00001 static char * readme_env[] = {
00002 "Unix Environment Variables Used by AFNI\n" ,
00003 "=======================================\n" ,
00004 "The AFNI program allows you to use several Unix environment variables\n" ,
00005 "to influence its behavior. The mechanics of setting an environment\n" ,
00006 "variable depend on which shell you are using. To set an environment\n" ,
00007 "variable named \"FRED\" to the string \"Elvis\":\n" ,
00008 "\n" ,
00009 " csh or tcsh: setenv FRED Elvis\n" ,
00010 " bash or ksh: FRED=Elvis ; export FRED\n" ,
00011 "\n" ,
00012 "Normally, these commands would go in your .cshrc or .profile files,\n" ,
00013 "so that they would be invoked when you login. If in doubt, consult\n" ,
00014 "your local Unix guru. If you don't have one, well....\n" ,
00015 "\n" ,
00016 "You don't NEED to set any of these variables -- AFNI will still work\n" ,
00017 "correctly. But they are an easy way to set up certain defaults to\n" ,
00018 "make AFNI a little easier on your neocortex and hippocampus.\n" ,
00019 "\n" ,
00020 "N.B.: Changes to environment variables AFTER you start a program will\n" ,
00021 " not be seen by that program, since each running program gets\n" ,
00022 " a private copy of the entire set of environment variables when\n" ,
00023 " it starts. This is a standard Unix feature, and is not specific\n" ,
00024 " to AFNI. Some variables can be set internally in AFNI using\n" ,
00025 " the \"Edit Environment\" control from the \"Datamode->Misc\" menu\n" ,
00026 " or from the image window Button-3 popup menu. Such variables\n" ,
00027 " are marked with \"(editable)\" in the descriptions below.\n" ,
00028 "\n" ,
00029 "N.B.: Some variables below are described as being of \"YES/NO\" type.\n" ,
00030 " This means that they should either be set to the value \"YES\"\n" ,
00031 " or to the value \"NO\".\n" ,
00032 "\n" ,
00033 "N.B.: You can now set environment variables on the 'afni' command\n" ,
00034 " line; for example:\n" ,
00035 " afni -DAFNI_EDGIZE_OVERLAY=YES -DAFNI_SESSTRAIL=3\n" ,
00036 " This may be useful for a 'one time' situation, or as an alias.\n" ,
00037 " -- RWCox - 22 Mar 2005\n" ,
00038 "\n" ,
00039 "N.B.: At the end of this file is a list of several environment variables\n" ,
00040 " that affect the program 3dDeconvolve, rather than the interactive\n" ,
00041 " AFNI program itself.\n" ,
00042 "\n" ,
00043 "********************************************************\n" ,
00044 "June 1999: Setting environment variables in file .afnirc\n" ,
00045 "********************************************************\n" ,
00046 "You can now set environment variables for an interactive AFNI run in the\n" ,
00047 "setup (.afnirc) file. This is provided as a convenience. An example:\n" ,
00048 "\n" ,
00049 "***ENVIRONMENT\n" ,
00050 " AFNI_HINTS = YES\n" ,
00051 " AFNI_SESSTRAIL = 3\n" ,
00052 "\n" ,
00053 "Note that the spaces around the \"=\" sign are required. See README.setup\n" ,
00054 "for more information about the possible contents of .afnirc besides the\n" ,
00055 "environment variables.\n" ,
00056 "\n" ,
00057 "A few other programs in the AFNI package also read the ***ENVIRONMENT\n" ,
00058 "section of the .afnirc file. This is needed so that environment settings\n" ,
00059 "that affect those programs (e.g., AFNI_COMPRESSOR for auto-compression of\n" ,
00060 "output datasets) can be properly initialized in .afnirc.\n" ,
00061 "\n" ,
00062 "At the same time, the routine in AFNI that initializes certain internal\n" ,
00063 "constants from X11 resources (usually in your .Xdefaults or .Xresources\n" ,
