Mercurial > hg > minc-tools
annotate README @ 2506:26b834cf2953
* removed GETTING_STARTED
* updated ancient history in README and INSTALL.minc
| author | rotor <rotor> |
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| date | Sat, 27 Mar 2010 15:42:09 +0000 |
| parents | e9f228e8ee85 |
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1 MINC - Medical Image NetCDF |
| 865 | 2 |
| 3 INTRODUCTION | |
| 4 ------------ | |
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5 The MINC file format is a highly flexible medical image file format |
| 2506 | 6 built on the HDF5 generalized data format. The format is |
| 865 | 7 simple, self-describing, extensible, portable and N-dimensional, with |
| 8 programming interfaces for both low-level data access and high-level | |
| 9 volume manipulation. On top of the libraries is a suite of generic | |
| 10 image-file manipulation tools. The format, libraries and tools are | |
| 11 designed for use in a medical-imaging research environment : they are | |
| 12 simple and powerful and make no attempt to provide a pretty interface | |
| 13 to users. | |
| 14 | |
| 15 Here's a list of some of the tools: | |
| 393 | 16 |
| 865 | 17 * rawtominc, minctoraw, mincextract - format conversion |
| 1581 | 18 * mincheader, mincdiff, mincinfo, minchistory - file information |
| 19 * mincedit, minc_modify_header - header manipulation | |
| 865 | 20 * mincresample - arbitrary volume resampling |
| 21 * mincreshape - extraction of volume sub-cubes, image flipping, | |
| 22 dimension re-ordering, type conversion | |
| 23 * mincconcat - concatenating or interleaving images from multiple | |
| 24 files | |
| 25 * mincmath - perform simple math on files | |
| 1455 | 26 * minccalc - perform more complicated math on files through an expression |
| 865 | 27 * mincaverage - average minc files |
| 1455 | 28 * mincstats - calculate statistics across voxels of a file |
| 865 | 29 * minclookup - lookup table operations for arbitrary re-mappings of |
| 30 intensities | |
| 31 * worldtovoxel, voxeltoworld - coordinate conversion | |
| 32 * xfmconcat, xfminvert - generalized transformation utilities | |
| 33 * mincview - simple image display using xv or ImageMagick | |
| 1581 | 34 * mincpik - generate picture from slice through volume |
| 35 | |
| 393 | 36 |
| 865 | 37 Additional tools are available from the Montreal Neurological |
| 38 Institute (MNI). These include register, a program designed for | |
| 39 manual, landmark-based volume registration using a tri-plane interface | |
| 40 that allows the user to roam simultaneously through two data volumes | |
| 41 plus the combined volume that overlays the data of the other two. Emma | |
| 42 is a minc interface to matlab (from The MathWorks) with functions to | |
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43 facilitate image processing and display. mni_autoreg provides automated |
| 1519 | 44 registration, both linear and nonlinear. |
| 45 | |
| 865 | 46 |
| 47 GETTING MINC | |
| 48 ------------ | |
| 1581 | 49 The minc package is available from |
| 1023 | 50 |
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51 http://packages.bic.mni.mcgill.ca/tgz |
| 865 | 52 |
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53 Minc requires that the NetCDF and HDF5 packages be built and installed first. |
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54 It is available from the Unidata Program centre at |
| 865 | 55 the University Corporation for Atmospheric Research (unidata.ucar.edu). |
| 393 | 56 |
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57 |
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58 SUPPORT FOR HDF5 "MINC 2.0" FORMAT FILES |
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59 ---------------------------------------- |
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60 |
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61 1.1 HDF5 |
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62 |
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63 This change requires that HDF5 must be installed before MINC can be |
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64 built. The latest version of HDF5 is 1.6.2. You can obtain HDF5 |
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65 here: |
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66 |
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67 http://hdf.ncsa.uiuc.edu/HDF5/release/obtain5.html |
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68 |
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69 You should NOT need to become an HDF5 expert to use MINC 2.0. |
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70 However, two tools included with HDF5 may prove useful, "h5dump" and |
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71 "h5ls". h5dump is roughly equivalent to netCDF's ncdump utility. |
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72 There is no exact netCDF tool analogous to h5ls. h5ls is useful for |
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73 exploring and extracting bits of the HDF5 hierarchy. |
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74 |
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75 1.2 New command Line options |
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76 |
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77 All MINC tools which produce output MINC files now take a "-2" option |
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78 which will tell the tool to output a MINC 2.0 format file. All MINC tools |
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79 also take a "-version" flag. |
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80 |
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81 1.3 Compatibility |
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82 |
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83 To the extent possible, the core MINC tools should operate "correctly" |
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84 on MINC 1.0 and 2.0 files. There are a few notable exceptions. |
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85 Scripts such as "mincdiff", "mincedit", and "mincheader" may not |
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86 work, or will produce odd results since they depend on the ASCII |
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87 format of the netCDF "ncdump" and "ncgen" utility. I'm open to |
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88 suggestions for the best way to handle this. We have an unfinished |
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89 "mincdump" tool which replaces "ncdump", but we do not yet have a |
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90 replacement for "ncgen". |
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91 |
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92 1.4 Conversion |
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93 |
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94 There is a new conversion utility called "mincconvert". This is just |
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95 a trivial library wrapper that can copy a file from the input to the |
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96 output while performing a conversion. |
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97 |
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98 2. REVISED ERROR MESSAGE HANDLING. |
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99 |
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100 I have somewhat revised the ways in which MINC decides when and how to |
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101 print error messages, with the hope to gradually improve the readability |
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102 and usefulness of these messages. In some cases I have probably been too |
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103 aggressive, and messages will now appear which really don't belong. Please |
