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.
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 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
- -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.
- -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 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.
- -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