00064 "file, and described in file AFNI.Xdefaults) has been modified to also\n" ,
00065 "allow the same constants to be set from Unix environment variables.\n" ,
00066 "For example, the gap (in pixels) between sub-graphs is set by the\n" ,
00067 "X11 resource \"AFNI*graph_ggap\", and can now be set by the environment\n" ,
00068 "variables \"AFNI_graph_ggap\" or \"AFNI_GRAPH_GGAP\", as in\n" ,
00069 "\n" ,
00070 " AFNI_graph_ggap = 6 // this is a comment\n" ,
00071 "\n" ,
00072 "If an X11 resource is actually set, it will take priority over the\n" ,
00073 "environment variable. Some of the variables that can be set in this\n" ,
00074 "way are:\n" ,
00075 "\n" ,
00076 " AFNI_ncolors = number of gray levels to use\n" ,
00077 " AFNI_gamma = gamma correction for image intensities\n" ,
00078 " AFNI_graph_boxes_thick = 0=thin lines, 1=thick lines, for graph boxes\n" ,
00079 " AFNI_graph_grid_thick = ditto for the graph vertical grid lines\n" ,
00080 " AFNI_graph_data_thick = ditto for the data graphs\n" ,
00081 " AFNI_graph_ideal_thick = ditto for the ideal graphs\n" ,
00082 " AFNI_graph_ort_thick = ditto for the ort graphs\n" ,
00083 " AFNI_graph_dplot_thick = ditto for the dplot graphs\n" ,
00084 " AFNI_graph_ggap = initial spacing between graph boxes\n" ,
00085 " AFNI_graph_matrix = initial number of sub-graphs\n" ,
00086 " AFNI_fim_polort = polynomial detrending order for FIM\n" ,
00087 " AFNI_fim_ignore = how many pts to ignore at start when doing FIM\n" ,
00088 " AFNI_montage_periodic = True allows periodic montage wraparound\n" ,
00089 " AFNI_purge = True allows automatic dataset memory purge\n" ,
00090 " AFNI_resam_vox = dimension of voxel (mm) for resampled datasets\n" ,
00091 " AFNI_resam_anat = One of NN, Li, Cu, Bk for Anat resampling mode\n" ,
00092 " AFNI_resam_func = ditto for Func resampling mode\n" ,
00093 " AFNI_resam_thr = ditto for Threshold resampling mode\n" ,
00094 " AFNI_pbar_posfunc = True will start color pbar as all positive\n" ,
00095 " AFNI_pbar_sgn_pane_count = # of panes to start signed color pbar with\n" ,
00096 " AFNI_pbar_pos_pane_count = # of panes to start positive color pbar with\n" ,
00097 "\n" ,
00098 "Some other such variables are described in file AFNI.Xdefaults. Note that\n" ,
00099 "values that actually affect the way the X11/Motif interface appears, such as\n" ,
00100 "AFNI*troughColor, must be set via the X11 mechanism and cannot be set using\n" ,
00101 "Unix environment variables. This is because they are interpreted by the\n" ,
00102 "Motif graphics library when it starts and not by any actual AFNI code.\n" ,
00103 "\n" ,
00104 "The following example is from my own .afnirc file on the Linux system on\n" ,
00105 "which I do most of the AFNI development. The first ones (in lower case)\n" ,
00106 "are described in AFNI.Xdefaults. The later ones (all upper case) are\n" ,
00107 "documented in this file. (You can tell from this file that I like to\n" ,
00108 "have things line up. You would never be able to tell this from the\n" ,
00109 "piles of paper in my office, though.)\n" ,
00110 "\n" ,
00111 " ***ENVIRONMENT\n" ,
00112 "\n" ,
00113 " AFNI_ncolors = 60 // number of gray levels\n" ,
00114 " AFNI_gamma = 1.5 // adjust for proper display\n" ,
00115 " AFNI_purge = True // purge datasets from memory when not used\n" ,
00116 " AFNI_chooser_doubleclick = Apply // like Apply button; could also be Set\n" ,
00117 " AFNI_chooser_listmax = 25 // max nonscrolling items in chooser lists\n" ,
00118 " AFNI_graph_width = 512 // initial width of graph window (pixels)\n" ,
00119 " AFNI_graph_height = 384 // initial height of graph window\n" ,
