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MINCSTATS(1)		       MINC User's Guide		  MINCSTATS(1)

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 sta-
       tistics 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  re-
       stricting  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 val-
       ues,  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	 aver-
       ages 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 his-
       togram can end up with some odd features	when using  the	 default  his-
       togram  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 au-
       tomatically, 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 his-
       togram 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 cal-
	      culations. This is the default.

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

       -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  in-
	      clude in statistic calculation.

       -ceil max1,max2,...
	      Comma-separated  list  of	upper bounds for ranges	of data	to in-
	      clude 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  his-
	      tograms  are written in this file, separated by blank lines. In-
	      formation	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 in-
	      put 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	-inte-
	      ger_histogram, except that the the histogram range is first con-
	      verted 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 vari-
	      ations 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  op-
	      tion 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 ex-
       actly 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. Further-
       more, 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  de-
	      scribed 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 (C) 2000 by Andrew Janke

       Man page: Copyright (C) 2001 by Peter Neelin

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

NAME | SYNOPSIS | DESCRIPTION | OPTIONS | General options | Invalid value options | Volume range options | Histogram options | Basic statistics | Histogram statistics | Generic options for all commands: | AUTHOR | COPYRIGHTS

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