JimStats - Usage

JimStats displays statistics about an image's intensities. Running the program without any arguments produces the following output:

JimStats: ERROR: specify the image name.
Usage: JimStats [options] image
 -?,--help                      Displays this help message.
 -a,--abs                       Convert all pixel intensities to absolute value
                                before computing the statistics.
 -c,--cog-mm                    Output the centre of gravity of the pixel
                                intensity in mm coordinates.
 -C,--cog-vox                   Output the centre of gravity of the pixel
                                intensity in voxel coordinates.
 -h,--histo <nbins>             Output a histogram of intensities with the
                                specified number of bins <nbins>.
 -l,--lthresh <thresh>          Set the lower intensity threshold to <thresh>.
                                All pixel intensities at or below the threshold
                                are disregarded.
 -m,--mean                      Output the mean pixel intensity.
 -M,--non-zero-mean             Output the mean pixel intensity for all voxels
                                that have non-zero intensity.
 -n,--nan                       Convert all NaN or Inf pixel intensities to
                                zeros before computing the statistics.
 -N,--histo-min <min>           Set the minimum intensity histogram bin value to
                                <min>.
 -p,--percentile <n>            Output the <n>th percentile in the intensity
                                histogram. <n> must be between in the range
                                [0..100]
 -P,--non-zero-percentile <n>   Output the <n>th percentile in the intensity
                                histogram for all voxels that have non-zero
                                intensity. <n> must be between in the range
                                [0..100]
 -r,--robust                    Output the robust minimum and maximum pixel
                                intensities.
 -R,--min-max                   Output the minimum and maximum pixel
                                intensities.
 -s,--sd                        Output the standard deviation of pixel
                                intensity.
 -S,--non-zero-sd               Output the standard deviation of pixel intensity
                                for all voxels that have non-zero intensity.
 -u,--uthresh <thresh>          Set the upper intensity threshold to <thresh>.
                                All pixel intensities at or above the threshold
                                are disregarded.
 -v,--vol                       Output the total number and total volume of all
                                voxels.
 -V,--non-zero-vol              Output the total number and total volume of all
                                voxels that have non-zero intensity.
 -ver,--version                 Prints the software build version, and exits.
 -X,--histo-max <max>           Set the maximum intensity histogram bin value to
                                <max>.