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>.