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MCX Documentation
1. Command Line Options
Required option
-f / --input
- Format
- A string
- Default value
- None, user must specify
- Restriction
- parameter can not be longer than 1024 characters (including the string ending mark '\0' )
- Description
-f filename.json
or
-f filename.inp
filename may contain absolute or relative path. If the filename has a '.json' extension, this input file is in the JSON format. If the input file name ends with '.inp', it is in the legacy format. If the file name contains space, one must use quotation marks to quote the full file name. In Windows, the quotation must be double quote (""). In Linux or Mac, either single or double quotation mark works.
If this flag is followed by an inline JSON string, such as -f '{...}', the parameter is parsed as an "inline JSON input file".
MC options
-n / --photon
- Format
- An integer or floating point number
- Default value
- 0
- Restriction
- the number can not exceed 2^63-1
- Description
-n N
where N can be either an integer, such as 100000 or a floating point number, such as 1e5. If N is a floating point number, it will be rounded to the largest integer below the current value.
-r / --repeat
- Format
- A positive or negative integer
- Default value
- 1
- Max Value
- the number can not exceed 2^32-1
- Description
-r N
where N is a positive integer. When use this option, mcx runs 'nphoton*N' photons with nphoton per batch.
If N is a negative integer, this option splits the total simulation into abs(N) number of smaller batches; in each batch, only nphoton/abs(N) number of photons are simulated.
This option is useful when one does not have access to a dedicated GPU, i.e. the GPU is used for both display and computation. In such case, the mcx computation time is limited to only 5 to 10 seconds due to the graphics driver. One can use the -r option to make the execution time per batch under the time limit set by the driver.
-b / --reflect
- Format
- A boolean, 0 or 1
- Default value
- 1
- Restriction
- must be 0 or 1
- Description
'-b' or '-b 1' to enable (default) or '-b 0' to disable
When enabled, mcx will either reflect or transmit the photon at the boundaries based on the Fresnel's equation.
By default, mcx considers refractive index mismatch at the boundaries.
-B / --reflectin (*depreciated)
- Format
- A boolean, 0 or 1
- Default value
- 1
- Restriction
- must be 0 or 1
- Description
-u / --unitinmm
- Format
- a floating point number
- Default value
- 1.0
- Restriction
- can not be less than or equal to 0
- Description
-u S
where S is a floating point number, denoting the edge length, in mm, of a voxel in the volume. For example, if the volume used in the simulation is 0.1x0.1x0.1 mm^3, then, one should use '-u 0.1' in the command line.
Only isotrpic voxels are currently supported by mcx.
-U / --normalize
- Format
- A boolean, 0 or 1
- Default value
- 1
- Restriction
- must be 0 or 1
- Description
'-U' or '-U 1' to enable (default) or '-U 0' to disable
For fluence, the normalization aims to generate a 'Green's function'. For other qualities, the normalization produces a stable solution by removing the dependency due to total photon numbers, voxel sizes, and time-gate settings. The detailed equations are explained in the MCX paper.
-E / --seed
- Format
- An integer or a string
- Default value
- -1
- Restriction
- must be an integer; if is a string, the specified file must exist
- Description
-E -1 // let MCX to automatically seed the CPU-RNG using system clock
-E n // n is a large positive integer, set the CPU-RNG's seed to n
-E filename.mch // replay detected photons using the seeds saved in the mch file
Setting a fixed RNG seed is expected to create reproducible results on NVIDIA cards if the thread/block size are kept the same.
-z / --srcfrom0
- Format
- A boolean, 0 or 1
- Default value
- 0
- Restriction
- must be 0 or 1
- Description
-z 0 (default)// assumes the lower-bottom corner of the first voxel as [1 1 1]
-z or -z 1 // assumes the lower-bottom corner of the first voxel as [0 0 0]
All source and detector positions are referenced from the origin, determined by this flag.
-R / --skipradius
- Format
- An integer
- Default value
- -2
- Restriction
- must be 0 or 1
- Description
-R -2 // this enables full atomic opertions in the entire volume (default)
-R n // when n is a positive integer, mcx uses atomic operations in the
// shared memory for a n x n x n sub-cubic domain centered at the source.
-R 0 // disable all atomic operations, data racing may exist, particularly
// near the source.
-R -1 //use crop0/crop1 to determine atomic zone
Using full atomic operations was very slow in very early CUDA devices, but for most later NVIDIA GPUs, the use of atomic operations is as efficient as the non-atomic version.
