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

NAME

       mincaverage - average minc files

SYNOPSIS

       mincaverage [<options>] <in1>.mnc [<in2>.mnc...] <out>.mnc

DESCRIPTION

       Mincaverage  averages minc files together. A range of optional behaviour is permitted as well: pre-normalizing volumes, creating a standard
       deviation volume, averaging over a specified dimension of the input files.

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
       -2     Create a MINC 2.0 format output file.

       -clobber
	      Overwrite an existing file.

       -noclobber
	      Don't overwrite an existing file (default).

       -verbose
	      Print out progress information for each chunk of data copied (default).

       -quiet Do not print out progress information.

       -debug Print extra information (e.g. normalization factors).

       -filelist filename
	      Specify a file containing a list of input file names. If "-" is given, then file names are read from stdin. If this option is given,
	      then there should be no input file names specified on the command line. Empty lines in the input file are ignored.

       -max_buffer_size_in_kb buffer-size
	      Specify the maximum size of the internal buffers (in kbytes). Default is 4096 kbytes.

Output type options
       These options control the storage precision and size of individual voxel values in the output file.

       -filetype
	      Don't do any type conversion (default).

       -byte  Write out 8-bit integer values.

       -short Write out 16-bit integer values.

       -int   Write out 32-bit integer values.

       -long  Superseded by -int.

       -float Write out single-precision floating point values.

       -double
	      Write out double-precision floating point values.

       -signed Write out values as signed integers (default for short and long). Ignored for floating point types.

       -unsigned
	      Write out values as unsigned integers (default for byte). Ignored for floating point types.

       -range min max
	      specifies  the  valid range of output voxel values in their integer representation. Default is the full range for the type and sign.
	      This option is ignored for floating point values. For it to have any effect, you must specify a type.

Averaging options
       -normalize
	      Normalize volumes to their global average before averaging them (based on the mean of voxels with value greater than  2  percent	of
	      full range above the minimum).

       -nonormalize
	      Do not normalize volumes (default).

       -sdfile sdfile.mnc
	      Specify the name of an output standard deviation file, to be calculated in addition the mean that is normally calculated.

       -copy_header
	      Copy all of the additional header information from the first input file (default for one input file).

       -nocopy_header
	      Do not copy additional header information (default for many input files).

       -avgdim dimname
	      Specify  the name of a dimension over which we should be averaging (or calculating standard deviation). If normalization is done, it
	      still only applies to separate files only - no normalization is done within a file.

       -binarize
	      Binarize the input volumes before calculating the average. The binarization is done by specifying a range of values that	contribute
	      1 to the average. Normalization of the input is not permitted when performing binarization.

       -binrange min max
	      Specify the range of values for binarization.

       -binvalue value
	      Specify  a  single  legal value (integer) for binarization. The range is set to be +/- 0.5 around this value to achieve an effective
	      rounding of input values.

       -weights <w1,w2,...>
	      Specify a series of weights for averaging. The number of weighting values must match the number of input files and the  values  must
	      be  provided  as a single argument with commas or spaces as separators. The sum of the weights must be non-zero. If weights are used
	      with an averaging dimension, then only one input file can be specified.

       -width_weighted
	      This option can only be used when averaging across a dimension (-avgdim option). It specifies that weighting should  be  done  using
	      the  width  variable  that corresponds to the averaging dimension. For example, using -width_weighted with -avgdim time will use the
	      time-width variable to weight the values.

Generic options for all commands:
       -help  Print summary of command-line options and exit.

       -version
	      Print the program's version number and exit.

AUTHOR

       Peter Neelin

COPYRIGHTS

       Copyright (C) 1995 by Peter Neelin

							   $Date: 2004-05-20 21:52:07 $ 					    MINCAVERAGE(1)