+
−.\"                                      Hey, EMACS: -*- nroff -*-
+
−.\" Copyright 1995 Peter Neelin, McConnell Brain Imaging Centre,
+
−.\" Montreal Neurological Institute, McGill University.
+
−.\" Permission to use, copy, modify, and distribute this
+
−.\" software and its documentation for any purpose and without
+
−.\" fee is hereby granted, provided that the above copyright
+
−.\" notice appear in all copies.  The author and McGill University
+
−.\" make no representations about the suitability of this
+
−.\" software for any purpose.  It is provided "as is" without
+
−.\" express or implied warranty.
+
−.\"
+
−.\" $Header: /private-cvsroot/minc/progs/mincaverage/mincaverage.man1,v 6.3 2004-05-20 21:52:07 bert Exp $
+
−.\"
+
−.TH MINCAVERAGE 1 "$Date: 2004-05-20 21:52:07 $" "" "MINC User's Guide"
+
−
+
−.SH NAME
+
−mincaverage - average minc files
+
−
+
−.SH SYNOPSIS
+
−.B mincaverage
+
−[<options>] <in1>.mnc [<in2>.mnc...] <out>.mnc
+
−
+
−.SH DESCRIPTION
+
−\fIMincaverage\fR 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.
+
−
+
−.SH 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.
+
−
+
−.SH General options
+
−.TP
+
−\fB\-2\fR
+
−Create a MINC 2.0 format output file.
+
−.TP
+
−\fB\-clobber\fR
+
−Overwrite an existing file.
+
−.TP
+
−\fB\-noclobber\fR
+
−Don't overwrite an existing file (default).
+
−.TP
+
−\fB\-verbose\fR
+
−Print out progress information for each chunk of data copied (default).
+
−.TP
+
−\fB\-quiet\fR
+
−Do not print out progress information.
+
−.TP
+
−\fB\-debug\fR
+
−Print extra information (e.g. normalization factors).
+
−.TP
+
−\fB\-filelist\fR \fIfilename\fR
+
−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.
+
−.TP
+
−\fB\-max_buffer_size_in_kb\fR \fIbuffer-size\fR
+
−Specify the maximum size of the internal buffers (in kbytes). Default is
+
−4096 kbytes.
+
−
+
−.SH Output type options
+
−These options control the storage precision and size of individual voxel
+
−values in the output file.
+
−.TP
+
−\fB-filetype\fR
+
−Don't do any type conversion (default).
+
−.TP
+
−\fB\-byte\fR
+
−Write out 8-bit integer values.
+
−.TP
+
−\fB\-short\fR
+
−Write out 16-bit integer values.
+
−.TP
+
−\fB-int\fR
+
−Write out 32-bit integer values.
+
−.TP
+
−\fB\-long\fR
+
−Superseded by -int.
+
−.TP
+
−\fB\-float\fR
+
−Write out single-precision floating point values.
+
−.TP
+
−\fB\-double\fR
+
−Write out double-precision floating point values.
+
−.P
+
−\fB\-signed\fR
+
−Write out values as signed integers (default for short and long). Ignored for
+
−floating point types.
+
−.TP
+
−\fB\-unsigned\fR
+
−Write out values as unsigned integers (default for byte). Ignored for
+
−floating point types.
+
−.TP
+
−\fB\-range\fR \fImin max\fR
+
−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.
+
−
+
−.SH Averaging options
+
−.TP
+
−\fB\-normalize\fR
+
−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).
+
−.TP
+
−\fB\-nonormalize\fR
+
−Do not normalize volumes (default).
+
−.TP
+
−\fB\-sdfile\fR \fIsdfile.mnc\fR
+
−Specify the name of an output standard deviation file, to be
+
−calculated in addition the mean that is normally calculated.
+
−.TP
+
−\fB\-copy_header\fR
+
−Copy all of the additional header information from the first input
+
−file (default for one input file).
+
−.TP
+
−\fB\-nocopy_header\fR
+
−Do not copy additional header information (default for many input files).
+
−.TP
+
−\fB\-avgdim\fR \fIdimname\fR
+
−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.
+
−.TP
+
−\fB\-binarize\fR
+
−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.
+
−.TP
+
−\fB\-binrange\fR \fImin max\fR
+
−Specify the range of values for binarization.
+
−.TP
+
−\fB\-binvalue\fR \fIvalue\fR
+
−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.
+
−.TP
+
−\fB\-weights\fR \fI<w1,w2,...>\fR
+
−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.
+
−.TP
+
−\fB\-width_weighted\fR
+
−This option can only be used when averaging across a dimension
+
−(\fB-avgdim\fR option). It specifies that weighting should be done using the
+
−width variable that corresponds to the averaging dimension. For
+
−example, using \fB\-width_weighted\fR with \fB\-avgdim\fR time will use the
+
−time-width variable to weight the values.
+
−
+
−.SH Generic options for all commands:
+
−.TP
+
−\fB-help\fR
+
−Print summary of command-line options and exit.
+
−.TP
+
−\fB\-version\fR
+
−Print the program's version number and exit.
+
−
+
−.SH AUTHOR
+
−Peter Neelin
+
−
+
−.SH COPYRIGHTS
+
−Copyright \(co 1995 by Peter Neelin
+
− 
+
−