mincaverage man page on DragonFly
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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-long Superseded by -int.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 inte‐
ger 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 averag‐
ing (or calculating standard deviation). If normalization is
done, it still only applies to separate files only - no normal‐
ization 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 con‐
tribute 1 to the average. Normalization of the input is not per‐
mitted 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 weight‐
ing 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
$Date: 2004-05-20 21:52:07 $ MINCAVERAGE(1)
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