00120 " AFNI_graph_data_thick = 1 // graph time series with thick lines\n" ,
00121 " AFNI_fim_ignore = 2 // default value for FIM ignore\n" ,
00122 " AFNI_graph_ggap = 7 // gap between sub-graphs (pixels)\n" ,
00123 " AFNI_pbar_hide = True // hide color pbar when it changes size\n" ,
00124 " AFNI_hotcolor = Violet // color to use on Done and Set buttons\n" ,
00125 " AFNI_SESSTRAIL = 2 // see below for these ...\n" ,
00126 " AFNI_RENDER_ANGLE_DELTA = 4.0 // |\n" ,
00127 " AFNI_RENDER_CUTOUT_DELTA = 4.0 // |\n" ,
00128 " AFNI_FIM_BKTHR = 25.0 // |\n" ,
00129 " AFNI_SPLASHTIME = 3.0 // v\n" ,
00130 "\n" ,
00131 "---------------------\n" ,
00132 "Variable: AFNI_ORIENT (editable)\n" ,
00133 "---------------------\n" ,
00134 "This is a string used to control the display of coordinates in the AFNI\n" ,
00135 "main control window. The string must be 3 letters, one each from the\n" ,
00136 "pairs {R,L} {A,P} {I,S}. The first letter in the string gives the\n" ,
00137 "orientation of the x-axis, the second the orientation of the y-axis,\n" ,
00138 "the third the z-axis:\n" ,
00139 "\n" ,
00140 " R = right-to-left L = left-to-right\n" ,
00141 " A = anterior-to-posterior P = posterior-to-anterior\n" ,
00142 " I = inferior-to-superior S = superior-to-inferior\n" ,
00143 "\n" ,
00144 "If AFNI_ORIENT is undefined, the default is RAI. This is the order\n" ,
00145 "used by DICOM, and means\n" ,
00146 "\n" ,
00147 " the -x axis is Right, the +x axis is Left,\n" ,
00148 " the -y axis is Anterior, the +y axis is Posterior,\n" ,
00149 " the -z axis is Inferior, the +z axis is Superior.\n" ,
00150 "\n" ,
00151 "As a special case, using the code 'flipped' is equivalent to 'LPI',\n" ,
00152 "which is the orientation used in many neuroscience journals.\n" ,
00153 "\n" ,
00154 "This variable is also recognized by program 3dclust, which will report\n" ,
00155 "the cluster coordinates in the (x,y,z) order given by AFNI_ORIENT.\n" ,
00156 "Both AFNI and 3dclust also recognize the command line switch\n" ,
00157 "\"-orient string\", where string is a 3 letter code that can be used\n" ,
00158 "to override the value of AFNI_ORIENT.\n" ,
00159 "\n" ,
00160 "The plugin \"Coord Order\" (plug_coord.c) allows you to interactively\n" ,
00161 "change the orientation of the variable display within AFNI.\n" ,
00162 "\n" ,
00163 "-------------------------\n" ,
00164 "Variable: AFNI_PLUGINPATH\n" ,
00165 "-------------------------\n" ,
00166 "This variable should be the directory in which AFNI should search\n" ,
00167 "for plugins. If there is more than one appropriate directory, they\n" ,
00168 "can be separated by colons, as in\n" ,
00169 "\n" ,
00170 " setenv AFNI_PLUGINPATH /directory/one:/directory/two\n" ,
00171 "\n" ,
00172 "If this variable is not set, then AFNI will use the PATH variable\n" ,
00173 "instead. This will waste time, since most directories in the PATH\n" ,
00174 "will not have plugins. On some systems, using the PATH has been\n" ,
00175 "known to cause problems when AFNI starts. I believe this is due to\n" ,
00176 "bugs in the system library routines (e.g., dlopen) used to manage\n" ,
00177 "dynamically loaded shared objects.\n" ,
00178 "\n" ,
00179 "------------------------\n" ,
00180 "Variable: AFNI_NOPLUGINS\n" ,
00181 "------------------------\n" ,
00182 "If this YES/NO variable is set to YES, then AFNI will not try to\n" ,
00183 "read plugins when it starts up. The command line switch \"-noplugins\"\n" ,
00184 "will have the same effect.\n" ,
00185 "\n" ,
00186 "--------------------------\n" ,
00187 "Variable: AFNI_YESPLUGOUTS\n" ,
00188 "--------------------------\n" ,