-k / --voidtime
- Format
- A boolean, 0 or 1
- Default value
- 0
- Restriction
- must be 0 or 1
- Description
-k 1 (default) // the time-of-flight of the photon starts at the launch time
-k 0 // the time-of-flight starts when a photon enters the first non-zero voxel.
-Y / --replaydet
- Format
- A positive integer
- Default value
- 0
- Restriction
- can not be negative
- Description
-Y n // n is a positive integer, denoting the index of the detectors to be replayed
-Y 0 // all detected photons will be replayed regardless of detector
If -Y is not specified, MCX replays all detected photons; otherwise, MCX only replays the detected photons from the specified detector. See -E for more details.
-P / --shapes
- Format
- A string
- Default value
- None, user must specify
- Restriction
- parameter can not be longer than 1024 characters (including the string ending mark '\0' )
- Description
-P '{"Shapes":[{"ZLayers":[[1,10,1],[11,30,2],[31,60,3]]}]}'
This defines a 3-layer medium: z slices 1-10 is filled with tissue label 1, z slices 11-30 is filled with label 2, and 31-60 is filled with label 3.
The shape definition always starts an array object named 'Shapes'. Each element in the 'Shapes' object defines a primitive object. The supported primitives include Name/Origin/Grid/Sphere/Box/Subgrid/{XYZ}Layers/{XYZ}Slabs/Cylinder/UpperSpace. Most objects have a sub-field 'Tag', specifying the tissue label (index to the property list). The details of the Shapes objects can be found in this link
-N / --reseed (*depreciated)
- Format
- An integer
- Default value
- 0
- Restriction
- can not be negative
- Description
-F / --faststep (*depreciated)
- Format
- A boolean, 0 or 1
- Default value
- 0
- Restriction
- must be 0 or 1
- Description
-e / --minenergy
- Format
- A floating point number
- Default value
- 0
- Restriction
- must be positive or 0.0
- Description
-e f // where f is a floating point number between 0 and 1.
-g / --gategroup
- Format
- A positive integer
- Default value
- 100
- Restriction
- can not be negative
- Description
Use -g to split a simulation containing many time gates into smaller but multiple sequential simulations. Format:
-g n // n is a positive integer
Only use this option when the GPU global memory can not hold the data for all required time gates, which only happens when one trys to simulate a very large domain with very dense time gates (very rare). If one's GPU can only hold the data for n time gates, while one has to simulate a total of N > n time gates, use -g n to split the total simulations into multiple runs: in the first run, MCX will record the results for 1~n time gates, in the second run, MCX will launch a new kernel to simulate photons for 1~2*n time gates, but only records the photon fluence for n+1 ~ 2*n time gates and so on. As one can see, this method introduces overhead in the later simulations. Therefore, it is recommended to avoid.
-a / --array
- Format
- A boolean, 0 or 1
- Default value
- 0
- Restriction
- must be 0 or 1
- Description
-a 0 (default) // the input volume is a MATLAB-array
-a 1 // the input volume is a C-array
If an MATLAB array is used, the fastest loop index is the left-most index of an array; while for a C array, it is the right-most index.
GPU options
-L / --listgpu
- Format
- A boolean, 0 or 1
- Default value
- 0
- Restriction
- must be 0 or 1
- Description
fangq@wazu:~/space/git/Project/mcx/example/quicktest$ ../../bin/mcx -L ============================= GPU Infomation ================================ Device 1 of 2: GeForce GTX 980 Ti Compute Capability: 5.2 Global Memory: 2147287040 B Constant Memory: 65536 B Shared Memory: 49152 B Registers: 65536 Clock Speed: 1.19 GHz Number of MPs: 22 Number of Cores: 2816 SMX count: 22 ============================= GPU Infomation ================================ Device 2 of 2: GeForce GT 730 Compute Capability: 3.5 Global Memory: 1073545216 B Constant Memory: 65536 B Shared Memory: 49152 B Registers: 65536 Clock Speed: 0.90 GHz Number of MPs: 2 Number of Cores: 384 SMX count: 2
-t / --thread
- Format
- An integer
- Default value
- 2^14=16384
- Restriction
- can not be negative
- Description
-t N
where N is a positive integer. The thread number N must be a multiple of 32 - the size of a warp - on all CUDA devices. If N is not a multiple of 32, mcx will round it to the nearest multiple less than N.
To achieve the best efficiency, it is recommended to launch a large number of threads to mazimize the utility of the GPU resources; a thread number larger than 10000 is generally sufficient.
