USAGE:
4DImageMath [--returnparameterfile <std::string>]
[--processinformationaddress <std::string>] [--xml]
[--echo] [--crop <std::vector<int>>] [--shred
<std::vector<int>>] [--compose] [--dotproduct] [--amin]
[--amax] [--sum] [--median] [--mean] [--norm <L2|L1|L0
|INF>] [-a <x|y|z|t|0|1|2|3>] [--sqrt] [--square] [--log]
[--exp] [--abs] [-f <std::string>] [--pow <std::string>]
[--min <std::string>] [--max <std::string>] [--mul
<std::string>] [--div <std::string>] [--sub <std::string>]
[--add <std::string>] [-v <int>] [--nt <int>] [--outformat
<NONE|4D|VECTOR>] [--box <std::vector<int>>] [-m
<std::string>] [--] [--version] [-h]
<std::vector<std::string>> ...
Where:
--returnparameterfile <std::string>
Filename in which to write simple return parameters (int, float,
int-vector, etc.) as opposed to bulk return parameters (image,
geometry, transform, measurement, table).
--processinformationaddress <std::string>
Address of a structure to store process information (progress, abort,
etc.). (value: 0)
--xml
Produce xml description of command line arguments (value: 0)
--echo
Echo the command line arguments (value: 0)
--crop <std::vector<int>>
Crop image by 8 parameters (x0,x1,y0,y1,z0,z1,t0,t1). (value: -1,-1,-1
,-1,-1,-1,-1,-1)
--shred <std::vector<int>>
Shred vector elements along axis according to offset, chunk size, and
space specified by parameters 1 to 3. (value: 0,0,0)
--compose
Compose images along axis (>=2 input images). (value: 0)
--dotproduct
Dot product along axis (2 input images) (value: 0)
--amin
minimal value along axis (value: 0)
--amax
maximal value along axis (value: 0)
--sum
Sum along axis (value: 0)
--median
Median along axis (value: 0)
--mean
Mean along axis (value: 0)
--norm <L2|L1|L0|INF>
Calculate norm of vector along axis. (value: L2)
-a <x|y|z|t|0|1|2|3>, --axis <x|y|z|t|0|1|2|3>
Axis (x/y/z/t, i.e., 0/1/2/3).
--sqrt
sqrt: square root, i.e., -f 'sqrt(x)' (value: 0)
--square
square, i.e., -f 'x*x' (value: 0)
--log
natural logarithm, i.e., -f 'log(x)' (value: 0)
--exp
exponential, i.e., -f 'exp(x)' (value: 0)
--abs
absolute value, i.e., -f 'abs(x)' (value: 0)
-f <std::string>, --func <std::string>
Perform functions on elements of the input images (one or more
inputs). Input images should have the same size, and it does not
change the size in the output image.
Note: it is slower (-f 'abs') than functions (--abs).
Example: cos(x)+3*x+abs(x)+2 +x^3
x[0]+x[1]*x[1]+3*x[2] // need >3 inputs
max(x[0],x[1],x[2]) // need >3 inputs
if (x>0.5) 1.0; else 0.0; // mask the input image using threshold 0.5
--pow <std::string>
Pow image file or a constant.
--min <std::string>
Take minimum of the input and the following image or constant.
--max <std::string>
Take maximum of the input and the following image or constant.
--mul <std::string>
Multiply image file or a constant.
--div <std::string>
Divide image file or a constant.
--sub <std::string>
Substract (minus) image file or a constant.
--add <std::string>
Add image file or a constant.
-v <int>, --verbose <int>
Verbose level. 0: no output log. 1: normal log. 2: log for debug log.
3: log for large matrix or vectors. (value: 1)
--nt <int>
Number of threads. If it not positive, then the default number for
multiple threads is used. (value: -1)
--outformat <NONE|4D|VECTOR>
Output format. NONE: same as the input. 4D: itk 4D image, VECTOR: 3D
vector image. (value: NONE)
--box <std::vector<int>>
only perform calculation in a given box (x0,x1,y0,y1,z0,z1). Set zero
out of the region. (value: -1,-1,-1,-1,-1,-1)
-m <std::string>, --mask <std::string>
Mask image file (3d or 4d image). Set zero out of the region.
--, --ignore_rest
Ignores the rest of the labeled arguments following this flag.
--version
Displays version information and exits.
-h, --help
Displays usage information and exits.
<std::vector<std::string>> (accepted multiple times)
Image list. At least two files (one or more input images, and one
output image)
Description: Perform math operators on 4D image (4D itk::Image or 3D
itk::VectorImage).
Examples:
4DImageMath image1.nii.gz out.nii.gz -f 'cos(x)+3*x+sqrt(abs(x))+sqrt(2)
+x^3' -m mask.nii.gz
4DImageMath image1.nii.gz out.nii.gz -f 'if (x>0.5) 1.0; else 0.0;' -m
mask.nii.gz
4DImageMath image1.nii.gz out.nii.gz --abs -m mask.nii.gz
4DImageMath image1.nii.gz out.nii.gz --exp -m mask.nii.gz
4DImageMath image1.nii.gz out.nii.gz --add image2.nii.gz -m mask.nii.gz
4DImageMath image1.nii.gz out.nii.gz --add 2.0 -m mask.nii.gz
4DImageMath image1.nii.gz image2.nii.gz out.nii.gz -f 'x[0]+x[1]' -m
mask.nii.gz
4DImageMath image1.nii.gz image2.nii.gz out.nii.gz -f 'x[0]^2+cos(x[1])'
-m mask.nii.gz
4DImageMath image1.nii.gz image2.nii.gz out.nii.gz --axis t --dotproduct
4DImageMath image1.nii.gz image2.nii.gz image3.nii.gz out.nii.gz -f
'max(x[0],x[1],x[2]/2.0)' -m mask.nii.gz
4DImageMath image1.nii.gz out.nii.gz --axis t --mean -m mask.nii.gz
4DImageMath image1.nii.gz out.nii.gz --axis x --norm L2 -m mask.nii.gz
4DImageMath image1.nii.gz image2.nii.gz image3.nii.gz out.nii.gz
--axis t --compose
Author(s): Jian Cheng (jian.cheng.1983@gmail.com)
Acknowledgements: Thank you everyone.
