mincaverage

mincaverage average minc files

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Superseded by -int.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.

AUTHOR

Peter Neelin