You should not manually specify the thread number using this option when you use the autopilot mode (-A).
-T / --blocksize
- Format
- An integer
- Default value
- 64
- Restriction
- can not be negative, must be multiples of 32
- Description
-T N
where N is a positive integer. The block size N must be a multiple of 32 - the size of a warp - on all CUDA devices. If N is not a multiple of 32, mcx will round it to the nearest multiple less than N.
Because mcx does not need inter-thread communication, a small block size, such as 32 or 64, is generally recommended.
You should not manually specify the block size using this option when you use the autopilot mode (-A).
-A / --autopilot
- Format
- A boolean, 0 or 1
- Default value
- 1
- Restriction
- must be 0 or 1
- Description
-A 1
When the autopilot mode is enabled, mcx will compute the 'optimal' thread number and block size using a heuristic algorithm.
-G / --gpu
- Format
- An integer or a string made of '0's and '1's
- Default value
- 1
- Restriction
- If integer, must be positive (>0); if string, can only have '0's and '1's.
- Description
-G 1 // use only the first GPU device (device orders based on 'mcx -L' output)
-G n // n is a positive integer, use only the n-th GPU device
-G 1110 // when -G is followed by a string made of only 0s and 1s, it specifies
// a mask for active GPUs, for example, 1110 means to use GPU 1-3
// together while the 4th GPU is not used.
When multiple GPU devices are specified, one need to use the -W/--workload flag to optimally partition the total photons to be simulated. By default, photons will be evenly distributed among multiple GPU devices.
-W / --workload
- Format
- A list of floating point/integer values, separated by commas
- Default value
- 100
- Restriction
- all values must be positive; no space is allowed; length must be equal or longer than number of activated GPUs (i.e. count of all '1's in -G)
- Description
-W w1,w2,w3,... // w_i is a numerical value, corresponding to the relative portions
// of the workload of the i-th GPU device. The total load
// is proportional to the sum of w_i.
For example, -W 10,20,20 indicates a 1:2:2 workload split between 3 active GPUs.If one needs to simulate 1e6 photons, the 1st GPU will run 2e5 photons, while the 2nd and the 3rd GPUs will run 4e5 photons each.
-I / --printgpu
- Format
- A boolean, 0 or 1
- Default value
- 0
- Restriction
- must be 0 or 1
- Description
The -I option lists all available GPU, same as -L, but it also run the actual simulation.
Output options
-s / --session
- Format
- A string
- Default value
- same as the input file name followed by the -f flag (without the path); it can not contain <>:"/|?*
- Restriction
- must be 0 or 1
- Description
-s session_name // session_name is a string, it can not contain <>:"/|?*
If -s is set, the output fluence file (.mc2), detected photon file (.mch) and the log file (.log) will be named as session_name.{mc2,mch,log}. Otherwise, the input file name following the -f option will be used in the place of session_name.
-d / --savedet
- Format
- A boolean, 0 or 1
- Default value
- 1
- Restriction
- must be 0 or 1
- Description
'-d' or '-d 1' to enable (default) or
'-d 0' to disable
When this option is enabled, a binary file, with a suffix of .mch, will be produced in additional to the '.mc2' output. The .mch file contains the partial path data for all photons enters the aperatures of the detectors.
-x / --saveexit
- Format
- A boolean, 0 or 1
- Default value
- 0
- Restriction
- must be 0 or 1
- Description
-X / --saveref
- Format
- A boolean, 0 or 1
- Default value
- 0
- Restriction
- must be 0 or 1
- Description
-q / --saveseed
- Format
- A boolean, 0 or 1
- Default value
- 0
- Restriction
- must be 0 or 1
- Description
-M / --dumpmask
- Format
- A boolean, 0 or 1
- Default value
- 0
- Restriction
- must be 0 or 1
- Description
-H / --maxdetphoton
- Format
- An integer
- Default value
- 1000000
- Restriction
- can not be negative
- Description
-H n // n is a positive integer, signifying mcx to allocate a buffer to hold n detected photons
By default, mcx can save up to 1e6 detected photons. If the detected photons exceed this limit, mcx will show a warning. Users may use the -H option to rerun the simulation and use the number in the warning to reallocate the buffer.