00189 "If this YES/NO variable is set to YES, then AFNI will try to listen\n" ,
00190 "for plugouts when it starts. The command line switch \"-yesplugouts\"\n" ,
00191 "will have the same effect. (Plugouts are an experimental feature\n" ,
00192 "that allow external programs to exchange data with AFNI.) It is now\n" ,
00193 "also possible to start plugout listening from the Datamode->Misc menu.\n" ,
00194 "\n" ,
00195 "---------------------\n" ,
00196 "Variable: AFNI_TSPATH\n" ,
00197 "---------------------\n" ,
00198 "This variable should be set to any directory which you want to have\n" ,
00199 "AFNI scan for timeseries files (*.1D -- see the AFNI manual). If\n" ,
00200 "more than one directory is desired, then colons can be used to\n" ,
00201 "separate them, as in AFNI_PLUGINPATH. Note that timeseries files\n" ,
00202 "are read from all session directories, so directories provided by\n" ,
00203 "AFNI_TSPATH are designed to contain extra timeseries files that\n" ,
00204 "you want loaded no matter what AFNI sessions and datasets are being\n" ,
00205 "viewed.\n" ,
00206 "\n" ,
00207 "------------------------\n" ,
00208 "Variable: AFNI_MODELPATH\n" ,
00209 "------------------------\n" ,
00210 "This variable should be set to the directory from which you want AFNI\n" ,
00211 "timeseries models to be loaded. These models are similar to plugins,\n" ,
00212 "and are used by programs 3dNLfim, 3dTSgen, and the plugin plug_nlfit\n" ,
00213 "(menu label \"NLfit & NLerr\") -- see documentation file 3dNLfim.ps.\n" ,
00214 "If AFNI_MODELPATH is not given, then AFNI_PLUGINPATH will be used\n" ,
00215 "instead.\n" ,
00216 "\n" ,
00217 "-----------------------------------------\n" ,
00218 "Variable: AFNI_IMSIZE_* (or MCW_IMSIZE_*)\n" ,
00219 "-----------------------------------------\n" ,
00220 "These variables (named AFNI_IMSIZE_1 to AFNI_IMSIZE_99) allow you\n" ,
00221 "to control how the AFNI programs read binary image files. The use of\n" ,
00222 "these is somewhat complicated, and is explained in detail at the end\n" ,
00223 "of the auxiliary programs manual (afni_aux.ps), in the section on \"3D:\"\n" ,
00224 "file specifications, and is also explained in the AFNI FAQ list.\n" ,
00225 "\n" ,
00226 "------------------------\n" ,
00227 "Variable: AFNI_SESSTRAIL (editable)\n" ,
00228 "------------------------\n" ,
00229 "This variable controls the number of directory levels shown when\n" ,
00230 "choosing between session directories with the \"Switch Session\"\n" ,
00231 "button. This variable should be set to a nonnegative integer.\n" ,
00232 "If a session directory name were\n" ,
00233 " this/is/a/directory/name/\n" ,
00234 "then the \"Switch Session\" chooser would display the following:\n" ,
00235 "\n" ,
00236 " AFNI_SESSTRAIL Display\n" ,
00237 " -------------- -------\n" ,
00238 " 0 name/\n" ,
00239 " 1 directory/name/\n" ,
00240 " 2 a/directory/name/\n" ,
00241 " 3 is/a/directory/name/\n" ,
00242 " 4 this/is/a/directory/name/\n" ,
00243 "\n" ,
00244 "That is, AFNI_SESSTRAIL determines how many trailing levels of\n" ,
00245 "the directory name are used for the display. If AFNI_SESSTRAIL\n" ,
00246 "is not set, then it is equivalent to setting it to 0 (which\n" ,
00247 "was the old method).\n" ,
00248 "\n" ,
00249 "--------------------\n" ,
00250 "Variable: AFNI_HINTS\n" ,
00251 "--------------------\n" ,
00252 "This is a string controlling whether or not the popup \"hints\" are\n" ,
00253 "displayed when AFNI starts. If the string is \"NO\", then the hints\n" ,
00254 "are disabled when AFNI starts, otherwise they are enabled. In\n" ,
