Provided by: minc-tools_2.3.00+dfsg-10build2_amd64 bug

NAME

       mincstats - calculate simple statistics across voxels of a minc file

SYNOPSIS

       mincstats [<options>] <in1>.mnc

DESCRIPTION

       Mincstats  will  calculate  simple  statistical measures across all voxels of a minc file.
       Note that these are global statistical  measures  and  not  voxel-by-voxel  measures  (see
       mincaverage  for  that).  By  default all statistics are calculated. If any statistics are
       requested via a command-line option, then only the requested statistics are printed.

       A very useful feature of this program is  the  ability  to  restrict  the  set  of  voxels
       included in the statistic calculation, either by restricting the range of included values,
       or by using a mask file with a restricted range. Multiple ranges for  the  input  file  or
       mask  file  can be specified. For each range of included volume values, and for each range
       of mask values, the relevant statistics are printed out (n*m values, where n is the number
       of volume ranges and m the number of mask ranges). These calculations are done in a single
       pass through the data, so specifying multiple ranges  is  much  faster  than  running  the
       program  repeatedly.  This is quite helpful when calculating many regional averages with a
       VOI mask volume.

       Special mention should be given  to  histograms  and  related  statistical  measures.  The
       default  range  of the histogram is from the smallest value in the file to the largest. In
       the not uncommon, but special, case when the number of histogram bins exactly matches  the
       number  of  possible  values  in  the  file  (e.g. 256 bins for full-range byte data), the
       histogram can end up with some odd features when using the default histogram  range.  This
       arises  from  the  discretization  of  the  data  that  are  then rebinned into a slightly
       mismatched histgram. For the example of byte data, the values that should be used are  256
       bins and a histogram range that extends half a bin below the smallest value and half a bin
       above the largest. Use option -discrete_histogram to work this out automatically,  or  use
       -integer_histogram  to  have  bins  of unit width if the input data are inherently integer
       (e.g. label data). In general, one should be careful about the  rebinning  of  discretized
       data to a histogram with a bin size that is close to the level of discretization.

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. 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

General options

       -clobber
              Overwrite an existing file.

       -noclobber
              Don't overwrite an existing file (default).

       -verbose
              Print out extra information (more than the default).

       -quiet Print out only the requested numbers

       -max_buffer_size_in_kb size
              Specify the maximum size of the internal buffers (in kbytes). Default is 4 MB.

Invalid value options

       -ignore_nan
              Exclude invalid values (outside valid range) from statistic calculations.  This  is
              the default.

       -include_nan
              Treat invalid values as zeros and include them in statistic calculations.

       -replace_nan value
              Replace  invalid  values  with  the  specified  value  and include the new value in
              statistic calculations.

Volume range options

       -floor min1,min2,...
              Comma-separated list of lower bounds for ranges of data  to  include  in  statistic
              calculation.

       -ceil max1,max2,...
              Comma-separated  list  of  upper  bounds for ranges of data to include in statistic
              calculation.

       -range min1,max1,min2,max2,...
              Comma-separated list of lower and upper bounds for ranges of  data  to  include  in
              statistic calculation.

       -binvalue val1,val2,...
              Comma-separated list of integer values to include in statistic calculation. A range
              of +/- 0.5 is defined around each specified value.

       -mask filename.mnc
              Name of file to be used for masking data included  in  statistic  calculation.  For
              this  to  have  any effect, you must specify a mask range with one of the following
              options.

       -mask_floor min1,min2,...:
              Like -floor, but applied to the mask file.

       -mask_ceil max1,max2,...
              Like -ceil, but applied to the mask file.

       -mask_range min1,max1,min2,max2,...
              Like -range, but applied to the mask file.

       -mask_binvalue val1,val2,...
              Like -binvalue, but applied to the mask file.

Histogram options

       -histogram filename
              Specify the name of a file into which the histogram is written. If multiple  ranges
              or  mask  ranges  are  specified,  then  all  histograms  are written in this file,
              separated by blank lines. Information describing each histogram is  written  before
              it  in  lines  starting  with the hash (pound) character. These files can be loaded
              into gnuplot.

       -hist_bins number-of-bins
              Specify the number of bins in the histogram.

       -bins number-of-bins
              Synonym for -hist_bins.

