
289 cut of production of secondary particles.
290
291 -----> Primary particles <------
292
293 The G4 General Particle Source (gps) is used to generate primary radiation field.
294 Macro primary.mac contains the definition of the primary radiation field.
