NAME

       minccmp - compare one or more minc file using comparator operators

SYNOPSIS

       minccmp [<options>] <in1.mnc> <in2.mnc> [<inn.mnc> ...]

DESCRIPTION

       minccmp  will  calculate  simple  statistical  measures  between two minc files or more by
       comparing all subsequent files to the first.  The results for each subseqent file are then
       returned  in order.  By default all statistics are calculated. If specifitc 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
       (-floor, -ceil or -range), or by using a mask file (-mask) with a restricted range.

       The comparison statistics available in minccmp are given below. Note  that  two  of  these
       (-xcorr and -zscore) are a very close approximation to what is used in minctracc.

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).

       -debug Dump a lot of extra information (for when things go haywire).

       -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.

       -check_dimensions
              Check that all input files have matching sampling in world dimensions (default).

       -nocheck_dimensions
              Ignore any differences in world dimensions sampling for input files .

Volume range options

       -floor min
              A lower bound for ranges of data to include in statistic calculations.

       -ceil max
              An upper bound for ranges of data to include in statistic calculations.

       -range min,max
              A lower and upper bound for the ranges of data to include in statistics.

       -mask filename.mnc
              Name of file to be used for masking data included in statistic calculations.

Basic statistics

       -all   Compute all statistical measures. This is the default.

       -ssq   Print the Sum Squared Difference between two input files
                 SSQ = Sum( (A-B)^2 )

       -rmse  Print the Root Mean Squared Error between two input files
                 RMSE = sqrt( 1/n * Sum((A-B)^2))

       -xcorr Print the Cross Correlation between two input files
                 XCORR = Sum((A*B)^2) / (sqrt(Sum(A^2)) * sqrt(Sum(B^2))

       -zscore
              Print the z-score difference between two input files
                 ZSCORE = Sum( |((A - mean(A)) / stdev(A)) -
                                ((B - mean(B)) / stdev(B))| ) / n

       -similarity
              Calculate the confusion  matrix,  assuming  that  the  volume  values  represent  a
              discrete  class of possible values. The maximum label value is currently limited to
              ten (10). Prints the Dice similarity statistic as well as specificity, sensitivity,
              accuracy, and kappa for each class and for the overall volumes.

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

       Copyright © 2010 by Andrew Janke

                                   $Date: 2010-03-02 12:12:20 $                        MINCCMP(1)