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Revised man pages
author bert <bert>
date Thu, 20 May 2004 21:52:07 +0000
parents 8c04b124e8e0
children
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1 .\" Hey, EMACS: -*- nroff -*-
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2 .\" Copyright 1995 Peter Neelin, McConnell Brain Imaging Centre,
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3 .\" Montreal Neurological Institute, McGill University.
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4 .\" Permission to use, copy, modify, and distribute this
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5 .\" software and its documentation for any purpose and without
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6 .\" fee is hereby granted, provided that the above copyright
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7 .\" notice appear in all copies. The author and McGill University
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8 .\" make no representations about the suitability of this
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9 .\" software for any purpose. It is provided "as is" without
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10 .\" express or implied warranty.
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11 .\"
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12 .\" $Header: /private-cvsroot/minc/progs/mincaverage/mincaverage.man1,v 6.3 2004-05-20 21:52:07 bert Exp $
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13 .\"
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14 .TH MINCAVERAGE 1 "$Date: 2004-05-20 21:52:07 $" "" "MINC User's Guide"
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15
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16 .SH NAME
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17 mincaverage - average minc files
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18
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19 .SH SYNOPSIS
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20 .B mincaverage
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21 [<options>] <in1>.mnc [<in2>.mnc...] <out>.mnc
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22
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23 .SH DESCRIPTION
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24 \fIMincaverage\fR averages minc files together. A range of optional
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25 behaviour is permitted as well: pre-normalizing volumes, creating a
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26 standard deviation volume, averaging over a specified dimension of the
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27 input files.
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28
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29 .SH OPTIONS
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30 Note that options can be specified in abbreviated form (as long as
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31 they are unique) and can be given anywhere on the command line.
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32
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33 .SH General options
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34 .TP
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35 \fB\-2\fR
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36 Create a MINC 2.0 format output file.
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37 .TP
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38 \fB\-clobber\fR
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39 Overwrite an existing file.
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40 .TP
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41 \fB\-noclobber\fR
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42 Don't overwrite an existing file (default).
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43 .TP
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44 \fB\-verbose\fR
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45 Print out progress information for each chunk of data copied (default).
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46 .TP
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47 \fB\-quiet\fR
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48 Do not print out progress information.
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49 .TP
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50 \fB\-debug\fR
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51 Print extra information (e.g. normalization factors).
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52 .TP
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53 \fB\-filelist\fR \fIfilename\fR
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54 Specify a file containing a list of input file names. If "-" is given, then
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55 file names are read from stdin. If this option is given, then there should be
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56 no input file names specified on the command line. Empty lines in the input
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57 file are ignored.
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58 .TP
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59 \fB\-max_buffer_size_in_kb\fR \fIbuffer-size\fR
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60 Specify the maximum size of the internal buffers (in kbytes). Default is
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61 4096 kbytes.
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62
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63 .SH Output type options
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64 These options control the storage precision and size of individual voxel
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65 values in the output file.
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66 .TP
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67 \fB-filetype\fR
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68 Don't do any type conversion (default).
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69 .TP
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70 \fB\-byte\fR
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71 Write out 8-bit integer values.
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72 .TP
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73 \fB\-short\fR
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74 Write out 16-bit integer values.
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75 .TP
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76 \fB-int\fR
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77 Write out 32-bit integer values.
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78 .TP
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79 \fB\-long\fR
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80 Superseded by -int.
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81 .TP
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82 \fB\-float\fR
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83 Write out single-precision floating point values.
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84 .TP
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85 \fB\-double\fR
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86 Write out double-precision floating point values.
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87 .P
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88 \fB\-signed\fR
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89 Write out values as signed integers (default for short and long). Ignored for
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90 floating point types.
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91 .TP
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92 \fB\-unsigned\fR
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93 Write out values as unsigned integers (default for byte). Ignored for
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94 floating point types.
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95 .TP
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96 \fB\-range\fR \fImin max\fR
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97 specifies the valid range of output voxel values in their integer
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98 representation. Default is the full range
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99 for the type and sign. This option is ignored for floating point
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100 values. For it to have any effect, you must specify a type.
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101
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102 .SH Averaging options
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103 .TP
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104 \fB\-normalize\fR
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105 Normalize volumes to their global average before averaging them (based
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106 on the mean of voxels with value greater than 2 percent of full range
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107 above the minimum).
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108 .TP
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109 \fB\-nonormalize\fR
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110 Do not normalize volumes (default).
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111 .TP
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112 \fB\-sdfile\fR \fIsdfile.mnc\fR
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113 Specify the name of an output standard deviation file, to be
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114 calculated in addition the mean that is normally calculated.
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115 .TP
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116 \fB\-copy_header\fR
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117 Copy all of the additional header information from the first input
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118 file (default for one input file).
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119 .TP
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120 \fB\-nocopy_header\fR
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121 Do not copy additional header information (default for many input files).
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122 .TP
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123 \fB\-avgdim\fR \fIdimname\fR
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124 Specify the name of a dimension over which we should be averaging (or
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125 calculating standard deviation). If normalization is done, it still
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126 only applies to separate files only - no normalization is done within
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127 a file.
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128 .TP
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129 \fB\-binarize\fR
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130 Binarize the input volumes before calculating the average. The
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131 binarization is done by specifying a range of values that contribute 1
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132 to the average. Normalization of the input is not permitted when
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133 performing binarization.
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134 .TP
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135 \fB\-binrange\fR \fImin max\fR
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136 Specify the range of values for binarization.
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137 .TP
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138 \fB\-binvalue\fR \fIvalue\fR
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139 Specify a single legal value (integer) for binarization. The range is
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140 set to be +/- 0.5 around this value to achieve an effective rounding
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141 of input values.
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142 .TP
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143 \fB\-weights\fR \fI<w1,w2,...>\fR
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144 Specify a series of weights for averaging. The number of weighting
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145 values must match the number of input files and the values must be
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146 provided as a single argument with commas or spaces as
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147 separators. The sum of the weights must be non-zero. If weights are
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148 used with an averaging dimension, then only one input file can be
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149 specified.
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150 .TP
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151 \fB\-width_weighted\fR
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152 This option can only be used when averaging across a dimension
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153 (\fB-avgdim\fR option). It specifies that weighting should be done using the
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154 width variable that corresponds to the averaging dimension. For
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155 example, using \fB\-width_weighted\fR with \fB\-avgdim\fR time will use the
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156 time-width variable to weight the values.
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157
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158 .SH Generic options for all commands:
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159 .TP
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160 \fB-help\fR
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161 Print summary of command-line options and exit.
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162 .TP
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163 \fB\-version\fR
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164 Print the program's version number and exit.
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165
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166 .SH AUTHOR
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167 Peter Neelin
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168
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169 .SH COPYRIGHTS
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170 Copyright \(co 1995 by Peter Neelin
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172