-S / --save2pt
- Format
- A boolean, 0 or 1
- Default value
- 1
- Restriction
- must be 0 or 1
- Description
-O / --outputtype
- Format
- A single character (case insensitive)
- Default value
- 'X'
- Restriction
- must be one of 'X,F,E,J,P', case insensitive
- Description
'X' - output time-resolved fluence rate (1/mm^2), i.e. TPSF 'F' - output time-resolved fluence rate integrated in each time-gate, 'E' - energy deposit at each voxel (normalized or unnormalized, depends on -n) 'J' - Jacobian (replay mode), 'P' - scattering event counts at each voxel (replay mode only)
-F / --outputformat
- Format
- A string
- Default value
- 'mc2'
- Restriction
- must be one of 'mc2', 'nii','hdr','ubj', case insensitive
- Description
mc2 - MCX mc2 format (binary 32bit float) (default)
nii - Nifti format (fluence after taking log10())
hdr - Analyze 7.5 hdr/img format
ubj - universal binary JSON format (currently not supported yet)
User IO options
-h / --help
- Format
- no follow-up parameter needed
- Default value
- Restriction
- None
- Description
Use the -h flag to print the built-in help of all supported command line flags
-v / --version
- Format
- no follow-up parameter needed
- Default value
- Restriction
- None
- Description
Use the -v flag to print the version of MCX
-l / --log
- Format
- A boolean, 0 or 1
- Default value
- 0
- Restriction
- must be 0 or 1
- Description
'-l' or '-l 1' to enable (default) or
'-l 0' to disable
The output file name is 'session_name.log' where 'session_name' is the string specified by the -s flag. If -l is used, no message will be printed in the command line.
-i / --interactive
- Format
- A boolean, 0 or 1
- Default value
- 0
- Restriction
- must be 0 or 1
- Description
mcx -i < input.inp
mcx -f input.inp
can produce the same answer.
Debug options
-D / --debug
- Format
- An integer or a string
- Default value
- 0
- Restriction
- If integer, must be positive; if string, must be made of any combinations of 'R','M','P' (case insensitive).
- Description
1 R debug RNG 2 M store photon trajectory info 4 P print progress bar
combine multiple items by using a string, or add selected numbers together
Additional options
--gscatter
- Format
- An integer
- Default value
- -1
- Restriction
- 1e9
- Description
--maxvoidstep
- Format
- An integer
- Default value
- 1000
- Restriction
- can not be negative
- Description
--maxjumpdebug
- Format
- An integer
- Default value
- 10000000
- Restriction
- can not be negative
- Description
2. Input File Format
JSON input file format
Starting from version 0.7.9, MCX accepts a JSON-formatted input file in addition to the conventional tMCimg-like input format. JSON (JavaScript Object Notation) is a portable, human-readable and "fat-free" text format to represent complex and hierarchical data. Using the JSON format makes a input file self-explanatory, extensible and easy-to-interface with other applications (like MATLAB).
A sample JSON input file can be found under the examples/quicktest folder. The same file, qtest.json, is also shown below:
{
"Help": {
"[en]": {
"Domain::VolumeFile": "file full path to the volume description file, can be a binary or JSON file",
"Domain::Dim": "dimension of the data array stored in the volume file",
"Domain::OriginType": "similar to --srcfrom0, 1 if the origin is [0 0 0], 0 if it is [1.0,1.0,1.0]",
"Domain::LengthUnit": "define the voxel length in mm, similar to --unitinmm",
"Domain::Media": "the first medium is always assigned to voxels with a value of 0 or outside of
the volume, the second row is for medium type 1, and so on. mua and mus must
be in 1/mm unit",
"Session::Photons": "if -n is not specified in the command line, this defines the total photon number",
"Session::ID": "if -s is not specified in the command line, this defines the output file name stub",
"Forward::T0": "the start time of the simulation, in seconds",
"Forward::T1": "the end time of the simulation, in seconds",
"Forward::Dt": "the width of each time window, in seconds",
"Optode::Source::Pos": "the grid position of the source, can be non-integers, in grid unit",
"Optode::Detector::Pos": "the grid position of a detector, can be non-integers, in grid unit",
"Optode::Source::Dir": "the unitary directional vector of the photon at launch",
"Optode::Source::Type": "source types, must be one of the following:
pencil,isotropic,cone,gaussian,planar,pattern,fourier,arcsine,disk,fourierx,fourierx2d",
"Optode::Source::Param1": "source parameters, 4 floating-point numbers",