       -hist_floor min
              Specify lower bound for histogram.

       -hist_ceil max
              Specify upper bound for histogram.

       -hist_range min max
              Specify a range for the histogram

       -integer_histogram
              Create bins of unit width, centred  around  integer  values.  This  is  useful  for
              integer data such as labels. The histogram range is rounded to the nearest integer,
              then the min is lowered and the max is raised by 0.5. The number of bins  is  taken
              as  the difference of these two values.  Note that 0.01 is added to the minimum and
              subtracted from the maximum prior to  the  rounding  in  order  to  ensure  that  a
              correctly  specified  range  (e.g.  [0.5,255.5])  is preserved. If you want to have
              integer bins that are wider than one, you will have to work out the histogram range
              and number of bins yourself and not use this option.

       -discrete_histogram
              Attempt  to  match  the  histogram to the discretization of the input data. This is
              appropriate for continuous data that are stored in an  integer  representation  and
              when  a  bin  width  close  to  the  discretization  is desired. This is similar to
              -integer_histogram, except that the the histogram range is first converted to voxel
              values  which are rounded and extended by half a bin on either side. This new voxel
              range is then converted back to real values. The number of bins  is  taken  as  the
              difference in the voxel value range. Note that this does not account for variations
              in slice-to-slice scaling, so odd histogram effects may still occur. This option is
              intended to give behaviour similar to that of volume_stats.

       -int_max_bins number-of-bins
              Specify  the  largest  histogram  that  can  be  automatically sized with the above
              options. The limit prevents accidental creation of huge  histograms.   This  option
              replaced the old -max_bins option in MINC 1.1.

Basic statistics

       -all   Compute all statistical measures. This is the default.

       -none  Synonym  for  -count  (for similarity to volume_stats). Note that although this was
              necessary for volume_stats, it is not needed here, since specifying  any  of  these
              options automatically turns off -all

       -count Count the number of voxels that are within the range and mask.

       -percent
              Print the percentage of voxels within the range and mask

       -volume
              Print the volume of the voxels within the range and mask (in mm-cubed).

       -min   Print the minimum value.

       -max   Print the maximum value.

       -sum   Print the sum of all values.

       -sum2  Print the sum of the squares of all values.

       -mean  Print the mean.

       -variance
              Print the variance.

       -stddev
              Print the standard deviation.

       -skewness
              Print the sample skewness (3rd moment) .

       -kurtosis
              Print the sample kurtosis (4th moment) .

       -CoM   Print  the  centre of mass. Both the voxel coordinate and the world coordinates are
              printed. The voxel  coordinates  are  printed  in  file  order,  whilst  the  world
              coordinates are printed in x,y,z order.

       -com   Synonym for -CoM.

       -world_only
              Print the centre of mass in world coordinates only.

Histogram statistics

       Note  that  histogram  statistics  are  derived  solely  from the histogram counts and bin
       centres, so results such as the median will not be exactly the same as the true value  for
       all  included  voxels.  For example, the error on the median can be as large as a half bin
       width. Furthermore, if the histogram range is less than that of included voxels, then  the
       result applies only to voxels included in the histogram.

       -hist_count
              Print  number  of  voxels  in  histogram.  This may be different from the number of
              included and masked voxels if the histogram range is less than  the  range  of  the
              included data.

       -hist_percent
              Print percentage of voxels included in histogram.

       -median
              Print the histogram median.

       -majority
              Print the bin centre (intensity value) for the bin with the most counts.

       -biModalT
              Print  the bi-modal threshold separating the volume into two classes The default is
              to use the otsu method (see options below)

       -otsu  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

       -kittler
              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.

       -kapur 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.

       -simple
              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.

       -pctT  Print the threshold needed for a particular critical percentage of the histogram.

       -entropy
              Print the Shannon entropy.

                   H(x) = - Sum(P(i) * log2(P(i))

              where P(i) is the bin probability

Generic options for all commands:

       -help  Print summary of command-line options and exit.

       -version
              Print the program's version number and exit.

AUTHOR

       Andrew Janke

COPYRIGHTS

       Program: Copyright © 2000 by Andrew Janke

       Man page: Copyright © 2001 by Peter Neelin

                                   $Date: 2004-05-20 21:52:09 $                      MINCSTATS(1)