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Man Pages


Manual Reference Pages  -  MINCAVERAGE (1)

NAME

mincaverage - average minc files

CONTENTS

Synopsis
Description
Options
General options
Output type options
Averaging options
Generic options for all commands:
Author
Copyrights

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-long Superseded by -int.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 © 1995 by Peter Neelin

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

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