"Optode::Source::Param2": "additional source parameters, 4 floating-point numbers"
}
},
"Domain": {
"VolumeFile": "semi60x60x60.bin",
"Dim": [60,60,60],
"OriginType": 1,
"LengthUnit": 1,
"Media": [
{"mua": 0.00, "mus": 0.0, "g": 1.00, "n": 1.0},
{"mua": 0.005,"mus": 1.0, "g": 0.01, "n": 1.0}
]
},
"Session": {
"Photons": 1000000,
"RNGSeed": 29012392,
"ID": "qtest"
},
"Forward": {
"T0": 0.0e+00,
"T1": 5.0e-09,
"Dt": 5.0e-09
},
"Optode": {
"Source": {
"Pos": [29.0, 29.0, 0.0],
"Dir": [0.0, 0.0, 1.0],
"Type": "pencil",
"Param1": [0.0, 0.0, 0.0, 0.0],
"Param2": [0.0, 0.0, 0.0, 0.0]
},
"Detector": [
{
"Pos": [29.0, 19.0, 0.0],
"R": 1.0
},
{
"Pos": [29.0, 39.0, 0.0],
"R": 1.0
},
{
"Pos": [19.0, 29.0, 0.0],
"R": 1.0
},
{
"Pos": [39.0, 29.0, 0.0],
"R": 1.0
}
]
}
}
A JSON input file requiers several root objects, namely "Domain", "Session", "Forward" and "Optode". Other root sections, like "Help", will be ignored. Each object is a data structure providing information indicated by its name. Each object can contain various sub-fields. The orders of the fields in the same level are flexible. For each field, you can always find the equivalent fields in the *.inp input files. For example, The "VolumeFile" field under the "Domain" object is the same as Line#6 in qtest.inp; the "RNGSeed" under "Session" is the same as Line#2; the "Optode.Source.Pos" is the same as the triplet in Line#3; the "Forward.T0" is the same as the first number in Line#5, etc.
An MCX JSON input file must be a valid JSON text file. You can validate your input file by running a JSON validator, for example http://jsonlint.com/ You should always use "" to quote a "name" and separate parallel items by ",".
MCX accepts an alternative form of JSON input, but using it is not recommended. In the alternative format, you can use
"rootobj_name.field_name": valueto represent any parameter directly in the root level. For example
{
"Domain.VolumeFile": "semi60x60x60.json",
"Session.Photons": 10000000,
...
}
You can even mix the alternative format with the standard format. If any input parameter has values in both formats in a single input file, the standard-formatted value has higher priority.
To invoke the JSON-formatted input file in your simulations, you can use the "-f" command line option with MCX, just like using an .inp file. For example:
mcx -A -n 20 -f onecube.json -s onecubejson
The input file must have a ".json" suffix in order for MCX to recognize. If the input information is set in both command line, and input file, the command line value has higher priority (this is the same for .inp input files). For example, when using "-n 20", the value set in "Session"/"Photons" is overwritten to 20; when using "-s onecubejson", the "Session"/"ID" value is modified. If your JSON input file is invalid, MCX will quit and point out where the format is incorrect.
inp input file format
Historically, MCX supports an extended version of the input file format used by tMCimg. The difference is that MCX allows comments in the input file. A typical MCX input file looks like this:
1000000 # total photon, use -n to overwrite in the command line
29012392 # RNG seed, negative to generate
30.0 30.0 0.0 1 # source position (in grid unit), the last num (optional) sets srcfrom0 (-z)
0 0 1 # initial directional vector
0.e+00 1.e-09 1.e-10 # time-gates(s): start, end, step
semi60x60x60.bin # volume ('unsigned char' binary format)
1 60 1 60 # x voxel size in mm (isotropic only), dim, start/end indices
1 60 1 60 # y voxel size, must be same as x, dim, start/end indices
1 60 1 60 # y voxel size, must be same as x, dim, start/end indices
1 # num of media
1.010101 0.01 0.005 1.37 # scat. mus (1/mm), g, mua (1/mm), n
4 1.0 # detector number and default radius (in grid unit)
30.0 20.0 0.0 2.0 # detector 1 position (real numbers in grid unit) and individual radius (optional)
30.0 40.0 0.0 # ..., if individual radius is ignored, MCX will use the default radius
20.0 30.0 0.0 #
40.0 30.0 0.0 #
pencil # source type (optional)
0 0 0 0 # parameters (4 floats) for the selected source
0 0 0 0 # additional source parameters
Note that the scattering coefficient mus=musp/(1-g).
JSON shape file format
Starting from v0.7.9, MCX can also use a shape description file in the place of the volume file. Using a shape-description file can save you from making a binary .bin volume. A shape file uses more descriptive syntax and can be easily understood and shared with others.
Samples on how to use the shape files are included under the example/shapetest folder.
