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.
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
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 invalid values with the specified value and include the
new value in statistic calculations.
Volume range options
Comma-separated list of lower bounds for ranges of data to
include in statistic calculation.
Comma-separated list of upper bounds for ranges of data to
include in statistic calculation.
Comma-separated list of lower and upper bounds for ranges of
data to include in statistic calculation.
Comma-separated list of integer values to include in statistic
calculation. A range of +/- 0.5 is defined around each specified
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.
Like -floor, but applied to the mask file.
Like -ceil, but applied to the mask file.
Like -range, but applied to the mask file.
Like -binvalue, but applied to the mask file.
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.
Specify number of bins in histogram.
Synonym for -hist_bins.
Specify lower bound for histogram.
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.
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.
-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
-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.
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.
Program: Copyright © 2000 by Andrew Janke
Man page: Copyright © 2001 by Peter Neelin
$Date: 2004-05-20 21:52:09 $