WarpCorrection - Usage

WarpCorrection is used to correct distortions in diffusion-weighted images cause by eddy-currents. Running the program with the option --help produces the following output:

Usage: WarpCorrection [options] image1 [image2] [image3] ...
 -?,--help                    Displays this help message.
 -c,--contiguous              Specify that the different diffusion weightings
                              are contiguous in the input image(s).
 -g,--grad-spec <xml-file>    Indicates that the gradient vector/B-matrix set
                              should be obtained from a gradient specification
                              XML file. If this option is not used, an attempt
                              will be made to obtain the gradient specification
                              from the input image(s).
 -h,--horizontal              Sets the phase-encoded direction to horizontal
                              (default: vertical).
 -l,--linear                  Sets the between-slice correction order to linear
                              (default: quadratic).
 -m,--motion-correct          Performs correction of subject motion as well as
                              warping.
 -n,--n-contrasts <integer>   Sets the number of diffusion weightings in the
                              single input image. Ignored if there is more than
                              one input image, or if the gradients are specified
                              in an XML file.
 -s,--sub-sampling <factor>   Sets the pixel subsampling factor used to speed up
                              processing (min: 1; max: 100; default: 1)
 -t,--threshold <number>      Sets the threshold for pixel exclusion. Only
                              pixels with intensity in the average
                              non-difusion-weighted image above the threshold
                              will be used in assessing the warps (default:
                              0.0).
 -u,--constant                Sets the between-slice correction order to
                              constant (default: quadratic).
 -v,--verbose                 Turns on verbose reporting to System.out.
 -ver,--version               Prints the software build version, and exits.
 -x,--max-iter <integer>      Sets the maximum number of iterations of the
                              minimisation before failing (default: 100).