mincaverage - average minc files
mincaverage [<options>] <in1>.mnc
[<in2>.mnc...] <out>.mnc
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.
Note that options can be specified in abbreviated form (as long as
they are unique) and can be given anywhere on the command line.
- -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.
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- Superseded by -int.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.
- -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 all of the additional header information from the first input file
(default for one input file).
- 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).
- -help
- Print summary of command-line options and exit.
- -version
- Print the program's version number and exit.
Copyright © 1995 by Peter Neelin