diff --git a/doc/mcx_help.html b/doc/mcx_help.html
index 6aaff93a..92d3869d 100644
--- a/doc/mcx_help.html
+++ b/doc/mcx_help.html
@@ -92,6 +92,7 @@
--bench
cube60
cube60b
cube60planar
+ cubesph60b
skinvessel
sphshell
spherebox
@@ -398,6 +399,10 @@ -K / --mediabyte
1 or byte
: 0-128 tissue labels
2 or short
: 0-65535 (max to 4000) tissue labels
4 or integer
: integer tissue labels
+ 96 or asgn_float
: mua/mus/g/n 4xfloat format
+ 97 or svmc
: split-voxel MC 8-byte format
+ 98 or mixlabel
: label1+label2+label1_percentage
+ 99 or labelplus
: 32bit composite voxel format
100 or muamus_float
: 2x 32bit floats for mua/mus
101 or mua_float
: 1 float per voxel for mua
102 or muamus_half
: 2x 16bit float for mua/mus
@@ -641,6 +646,7 @@ -d / --savedet
'-d' or '-d 1' to enable (default) or
'-d 0' to disable
+ '-d 3' terminate simulation when detected
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 apertures of the detectors.
@@ -804,10 +810,10 @@
-F / --outputformat
the bnii/jnii formats support compression (-Z) and generate small files
load jnii (JSON) and bnii (UBJSON) files using below lightweight libraries in MATLAB or Python:
@@ -930,7 +936,8 @@
-D / --debug
1 R debug RNG
2 M store photon trajectory info (saved in a .mct
file, can be loaded with loadmch.m
)
- 4 P print progress bar
+ 4 P print progress bar
+ 8 T save trajectory data only, disable flux/detp
combine multiple items by using a string, or add selected numbers together
@@ -1002,7 +1009,7 @@
2.1. JSON input file format
"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::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",
@@ -1021,38 +1028,38 @@ 2.1. JSON input file format
}
},
"Domain": {
- "VolumeFile": "semi60x60x60.bin",
+ "VolumeFile": "semi60x60x60.bin",
"Dim": [60,60,60],
"OriginType": 1,
- "LengthUnit": 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"
+ "Photons": 1000000,
+ "RNGSeed": 29012392,
+ "ID": "qtest"
},
"Forward": {
- "T0": 0.0e+00,
- "T1": 5.0e-09,
- "Dt": 5.0e-09
+ "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
- },
+ "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
@@ -1065,7 +1072,7 @@ 2.1. JSON input file format
"Pos": [39.0, 29.0, 0.0],
"R": 1.0
}
- ]
+ ]
}
}