00255 "either case, they can be turned off and on interactively from the\n" ,
00256 "Define Datamode->Misc menu.\n" ,
00257 "\n" ,
00258 "Hints can be permanently disabled by setting the C macro\n" ,
00259 "DONT_USE_HINTS in machdep.h and recompiling AFNI. They can also\n" ,
00260 "be disabled at runtime by setting AFNI_HINTS to \"KILL\".\n" ,
00261 "\n" ,
00262 "-------------------------\n" ,
00263 "Variable: AFNI_COMPRESSOR (cf. AFNI_AUTOGZIP) (editable)\n" ,
00264 "-------------------------\n" ,
00265 "This variable is used to control automatic compression of .BRIK files on\n" ,
00266 "output. The legal values are \"COMPRESS\", \"GZIP\", and \"BZIP2\", which\n" ,
00267 "respectively invoke programs \"compress\", \"gzip\", and \"bzip2\" (the program\n" ,
00268 "must be in your path for compression to work). If AFNI_COMPRESSOR is\n" ,
00269 "equal to one of these, then all AFNI programs will automatically pass\n" ,
00270 ".BRIK data through the appropriate compression program as it is written\n" ,
00271 "to disk. Note that this will slow down dataset write operations. Note\n" ,
00272 "also that compressed datasets cannot be mapped directly from disk into\n" ,
00273 "memory ('mmap'), but must occupy actual memory (RAM) and swap space. For\n" ,
00274 "more details, see file README.compression.\n" ,
00275 "\n" ,
00276 "Note that compressed (.BRIK.Z, .BRIK.gz, and .BRIK.bz2) datasets will\n" ,
00277 "automatically be uncompressed on input, no matter what the setting of\n" ,
00278 "this variable. AFNI_COMPRESSOR only controls how the datasets are\n" ,
00279 "written.\n" ,
00280 "\n" ,
00281 "------------------------\n" ,
00282 "Variable: AFNI_BYTEORDER\n" ,
00283 "------------------------\n" ,
00284 "This variable is used to control the byte order for output files.\n" ,
00285 "If you use it, the two legal values are \"LSB_FIRST\" and \"MSB_FIRST\".\n" ,
00286 "If you don't use it, the default order on your CPU will be used.\n" ,
00287 "The main purpose of this would be if you were using a mixture of\n" ,
00288 "CPU types reading shared disks (i.e., using NFS). If the majority\n" ,
00289 "of the systems were MSB_FIRST (e.g., SGI, HP, Sun), but there were\n" ,
00290 "a few LSB_FIRST systems (e.g., Intel, DEC Alpha), then you might\n" ,
00291 "want to do 'setenv AFNI_BYTEORDER MSB_FIRST' on all of the MSB_FIRST\n" ,
00292 "systems to make sure that the datasets that they write out are\n" ,
00293 "readable by the other computers.\n" ,
00294 "\n" ,
00295 "Note that AFNI programs can now check the .HEAD file for the byte\n" ,
00296 "order of a dataset, and will swap the bytes on input, if needed.\n" ,
00297 "If you wish to mark all of the datasets on a given system as\n" ,
00298 "being in a particular order, the following command should work:\n" ,
00299 "\n" ,
00300 " find /top/dir -name \\*.HEAD -exec 3drefit -byteorder NATIVE_ORDER {} \\;\n" ,
00301 "\n" ,
00302 "Here, '/top/dir' is the name of the top level directory under\n" ,
00303 "which you wish to search for AFNI datasets. The string NATIVE_ORDER\n" ,
00304 "means to set all datasets to the CPU default order, which is probably\n" ,
00305 "what you are using now. (You can use the program 'byteorder' to\n" ,
00306 "find out the native byte ordering of your CPU.)\n" ,
00307 "\n" ,
00308 "------------------------------\n" ,
00309 "Variable: AFNI_BYTEORDER_INPUT\n" ,
00310 "------------------------------\n" ,
00311 "This variable is used to control the byte order for input files.\n" ,
00312 "If you use it, the two legal values are \"LSB_FIRST\" and \"MSB_FIRST\".\n" ,
00313 "The value of this variable is only used for old datasets that do\n" ,
