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

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

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 (C) 2010 by Andrew Janke

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