The sample shape file, shapes.json, is shown below:
{
"MCX_Shape_Command_Help":{
"Shapes::Common Rules": "Shapes is an array object. The Tag field sets the voxel value for each
region; if Tag is missing, use 0. Tag must be smaller than the maximum media number in the
input file.Most parameters are in floating-point (FP). If a parameter is a coordinate, it
assumes the origin is defined at the lowest corner of the first voxel, unless user overwrite
with an Origin object. The default origin of all shapes is initialized by user's --srcfrom0
setting: if srcfrom0=1, the lowest corner of the 1st voxel is [0,0,0]; otherwise, it is [1,1,1]",
"Shapes::Name": "Just for documentation purposes, not parsed in MCX",
"Shapes::Origin": "A floating-point (FP) triplet, set coordinate origin for the subsequent objects",
"Shapes::Grid": "Recreate the background grid with the given dimension (Size) and fill-value (Tag)",
"Shapes::Sphere": "A 3D sphere, centered at C0 with radius R, both have FP values",
"Shapes::Box": "A 3D box, with lower corner O and edge length Size, both have FP values",
"Shapes::SubGrid": "A sub-section of the grid, integer O- and Size-triplet, inclusive of both ends",
"Shapes::XLayers/YLayers/ZLayers": "Layered structures, defined by an array of integer triples:
[start,end,tag]. Ends are inclusive in MATLAB array indices. XLayers are perpendicular to x-axis, and so on",
"Shapes::XSlabs/YSlabs/ZSlabs": "Slab structures, consisted of a list of FP pairs [start,end]
both ends are inclusive in MATLAB array indices, all XSlabs are perpendicular to x-axis, and so on",
"Shapes::Cylinder": "A finite cylinder, defined by the two ends, C0 and C1, along the axis and a radius R",
"Shapes::UpperSpace": "A semi-space defined by inequality A*x+B*y+C*z>D, Coef is required, but not Equ"
},
"Shapes": [
{"Name": "Test"},
{"Origin": [0,0,0]},
{"Grid": {"Tag":1, "Size":[40,60,50]}},
{"Sphere": {"Tag":2, "O":[30,30,30],"R":20}},
{"Box": {"Tag":0, "O":[10,10,10],"Size":[10,10,10]}},
{"Subgrid": {"Tag":1, "O":[13,13,13],"Size":[5,5,5]}},
{"UpperSpace":{"Tag":3,"Coef":[1,-1,0,0],"Equ":"A*x+B*y+C*z>D"}},
{"XSlabs": {"Tag":4, "Bound":[[5,15],[35,40]]}},
{"Cylinder": {"Tag":2, "C0": [0.0,0.0,0.0], "C1": [15.0,8.0,10.0], "R": 4.0}},
{"ZLayers": [[1,10,1],[11,30,2],[31,50,3]]}
]
}
A shape file must contain a "Shapes" object in the root level. Other root-level fields are ignored. The "Shapes" object is a JSON array, with each element representing a 3D object or setting. The object-class commands include "Grid", "Sphere", "Box" etc. Each of these object include a number of sub-fields to specify the parameters of the object. For example, the "Sphere" object has 3 subfields, "O", "R" and "Tag". Field "O" has a value of 1x3 array, representing the center of the sphere; "R" is a scalar for the radius; "Tag" is the voxel values. The most useful command is "[XYZ]Layers". It contains a series of integer triplets, specifying the starting index, ending index and voxel value of a layered structure. If multiple objects are included, the subsequent objects always overwrite the overlapping regions covered by the previous objects.
There are a few ways for you to use shape description records in your MCX simulations. You can save it to a JSON shape file, and put the file name in Line#6 of yoru .inp file, or set as the value for Domain.VolumeFile field in a .json input file. In these cases, a shape file must have a suffix of .json.
You can also merge the Shapes section with a .json input file by simply appending the Shapes section to the root-level object. You can find an example, jsonshape_allinone.json, under examples/shapetest. In this case, you no longer need to define the "VolumeFile" field in the input.
Another way to use Shapes is to specify it using the -P (or --shapes) command line flag. For example:
mcx -f input.json -P '{"Shapes":[{"ZLayers":[[1,10,1],[11,30,2],[31,60,3]]}]}'
This will first initialize a volume based on the settings in the input .json file, and then rasterize new objects to the domain and overwrite regions that are overlapping.
For both JSON-formatted input and shape files, you can use the JSONlab toolbox [4] to load and process in MATLAB.