00314 "not have the byte order encoded in their headers. If this variable\n" ,
00315 "is not present, then the CPU native byte order is used. If this\n" ,
00316 "variable is present, and its value differs from the native byte\n" ,
00317 "order, then 2 byte dataset BRIKs (short) are 2-swapped (as in\n" ,
00318 "\"ab\" -> \"ba\") when they are read from disk, and 4 byte datasets\n" ,
00319 "(float, complex) are 4-swapped (\"abcd\" -> \"dcba\").\n" ,
00320 "\n" ,
00321 "[per the request of John Koger]\n" ,
00322 "\n" ,
00323 "---------------------\n" ,
00324 "Variable: AFNI_NOMMAP\n" ,
00325 "---------------------\n" ,
00326 "This YES/NO variable can be used to turn off the mmap feature by which\n" ,
00327 "AFNI can load datasets into memory using the map-file-to-memory\n" ,
00328 "functionality of Unix. (Dataset .BRIK files will only be mmap-ed if\n" ,
00329 "they are not compressed and are in the native byte order of the CPU.)\n" ,
00330 "On some systems, mmap doesn't seem to work very well (e.g., Linux kernel\n" ,
00331 "version 1.2.13). You can disable mmap by 'setenv AFNI_NOMMAP YES'.\n" ,
00332 "\n" ,
00333 "The penalty for disabling mmap is that all datasets must be loaded\n" ,
00334 "into actual RAM. AFNI does not have the ability to load a dataset\n" ,
00335 "only partially, so if a 20 Megabyte .BRIK file is accessed, all of\n" ,
00336 "it will be loaded into RAM. With mmap, the Unix operating system will\n" ,
00337 "decide how much of the file to load. In this way, it is possible to\n" ,
00338 "deal with more files than you have swap space on your computer\n" ,
00339 "(since .BRIK files are mmap-ed in readonly mode).\n" ,
00340 "\n" ,
00341 "The moral of the story: buy more memory, it's cheap. At the time\n" ,
00342 "I write this line [Aug 1998], I have a PC with 384 MB of RAM, and\n" ,
00343 "it is great to use with AFNI.\n" ,
00344 "\n" ,
00345 "[Feb 2004] I now have a Mac G5 with 8 GB of RAM, and it is even greater!\n" ,
00346 "\n" ,
00347 "----------------------\n" ,
00348 "Variable: AFNI_PSPRINT (editable)\n" ,
00349 "----------------------\n" ,
00350 "This variable is used to define a command that will print the\n" ,
00351 "standard input (stdin) to a PostScript printer. If it is defined,\n" ,
00352 "the \"->printer\" button on the timeseries \"Plot\" windows will work.\n" ,
00353 "For some Unix systems, the following should work:\n" ,
00354 " setenv AFNI_PSPRINT \"lp -\"\n" ,
00355 "For others, this may work\n" ,
00356 " setenv AFNI_PSPRINT \"lpr -\"\n" ,
00357 "It all depends on the printer software setup you have. To send the\n" ,
00358 "output into GhostView\n" ,
00359 " setenv AFNI_PSPRINT \"ghostview -landscape -\"\n" ,
00360 "\n" ,
00361 "In the (very far distant) future, other windows (e.g., image and graph\n" ,
00362 "displays) may get the ability to print to a PostScript file or printer.\n" ,
00363 "\n" ,
00364 "---------------------------\n" ,
00365 "Variable: AFNI_LEFT_IS_LEFT (editable)\n" ,
00366 "---------------------------\n" ,
00367 "Setting this YES/NO variable to YES tells AFNI to display images with\n" ,
00368 "the left side of the subject on the left side of the window. The default\n" ,
00369 "mode is to display the right side of the subject on the left side of\n" ,
00370 "the window - the radiology convention. This \"handedness\" can also be\n" ,
00371 "controlled with the \"-flipim\" and \"-noflipim\" command line options to AFNI.\n" ,
00372 "\n" ,
00373 "--------------------------\n" ,
00374 "Variable: AFNI_ALWAYS_LOCK\n" ,
00375 "--------------------------\n" ,
00376 "Setting this YES/NO variable to YES tells AFNI to start up with all\n" ,
