Updated man page to match new options.

Updated man page to match the new options that Bert has added over time. For thresholding of histogram and calculation of skewness and kurtosis of histogram

progs/mincstats/mincstats.man1

@@ -1,4 +1,3 @@
-.\"                                      Hey, EMACS: -*- nroff -*-
 .\" Copyright 2001 Peter Neelin, McConnell Brain Imaging Centre,
 .\" Montreal Neurological Institute, McGill University.
 .\" Permission to use, copy, modify, and distribute this
@@ -9,8 +8,6 @@
 .\" software for any purpose.  It is provided "as is" without
 .\" express or implied warranty.
 .\"
-.\" $Header: /private-cvsroot/minc/progs/mincstats/mincstats.man1,v 1.5 2004-05-20 21:52:09 bert Exp $
-.\"
 .TH MINCSTATS 1 "$Date: 2004-05-20 21:52:09 $" "" "MINC User's Guide"
 
 .SH NAME
@@ -59,7 +56,9 @@ discretization.
 
 .SH OPTIONS
 Note that options can be specified in abbreviated form (as long as
-they are unique) and can be given anywhere on the command line.
+they are unique) and can be given anywhere on the command line. The order
+in which the statistics are printed will be always the same irrespective
+or the order in which they are requested on the command line
 
 .SH General options
 .TP
@@ -137,7 +136,7 @@ describing each histogram is written before it in lines starting with
 the hash (pound) character. These files can be loaded into gnuplot.
 .TP
 \fB\-hist_bins\fR \fInumber-of-bins\fR
-Specify number of bins in histogram.
+Specify the number of bins in the histogram.
 .TP
 \fB-bins\fR \fInumber-of-bins\fR
 Synonym for \fB\-hist_bins\fR.
@@ -221,6 +220,12 @@ Print the variance.
 \fB\-stddev\fR
 Print the standard deviation.
 .TP
+\fB\-skewness\fR
+Print the sample skewness (3rd moment) .
+.TP
+\fB\-kurtosis\fR
+Print the sample kurtosis (4th moment) .
+.TP
 \fB\-CoM\fR
 Print the centre of mass. Both the voxel coordinate and the world
 coordinates are printed. The voxel coordinates are printed in file
@@ -257,9 +262,30 @@ Print the histogram median.
 Print the bin centre (intensity value) for the bin with the most counts.
 .TP
 \fB\-biModalT\fR
-Print the bi-modal threshold calculated using the method described in
-Otsu N, "A Threshold Selection Method from Grey-level Histograms",
-IEEE Trans on Systems, Man and Cybernetics. 1979, 9:1; 62-66.
+Print the bi-modal threshold separating the volume into two classes
+The default is to use the otsu method (see options below)
+.TP
+\fB\-otsu\fR
+Use the method described in Otsu N, "A Threshold Selection Method 
+from Grey-level Histograms", IEEE Trans on Systems, Man and Cybernetics. 
+1979, 9:1; 62-66 to calculate the threshold
+.TP
+\fB\-kittler\fR
+Use the Kittler&Illingworth '86 algorithm to calculate the for bimodal
+threshold. Kittler, J. & Illingworth J., "Minimum error thresholding", 
+Pattern Recognition, vol 19, pp 41-47, 1986.
+.TP
+\fB\-kapur\fR
+Use the Kapur et al. '85 algorithm to calculate the bimodal threshold.
+Kapur, Sahoo & Wong "A new method for Gray-level picture thresholding 
+using the entropy of the histogram", Computer Vision, Graphics, and 
+Image Processing, vol 29, pp 273-285, 1985.
+.TP
+\fB\-simple\fR
+Use simple mean-of-means algorithm to calculate the bimodal threshold
+This is more computationally expensive than some of the alternatives, 
+and doesn't seem to do a great job. But it does seem more robust than 
+some of the other methods.
 .TP
 \fB\-pctT\fR
 Print the threshold needed for a particular critical percentage of the