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).
-filelistfilename
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_kbbuffer-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Superseded by -int.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.
-rangemin 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).
-sdfilesdfile.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).
-avgdimdimname
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.
-binrangemin max
Specify the range of values for binarization.
-binvaluevalue
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.