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       mincstats - calculate simple statistics across voxels of a minc file


       mincstats [<options>] <in1>.mnc


       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


       Note that options can be specified in abbreviated form (as long as they
       are unique) and can be given anywhere on the command line.

General options

              Overwrite an existing file.

              Don’t overwrite an existing file (default).

              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

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

              Treat  invalid  values  as  zeros  and include them in statistic

       -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

       -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 number of bins in 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

              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.

              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.

              Print the percentage of voxels within the range and mask

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

       -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.

              Print the variance.

              Print the standard deviation.

       -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

       -com   Synonym for -CoM.

              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

              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.

              Print percentage of voxels included in histogram.

              Print the histogram median.

              Print the bin centre (intensity value) for the bin with the most

              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.

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

              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.

              Print the program’s version number and exit.


       Andrew Janke


       Program: Copyright © 2000 by Andrew Janke

       Man page: Copyright © 2001 by Peter Neelin

                         $Date: 2004-05-20 21:52:09 $