4DImageMath
===========

.. code-block:: none

  
  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.