Asymmetry - Usage

Asymmetry analyses the asymmetry of the Z-spectrum with respect to the water frequency in CEST analysis. Running the program without any arguments produces the following output:

Usage: Asymmetry [options] image1 [image2 image3 ... imageN]
 -?,--help                                                   Displays this help
                                                             message.
 -b0,--b0-map <b0-map-image>                                 Specifies the B0
                                                             inhomogeneity map,
                                                             in ppm.
 -c,--contiguous                                             Specify that the
                                                             different frequency
                                                             offsets are
                                                             contiguous in the
                                                             input image(s).
 -f,--freq-off <Off1,Off2,..,Offn | FirstOff:LastOff:nOff>   Specifies the
                                                             frequency offsets
                                                             in ppm. By default,
                                                             an attempt is made
                                                             to read these from
                                                             the image header.
 -m,--mask <image>                                           Mask the output
                                                             images using the
                                                             image mask <image>.
 -M,--roi-mask <roi-file>                                    Mask the output
                                                             images using the
                                                             ROI mask
                                                             <roi-file>.
 -n,--n-slices <integer>                                     Specify the number
                                                             of physical slice
                                                             locations. Default:
                                                             1.
 -o,--offset <offset | minOffset:maxOffset>                  Specifies the
                                                             offset frequency
                                                             (or range) at which
                                                             to assess the
                                                             Z-spectrum
                                                             asymmetry, in ppm.
                                                             Compulsory option.
                                                             Either Offset or
                                                             MinOffset:MaxOffset
                                                             .
 -s0,--s0-map <s0-map-image>                                 Specifies the S0
                                                             image (with no
                                                             saturation pulses).
 -t,--threshold <number>                                     Sets a threshold:
                                                             if pixels
                                                             intensities at a
                                                             given location are
                                                             below <number> in
                                                             all input images,
                                                             then the output is
                                                             set to zero in that
                                                             pixel location.
 -v,--verbose                                                Turns on verbose
                                                             reporting to
                                                             System.out.
 -ver,--version                                              Prints the software
                                                             build version, and
                                                             exits.