1. P HI T S PHITS Tutorial for making Voxel Phantom Multi-Purpose Particle and Heavy Ion Transport code System title1 Last revised 2014/8

2. What is Voxel Phantom? Introduction2 Reproduce a complex structure such as human body based on repeated rectangles filled with a certain material (See Manual 5.7.5) Low resolution High resolution You can make voxel phantom in PHITS virtual space using Universe and Lattice functions (See Manual 5.7.3 and 5.7.4)

3. Examples of PHITS calculations using voxel phantom 3 Biological dose estimation for charged-particle therapy Treatment planning for BNCT T. Sato et al. Radiat. Res. (2009) H. Kumada et al. J. Phys.: Conf. Ser. (2007) Introduction

4. Table of Contents4 1.Universe 2.Lattice 3.Simple voxel phantom 4.Conversion from DICOM format 5.Summary 6.Appendix

5. What is Universe? Universe5 You can define many universes in PHITS virtual space But only 1 universe (main space) is the stage of particle transport simulation Other universes are used for replacing some parts of the main space using “fill” command Some parts of the main space (inside the boxes) are filled with universe 1 Universe1 Main space → Virtual space in PHITS

6. Example of Universe Universe6 universe.inp [ C e l l ] $ Main space 1 0 11 -12 13 -14 15 -17 FILL=1 2 0 11 -12 13 -14 17 -16 FILL=2 9 -1 #1 #2 $ Universe 1 101 1 -1.00 -10 13 -14 U=1 102 0 #101 U=1 $ Universe 2 201 2 -7.86 -10 13 -14 U=2 202 1 -1.00 #201 U=2 [ S u r f a c e ] 10 CY 5 11 PX -6 12 PX 6 13 PY -6 14 PY 6 15 PZ -6 16 PZ 6 17 PZ 0 Declare universe 1 always void PX -3 PX 9 Filled with Universe1 Figure 5.13 (a) Two rectangular solids. (b) Cylinder filled with water. (c) Iron cylinder in water

7. Table of Contents7 1.Universe 2.Lattice 3.Simple voxel phantom 4.Conversion from DICOM format 5.Summary 6.Appendix

8. What is Lattice? Lattice8 → Repeated structure used in PHITS virtual space It is troublesome to define all surfaces and cells used in repeated structure Define only surfaces and cells used in fundamental structure Examples of Lattice in PHITS Express the repeated structure using “lat” command

9. How to define lattice? 9 Only repeated structure can be defined in lattice universe You have to fill lattice with other universe It is better to define lattice not in main space but in a universe You cannot directly define the contents inside lattice Define repeated structure using more than 2 universes Universe1 (Lattice structure) Universe2 (fundamental structure) fill Main space fill Lattice

10. 10 lattice.inp [ S u r f a c e ] 1 rpp -5 5 -5 5 -1 1 2 rpp -6 6 -6 6 -2 1 99 so 100 101 rpp -1 1 -1 1 -1 1 201 sph 0 0 0 1 [ C e l l ] $ Main space 1 3 -8.96 1 -2 2 0 -1 fill=1 98 0 -99 2 99 -1 99 $ Universe 1 101 0 -101 lat=1 u=1 fill=-2:2 -2:2 0:0 2 2 2 2 2 $ Universe 2 201 1 -19.32 -201 u=2 202 0 201 u=2 Declare lattice type 1 (Rectangle) Define the region of basic lattice Define the number of repeated structure Universe number to be filled with （ 5×5×1 matrix ） Location should be adjusted to that of the basic lattice Basic lattice （ 0,0,0 ） -5 X 5 （ 2,2,0 ） Region 101 -5 Y 5 （ -2,-2,0 ） PHITS input Lattice

11. Change the contents of lattice 11 lattice1.inp [ C e l l ] $ Main space 1 3 -8.96 1 -2 2 0 -1 fill=1 98 0 -99 2 99 -1 99 $ Universe 1 101 0 -101 lat=1 u=1 fill=-2:2 -2:2 0:0 3 2 2 2 2 2 2 2 2 2 $ Universe 2 201 1 -19.32 -201 u=2 202 0 201 u=2 $ Universe 3 302 0 -99 u=3 Before (lattice.inp) Lattice After (lattice1.inp) Change 1 st box from golden ball to void

