Provided by: minc-tools_2.3.00+dfsg-3build1_amd64 bug

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       -long  Superseded by -int.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)