JimStats - Usage

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

JimStats: please 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,--non-zero-mean             Output the mean pixel intensity for all
                                voxels that have non-zero intensity.
 -m,--mean                      Output the mean pixel intensity.
 -n,--nan                       Convert all NaN or Inf pixel intensities
                                to zeros before computing the statistics.
 -N,--histo-min <min>           Set the minumum intensity histogram bin
                                value to <min>.
 -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]
 -p,--percentile <n>            Output the <n>th percentile in the
                                intensity histogram. <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>.
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