12. Table of Contents12 Table of Contents 1.Universe 2.Lattice 3.Simple voxel phantom 4.Conversion from DICOM format 5.Summary 6.Appendix

13. How to define voxel phantom? 13 Universe1 (void) Simple Voxel Phantom ① Make universes filled with an unique material such as bone and soft tissue Universe2 (water) Universe3 (Aluminum) ② Make voxel phantom by repeating those universes Universe10 (Voxel Phantom) Main Space ③ Fill some part of the main space with the voxel phantom

14. PHITS input file 14Simple Voxel Phantom robot.inp [ C e l l ] $ Material universe 1 0 -99 u=1 2 1 -1.00 -99 u=2 3 2 -2.70 -99 u=3 $ Voxel universe 101 0 -101 lat=1 u=10 fill=0:4 0:4 0:4 1 1 1 1 1 1 2 1 2 1 1 1 1 1 1 … repeat 4 times $ Main space 201 0 -201 fill=10 202 0 201 -202 203 3 -8.96 202 -203 204 0 -99 201 203 205 -1 99 [ S u r f a c e ] $ fundamental voxel 1 px -5 2 px -3 3 py 3 4 py 5 5 pz 3 6 pz 5 99 so 100 $ Main space 201 rpp -5 5 -5 5 -5 5 202 rcc 0 0 -5 0 0 4 8 203 rcc 0 0 -6 0 0 5 9 Lattice order: X+, Y+, Z+ (start with left&lower voxel) Surfaces for the basic lattice Any large region is OK x y z

15. Change materials 15Simple Voxel Phantom robot1.inp [ C e l l ] $ Material universe 1 0 -99 u=1 2 1 -1.00 -99 u=2 3 2 -2.70 -99 u=3 4 3 -8.96 -99 u=4 $ Voxel universe 101 0 -2 1 3 -4 5 -6 lat=1 u=10 fill=0:4 0:4 0:4... last one 1 1 1 1 1 1 1 4 1 1 1 1 1 1 1 … repeat 4 times $ Main space 201 0 -201 fill=10 202 0 201 -202 203 3 -8.96 202 -203 204 0 -99 201 203 205 -1 99 Before (robot.inp) After (robot1.inp) Change the material of the phantom head from water to copper

16. Example of dose calculation 16Simple Voxel Phantom [t-heat] tally using mesh = xyz [t-heat] tally using mesh = reg robot-heat-reg.out Visualize the dose distribution Calculate dose for each region (Head, torso, and arm&leg) x: Serial Num. of Region y: Heat [MeV/source] h: x n n y(total),l3 n # num reg volume heat r.err 1 2 1.0000E+00 9.5978E-01 0.1277 2 3 1.0000E+00 3.4847E+01 0.0000 3 4 1.0000E+00 5.1924E+01 0.0000 robot-heat-xz.eps Useful for calculating dose inside tumor region

17. Table of Contents17 Table of Contents 1.Universe 2.Lattice 3.Simple voxel phantom 4.Conversion from DICOM format 5.Summary 6.Appendix

18. DICOM format (Binary) 18 ① Header (Information on time, voxel size etc.) ② CT values （ 1,1→2,1→3,1→…→n x -1, n y → n x, n y ） Data for 1 slice （ sample001.dcm ） Several files are contained in one folder to represent an object cross sectional view 3D view Dicom to PHITS It is necessary to convert from DICOM to PHITS-input format (CT value, binary) (Universe number, text)

19. "data/HumanVoxelTable.data" Conversion table "DICOM/" DICOM files are automatically identified in this directory "PHITSinputs" Directory for PHITS inputs to be created 1 20 Slices to be used (1<=z<=20) 70 430 90 460 Clipping (70<=x<=430, 90<=y<=460) 4 4 1 Coarse graining (Average on 4 times 4 voxels in x and y direction) 0 Origin option: 0:Center of data 1:Reading from DICOM header 0 PHITS parameter: 0:Minimal 1:Photon therapy 2:Particle therapy 1 Reading slice order: +1:Ascending order or -1:Descending order Conversion (DICOM2PHITS) 19 Convert from Dicom data to PHITS input format (voxel phantom) 1. Make an input file for DICOM2PHITS （ dicom2phits.inp ） 2. Execute Windows: Drag dicom2phits.inp and drop into dicom2phits.bat Mac: Double click dicom2phits.command and type dicom2phits.inp + enter DICOM2PHITS HowTo Refer to “PHITS Tutorial How to use DICOM2PHITS” phits/utility/dicom2phits/phits-lec-dicom2phits-jp.ppt A sample input file will be created in PHITSinputs/ directory

