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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       -long  Superseded by -int.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)