00377 "the controller windows locked together. If you mostly use multiple\n" ,
00378 "controllers to view datasets in unison, then this will be useful.\n" ,
00379 "Notice that the Time Lock feature is not automatically enabled\n" ,
00380 "by this -- you must still actuate it manually from the Lock menu\n" ,
00381 "on the Define Datamode panel.\n" ,
00382 "\n" ,
00383 "------------------------\n" ,
00384 "Variables: AFNI_RENDER_* (editable)\n" ,
00385 "------------------------\n" ,
00386 "These variables set some defaults in the \"Render Dataset\" (volume\n" ,
00387 "rendering) plugin. The first two variables are\n" ,
00388 "\n" ,
00389 " AFNI_RENDER_ANGLE_DELTA = stepsize for viewing angles, in degrees\n" ,
00390 " AFNI_RENDER_CUTOUT_DELTA = stepsize for cutout dimensions, in mm\n" ,
00391 "\n" ,
00392 "These stepsizes control how much the control parameters change when\n" ,
00393 "one of their up- or down-arrows is pressed. Both of these stepsize\n" ,
00394 "values default to 5.0.\n" ,
00395 "\n" ,
00396 "The third variable is\n" ,
00397 "\n" ,
00398 " AFNI_RENDER_PRECALC_MODE = \"Low\", \"Medium\", or \"High\"\n" ,
00399 "\n" ,
00400 "This is used to set the initial precalculation mode for the renderer\n" ,
00401 "(this mode can be altered interactively, unlike the stepsizes).\n" ,
00402 "\n" ,
00403 "The fourth variable is\n" ,
00404 "\n" ,
00405 " AFNI_RENDER_SHOWTHRU_FAC = some number between 0.0 and 1.0\n" ,
00406 "\n" ,
00407 "This is used to control the way in which the \"ShowThru\" Color Opacity\n" ,
00408 "option renders images. See the rendering plugin Help window for more\n" ,
00409 "information.\n" ,
00410 "\n" ,
00411 "-------------------------\n" ,
00412 "Variable: AFNI_NOREALPATH\n" ,
00413 "-------------------------\n" ,
00414 "Normally, when AFNI reads a list of session directories, it converts\n" ,
00415 "their names to the \"real path\" form, which follows symbolic links, and\n" ,
00416 "removes '/./' and '/../' components. These converted names are used\n" ,
00417 "for display purposes in the \"Switch Session\" chooser and in other\n" ,
00418 "places. If you wish to have the names NOT converted to the \"real path\"\n" ,
00419 "format, set this YES/NO environment variable to YES, as in\n" ,
00420 "\n" ,
00421 " setenv AFNI_NOREALPATH YES\n" ,
00422 "\n" ,
00423 "(For more information on the \"real path\" conversion, see the Unix\n" ,
00424 "man page for the realpath() function.) Note that if you use this\n" ,
00425 "feature, then the effect of AFNI_SESSTRAIL will be limited to what\n" ,
00426 "you type on the command line, since it is the realpath() function\n" ,
00427 "that provides the higher level hierarchies of the session names.\n" ,
00428 "\n" ,
00429 "----------------------------\n" ,
00430 "Variable: AFNI_NO_MCW_MALLOC\n" ,
00431 "----------------------------\n" ,
00432 "AFNI uses a set of \"wrapper\" macros and functions to let itself keep\n" ,
00433 "track of the memory allocated and freed by the C malloc() library.\n" ,
00434 "This is useful for debugging purposes (see the last items on the 'Misc'\n" ,
00435 "menu in the AFNI 'Define Datamode' control panel), but carries a small\n" ,
00436 "overhead (both in memory and speed). Setting this YES/NO environment\n" ,
00437 "variable to YES provides one way to disable this facility, as in\n" ,
00438 "\n" ,
00439 " setenv AFNI_NO_MCW_MALLOC YES\n" ,
00440 "\n" ,
00441 "Another way to permanently disable this capability (so that it isn't\n" ,
00442 "even compiled) is outlined in the file machdep.h. Also, the interactive\n" ,