20. Reduce computational time 20 It converts its input file to binary, and re-reads the binary file Make binary file of voxel phantom prior to the PHITS execution Purpose Procedure ① Insert the following 2 lines in the [Parameters] section ivoxel = 2 # Convert the “fill” part of lattice to binary and output to file(18) file(18) = voxel.bin # Output file name for binary voxel phantom ② Execute PHITS → Binary file was successfully generated!! ③ Change “ivoxel = 1”, and comment out “infl” command ivoxel = 1 # Read the “fill” part of lattice from file(18) $ infl:{voxel1.inp} Speed up! Dicom to PHITS It is better to… Every time PHITS runs…

21. Table of Contents21 Table of Contents 1.Universe 2.Lattice 3.Simple voxel phantom 4.Conversion from DICOM format 5.Summary 6.Appendix

22. Summary 22Summary ① Voxel phantom can be implemented in PHITS using Universe and Lattice concepts ② DICOM format must be converted into PHITS input format using DICOM2PHITS ③ Computational time can be reduced by using “ivoxel” parameter

23. Table of Contents23 Table of Contents 1.Universe 2.Lattice 3.Simple voxel phantom 4.Conversion from DICOM format 5.Summary 6.Appendix

24. How to Deal with High-Resolution Phantom? 24 High resolution voxel phantom requires numerous memory Default setting of PHITS is allowed to use memory only less than 2 Byte e.g.) Whole body voxel phantom (180cm×30cm×50cm) with 1mm 3 resolution consists of 270,000,000 voxels, and costs 5.4 GByte memory, since PHITS uses memory approximately 20 Byte / voxel Change “param.inc” included in “src” folder How to deal with the situation? increase mdas: Maximum memory allowed to be used by PHITS (Byte) / 8 increase latmax: Maximum number of lattice in a cell declare integer*8 for several parameters (see next page in detail) Divide voxel phantom into several regions to reduce the area to be voxelized Memory is insufficient? Combine several CT pixels into one voxel to decrease the resolution of phantom Delete all object files (*.o) and re-compile PHITS* *For Windows PC, gfortran is recommended to be used for this purpose, because PHITS executable file compiled by Intel Fortran may cause “stack overflow” for large voxel phantom

25. 25Appendix If #voxels is greater than 50 millions, many changes are necessary e.g. total #voxel = 150 millions, max #voxel per cell = 40 millions Change include files in “src” folder Add compiler options （ e.g. for Intel Fortran in Linux ） param.inc integer*8 mdas,mcmx,mci,mmdas,mmmax,nbnds,mct ! avoid overflow (integer*4 =< 2147483647 ） parameter ( mdas = 500000000 ) ! Maximum memory allowed to be used by PHITS (Byte) / 8 parameter ( latmax = 47000000 ) ! Maximum number of lattice in a cell angel00.inc integer*8 mdas,mmdas,mmmax ! avoid overflow (integer*4 =< 2147483647 ） parameter ( mdas = 350000000 ) ! Maximum memory allowed to be used by ANGEL (Byte) / 8 makefile F77 = ifort FCFLAGS = -noautomatic -mcmodel=large -i-dynamic -i-dynamic: Dynamic link to libraries -mcmodel=large: no limitation in memory use (this option is only valid for Linux) How to Deal with High-Resolution Phantom?

26. Change the order of lattice 26 lattice2.inp [ S u r f a c e ] (pick up partially) 101 px -1 102 px 1 103 py -1 104 py 1 105 pz -1 106 pz 1 [ C e l l ] (pick up partially) $ Universe 1 101 0 -102 101 -104 103 -106 105 lat=1 u=1 fill=-2:2 -2:2 0:0 3 2 2 2 2 2 2 2 2 2 -102 101 103 -104 -106 105 X: +, Y: –, Z:+ Appendix RPP is divided into each surface Order is important! -102 101 -104 103 -106 105 X:+, Y:+, Z:+ 101 -102 -104 103 -106 105 X: –, Y:+, Z: + 101 -102 103 -104 -106 105 X: –, Y: –, Z: + Prior surface faces to the forward direction Same as RPP, BOX