Tractography - Usage

Tractography is used to perform tractography from diffusion tensor images. Running the program with the option --help produces the following output:

Usage: Tractography [options] DTImage seedROIFile
 -?,--help                   Displays this help message.
 -a,--accuracy <accuracy>    Sets the tract propagation accuracy to one of:
                             FASTEST, MEDIUM, MOST_ACCURATE (default: MEDIUM).
 -b,--name <basename>        Set the base name for the tracts/tract stats output
                             files.
 -c,--min-curv <radius>      Sets the minimum radius of curvature tract
                             termination criterion.
 -f,--fa <fa>                Sets the minimum fractional anisotropy tract
                             termination criterion.
 -i,--interval <interval>    Sets the interval (in mm) between points when
                             writing out the tracts and tracts statistics.
 -o,--overwrite-tracts       Specifies that the tract file should be
                             overwritten, not appended.
 -O,--overwrite-stats        Specifies that the tract stats file should be
                             overwritten, not appended.
 -r,--rep-factor <factor>    Sets the seed replication factor to one of 1, 2 or
                             3 (default: 1).
 -s,--filter-size <width>    Sets the size (in mm, FWHM) of the Gaussian
                             smoothing filter for smoothing tracts. The filter
                             is applied to the DT images before tracking.
 -t,--target <roiFileName>   Sets the name for the optional ROI file that
                             contains the target area. Only tracts that pass
                             through the target area will be retained.
 -v,--verbose                Turns on verbose reporting to System.out.
 -ver,--version              Prints the software build version, and exits.
 -w,--write-tracts           Causes tracts to be written to disk in XML file
                             format.
 -W,--write-stats            Causes tract stats to be written to disk.
 -X,--x-reversed             Indicates that the x-gradient sign is opposite to
                             convention.
 -Y,--y-reversed             Indicates that the y-gradient sign is opposite to
                             convention.
 -Z,--z-reversed             Indicates that the z-gradient sign is opposite to
                             convention.