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104 let me know which ones are most annoying, and I'll try to get rid of them. |
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105 |
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106 3. TENTATIVE ".mincrc" AND ENVIRONMENT VARIABLE SUPPORT |
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107 |
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108 I've implemented this as a way to control certain behaviors of the library |
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109 which are not readily available through other means. These variables may |
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110 be defined either in your environment, or in the .mincrc file in your |
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111 home directory. The value in the environment should override the one in |
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112 .mincrc. |
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113 |
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114 Here's what exists so far: |
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115 |
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116 # Force output files to MINC 2.0 format, regardless of the "-2" option. |
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117 # |
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118 MINC_FORCE_V2 = {1, 0} |
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119 |
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120 # Desired ZLIB compression level. Zero implies no compression, a value |
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121 # of 4 gives a good tradeoff of compression and performance. |
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122 # |
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123 MINC_COMPRESS = {0..9} |
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124 |
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125 # Desired HDF5 chunking dimension. This controls the size of the |
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126 # "hypercube" used by HDF5 to store the file. If set to zero, the |
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127 # file will not be stored in a chunked format, unless compression is |
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128 # enabled. The chunk size will automatically be reduced if it exceeds |
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129 # any actual dimension of the volume. If chunking is enabled |
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130 # automatically because of compression, the default chunk dimension is |
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131 # 32. |
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132 # |
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133 MINC_CHUNKING = {0..N} |
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134 |
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135 # Log file - path to the desirned output file for messages. The default |
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136 # is the standard error (stderr) stream. To redirect to standard output, |
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137 # set this variable to "stdout" or "-". Otherwise the variable is taken |
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138 # to be the path to the desired log file. If the path name begins with |
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139 # a '+' character, the log file should be appended rather than recreated. |
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140 # |
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141 MINC_LOGFILE = [+]<pathname>|stdout|- |
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142 |
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143 # Logging level. Not really useful yet, but intended to allow setting |
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144 # of 'verbosity' of messages. A value of zero would inhibit all but |
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145 # fatal messages, a value of 4 would allow debugging messages. |
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146 # |
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147 MINC_LOGLEVEL = 0-4 |
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148 |
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149 4. NEW PROGRAMMING INTERFACE |
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150 |
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151 4.1. New MINC 1.0 calls |
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152 |
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153 A couple of new things have been added to libminc: |
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154 |
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155 /* Returns a printable library version string */ |
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156 const char * miget_version(); |
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157 |
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158 /* Appends "new_history" to the file's history attribute. */ |
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159 int miappend_history(int fd, const char *new_history); |
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160 |
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161 4.2. New MINC 2.0 calls |
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162 |
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163 This is a new set of calls, defined in "minc2.h" and the assorted source |
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164 files found in the libsrc2 directory. |
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165 |
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166 The general philosophy is to provide a higher level interface than "libminc", |
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167 but without some of the constraints and memory management of "volume_io". |
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168 |
| 2506 | 169 |
| 170 DOCUMENTATION | |
| 171 ------------- | |
| 172 | |
| 173 http://en.wikibooks.org/wiki/MINC | |
| 174 | |
| 175 | |
| 176 PROGRAMMING WITH THE MINC API | |
| 177 ----------------------------- | |
| 178 | |
| 179 1) NetCDF and HDF5 are basis, providing a C callable | |
| 180 library for accessing data structures in a file at a low-level. | |
| 181 | |
| 182 2) The low-level MINC library is used to do medical-image specific | |
| 183 things. It provides some enhancements to NetCDF and HDF5 | |
| 184 as well as image conversion routines for dealing with image pixel | |
| 185 value issues as well as image size and orientation. Documentation | |
| 186 consists of a programmer's guide and reference (minc_user.tex and | |
| 187 minc_reference.tex in the doc directory). Example C programs exist | |
| 188 in progs/mincexample. | |
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189 |
| 2506 | 190 3) A high-level C library called volume_io provides a Volume data |
| 191 type, with functions like input_volume to give simple access to data | |
| 192 while handling issues of pixel range conversion and voxel-to-world | |
| 193 coordinate conversion. Documentation consists of a programmer's | |
| 194 reference volume_io/Documentation/volume_io.tex. Example programs | |
| 195 exist in volume_io/Testing. | |
| 196 | |
| 197 The LaTeX documentation is not built by default. You can build these | |
| 198 documents using | |
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199 |
| 2506 | 200 cd doc; make docs |
| 201 cd volume_io/Documentation; make docs | |
| 202 | |
| 203 latex and dvips are required. | |
| 204 | |
| 205 | |
| 206 Applications that use MINC alone need to #include <minc.h> and | |
| 207 link with "-lminc2 -lnetcdf -lhdf5 -lz -lm". | |
| 208 | |
| 209 Applications built with VolumeIO need to #include <volume_io.h> | |
| 210 and link with "-lvolume_io2 -lminc2 -lnetcdf -lhdf5 -lz -lm". | |
| 211 | |
| 212 |