PHITS Multi-Purpose Particle and Heavy Ion Transport code System PHITS Tutorial for making Voxel Phantom Last revised 2014/8 title 1 What is Voxel Phantom? 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) Introduction 2 Examples of PHITS calculations using voxel phantom Biological dose estimation for charged-particle therapy T. Sato et al. Radiat. Res. (2009) Treatment planning for BNCT H. Kumada et al. J. Phys.: Conf. Ser. (2007) Introduction 3 Table of Contents 1. Universe 2. Lattice 3. Simple voxel phantom 4. Conversion from DICOM format 5. Summary 6. Appendix Table of Contents 4 What is Universe? → Virtual space in PHITS Universe1 You can define many universes in PHITS virtual space But only 1 universe (main space) is the stage of particle transport simulation Main space Some parts of the main space (inside the boxes) are filled with universe 1 Universe Other universes are used for replacing some parts of the main space using “fill” command 5 always void universe.inp Example of Universe [Cell] Filled with $ Main space 1 0 11 -12 13 -14 15 -17 FILL=1 Universe1 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 Declare universe 1 $ Universe 2 201 2 -7.86 -10 13 -14 U=2 202 1 -1.00 #201 U=2 [Surface] 10 CY 5 PX -3 11 PX -6 12 PX 6 PX 9 13 PY -6 14 PY 6 15 PZ -6 16 PZ 6 17 PZ 0 Figure 5.13 (a) Two rectangular solids. (b) Cylinder filled with water. (c) Iron cylinder in water Universe 6 Table of Contents 1. Universe 2. Lattice 3. Simple voxel phantom 4. Conversion from DICOM format 5. Summary 6. Appendix Table of Contents 7 What is Lattice? → 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 Lattice 8 How to define lattice? Only repeated structure can be defined in lattice universe You cannot directly define the contents inside lattice It is better to define lattice not in main space but in a universe You have to fill lattice with other universe Define repeated structure using more than 2 universes fill Main space fill Universe1 Universe2 (Lattice structure) (fundamental structure) Lattice 9 5 (2,2,0) Y [Surface] 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 [Cell] $ 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 22222 22222 22222 22222 22222 $ Universe 2 201 1 -19.32 -201 u=2 202 0 201 u=2 PHITS input Basic lattice(0,0,0) (-2,-2,0) -5 lattice.inp -5 X Region 101 5 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 Lattice 10 Change the contents of lattice lattice1.inp [Cell] $ 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 32222 22222 22222 22222 22222 $ Universe 2 201 1 -19.32 -201 u=2 202 0 201 u=2 $ Universe 3 302 0 -99 u=3 Change 1st box from golden ball to void Before (lattice.inp) Lattice After (lattice1.inp) 11 Table of Contents 1. Universe 2. Lattice 3. Simple voxel phantom 4. Conversion from DICOM format 5. Summary 6. Appendix Table of Contents 12 How to define voxel phantom? ① Make universes filled with an unique material such as bone and soft tissue ② Make voxel phantom by repeating those universes Universe1 (void) Universe2 (water) Universe3 (Aluminum) ③ Fill some part of the main space with the voxel phantom Universe10 (Voxel Phantom) Main Space Simple Voxel Phantom 13 PHITS input file robot.inp [Cell] $ 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 11111 12121 12121 11111 11111 … 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 Surfaces for the basic lattice Any large region is OK Lattice order: X+, Y+, Z+ (start with left&lower voxel) [Surface] $ 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 z y x Simple Voxel Phantom 14 robot1.inp Change materials [Cell] $ 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 11111 11111 11411 11111 11111 … 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 Change the material of the phantom head from water to copper Before (robot.inp) Simple Voxel Phantom After (robot1.inp) 15 Example of dose calculation robot-heat-xz.eps robot-heat-reg.out 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 [t-heat] tally