

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.
 
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.
floor min1,min2,... Commaseparated list of lower bounds for ranges of data to include in statistic calculation. ceil max1,max2,... Commaseparated list of upper bounds for ranges of data to include in statistic calculation. range min1,max1,min2,max2,... Commaseparated list of lower and upper bounds for ranges of data to include in statistic calculation. binvalue val1,val2,... Commaseparated 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 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 numberofbins Specify number of bins in histogram. bins numberofbins 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 slicetoslice scaling, so odd histogram effects may still occur. This option is intended to give behaviour similar to that of volume_stats. int_max_bins numberofbins 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 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 mmcubed). 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.
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 bimodal threshold calculated using the method described in Otsu N, "A Threshold Selection Method from Greylevel Histograms", IEEE Trans on Systems, Man and Cybernetics. 1979, 9:1; 6266. 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
help Print summary of commandline options and exit. version Print the program’s version number and exit.
Andrew Janke
Program: Copyright © 2000 by Andrew Janke
Man page: Copyright © 2001 by Peter Neelin
MINCSTATS (1)  $Date: 20040520 21:52:09 $ 
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