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       -long  Superseded by -int.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.

       -weightfile weightfile.mnc
              Specify an output cumulative voxel weight file (default=none).

       -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.

       -ignore_below value
              Do not include voxels below this value in the average and sd

       -ignore_above value
              Do not include voxels above this value in the average and sd

       -floor value
              Synonym for -ignore_below

       -ignore_above value
              Synonym for -ignore_above

       -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.

       -min_weight value
              This  specifies  the  minimum  weight  (number  of volumes if no weights are specified) needed for
              calculating a valid average. If the cumulative weight for a voxel is  below  this  threshold,  the
              average and sd reported will be 0. This would typically be useful if values are excluded using any
              of the -ignore options, or by NaN values in the input volume(s).

       -min_weight_fraction value
              Same as -min_weight, but specified as a fraction of the sum of the input weights (or the number of
              input volumes, if no weight is specified).

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 © 1995 by Peter Neelin

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