using mesh = reg Calculate dose for each region (Head, torso, and arm&leg) [t-heat] tally using mesh = xyz Visualize the dose distribution Useful for calculating dose inside tumor region Simple Voxel Phantom 16 Table of Contents 1. Universe 2. Lattice 3. Simple voxel phantom 4. Conversion from DICOM format 5. Summary 6. Appendix Table of Contents 17 DICOM format (Binary) Data for 1 slice (sample001.dcm) ① Header (Information on time, voxel size etc.) ② CT values(1,1→2,1→3,1→…→nx-1, ny → nx, ny) Several files are contained in one folder to represent an object 3D view cross sectional view It is necessary to convert from DICOM to PHITS-input format (CT value, binary) (Universe number, text) Dicom to PHITS 18 Conversion (DICOM2PHITS) Convert from Dicom data to PHITS input format (voxel phantom) Refer to “PHITS Tutorial How to use DICOM2PHITS” phits/utility/dicom2phits/phits-lec-dicom2phits-jp.ppt 1. Make an input file for DICOM2PHITS (dicom2phits.inp) "data/HumanVoxelTable.data" "DICOM/" "PHITSinputs" 1 20 70 430 90 460 4 4 1 0 0 1 Conversion table DICOM files are automatically identified in this directory Directory for PHITS inputs to be created Slices to be used (1<=z<=20) Clipping (70<=x<=430, 90<=y<=460) Coarse graining (Average on 4 times 4 voxels in x and y direction) Origin option: 0:Center of data 1:Reading from DICOM header PHITS parameter: 0:Minimal 1:Photon therapy 2:Particle therapy Reading slice order: +1:Ascending order or -1:Descending order 2. Execute Windows: Drag dicom2phits.inp and drop into dicom2phits.bat Mac: Double click dicom2phits.command and type dicom2phits.inp + enter A sample input file will be created in PHITSinputs/ directory DICOM2PHITS HowTo 19 Reduce computational time Purpose It converts its input file to binary, and re-reads the binary file Every time PHITS runs… It is better to… Make binary file of voxel phantom prior to the PHITS execution 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) Speed up! $ infl:{voxel1.inp} Dicom to PHITS 20 Table of Contents 1. Universe 2. Lattice 3. Simple voxel phantom 4. Conversion from DICOM format 5. Summary 6. Appendix Table of Contents 21 Summary 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 Summary 22 Table of Contents 1. Universe 2. Lattice 3. Simple voxel phantom 4. Conversion from DICOM format 5. Summary 6. Appendix Table of Contents 23 How to Deal with High-Resolution Phantom? High resolution voxel phantom requires numerous memory e.g.) Whole body voxel phantom (180cm×30cm×50cm) with 1mm3 resolution consists of 270,000,000 voxels, and costs 5.4 GByte memory, since PHITS uses memory approximately 20 Byte / voxel Default setting of PHITS is allowed to use memory only less than 2 Byte How to deal with the situation? Change “param.inc” included in “src” folder • 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) Delete all object files (*.o) and re-compile PHITS* Memory is insufficient? Divide voxel phantom into several regions to reduce the area to be voxelized Combine several CT pixels into one voxel to decrease the resolution of phantom *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 24 How to Deal with High-Resolution Phantom? 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 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 Add compiler options (e.g. for Intel Fortran in Linux) 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) Appendix 25 Change the order of lattice lattice2.inp [ S u r f a c e ] (pick up partially) 101 px -1 102 px 1 RPP is divided 103 py -1 104 py 1 into each surface 105 pz -1 106 pz 1 [ C e l l ] (pick up partially) -102 $ Universe 1 101 0 -102 101 -104 103 -106 105 lat=1 u=1 Order is fill=-2:2 -2:2 0:0 important! 32222 22222 22222 22222 22222 Same as RPP, BOX 101 -104 103 -106 105 X:+, Y:+, Z:+ 101 -102 -104 103 -106 105 X: –, Y:+, Z: + Prior surface faces to -102 101 103 -104 -106 105 the forward direction X: +, Y: –, Z:+ 101 -102 103 -104 -106 105 X: –, Y: –, Z: + Appendix 26