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mincaverage - Online in the Cloud

Run mincaverage in OnWorks free hosting provider over Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator

This is the command mincaverage that can be run in the OnWorks free hosting provider using one of our multiple free online workstations such as Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator

PROGRAM:

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-long Superseded by -int.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.

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