00443 "AFNI program takes the command line switch \"-nomall\", which will turn\n" ,
00444 "off these functions for the given run.\n" ,
00445 "\n" ,
00446 "N.B.: Setting this variable in the .afnirc file will have no effect,\n" ,
00447 " since the decision whether to use the routines in mcw_malloc.c\n" ,
00448 " is made at the very start of the program, before .afnirc is\n" ,
00449 " scanned. Therefore, to use this variable, you must set it\n" ,
00450 " externally, perhaps in your .cshrc or .profile initialization\n" ,
00451 " file.\n" ,
00452 "\n" ,
00453 "------------------------\n" ,
00454 "Variable: AFNI_FIM_BKTHR\n" ,
00455 "------------------------\n" ,
00456 "This sets the threshold for the elimination of the background voxels\n" ,
00457 "during the interactive FIM calculations. The average intensity of\n" ,
00458 "all voxels in the first 3D volume used in the correlation is calculated.\n" ,
00459 "Voxels with intensity below 0.01 * AFNI_FIM_BKTHR * (this average)\n" ,
00460 "will not have the correlation computed. The default value is 10.0, but\n" ,
00461 "values as large as 50.0 may be useful. This parameter may be changed\n" ,
00462 "interactively from the FIM->Edit Ideal submenu in a graph viewer.\n" ,
00463 "\n" ,
00464 "------------------------\n" ,
00465 "Variable: AFNI_FLOATSCAN (editable)\n" ,
00466 "------------------------\n" ,
00467 "If this YES/NO variable is set to YES, then floating point bricks\n" ,
00468 "are checked for illegal values (NaN and Infinity) when they are\n" ,
00469 "read into an AFNI program -- illegal values will be replaced by\n" ,
00470 "zeros. If a dataset brick contains such illegal values that go\n" ,
00471 "undetected, AFNI programs will probably fail miserably, and have\n" ,
00472 "been known to go into nearly-infinite loops.\n" ,
00473 "\n" ,
00474 "Setting this variable implies setting AFNI_NOMMAP to YES, since\n" ,
00475 "only in-memory bricks can be altered (mmap-ed bricks are readonly).\n" ,
00476 "\n" ,
00477 "The command line program 'float_scan' can be used to check and\n" ,
00478 "patch floating point files.\n" ,
00479 "\n" ,
00480 "[14 Sep 1999] The program to3d will scan input float and complex\n" ,
00481 "files for illegal values, and patch illegal input numbers with\n" ,
00482 "zeros in the output dataset. If this behavior is not desired for\n" ,
00483 "some bizarre reason, the '-nofloatscan' command line option to\n" ,
00484 "to3d must be used.\n" ,
00485 "\n" ,
00486 "-----------------------\n" ,
00487 "Variable: AFNI_NOSPLASH\n" ,
00488 "-----------------------\n" ,
00489 "If this YES/NO variable is set to YES, then the AFNI splash screen\n" ,
00490 "will not be displayed when the program starts. I'm not sure WHY\n" ,
00491 "you would want to disable this thing of beauty (which is a joy\n" ,
00492 "forever), but if your soul is thusly degraded, so be it.\n" ,
00493 "\n" ,
00494 "------------------------\n" ,
00495 "Variable: AFNI_SPLASH_XY\n" ,
00496 "------------------------\n" ,
00497 "If set, this variable should be in the form \"100:37\" (two integers\n" ,
00498 "separated by a colon). These values specify the (x,y) screen location\n" ,
00499 "where the splash window's upper left corner will be placed. If not\n" ,
00500 "set, x will be set to center the splash window on the display and\n" ,
00501 "y will be 100.\n" ,
00502 "\n" ,
00503 "-------------------------\n" ,
00504 "Variable: AFNI_SPLASHTIME\n" ,
00505 "-------------------------\n" ,
00506 "The value of this variable determines how long the AFNI splash screen\n" ,
00507 "will stay popped up, in seconds (default value = 5.0). The splash\n" ,
00508 "screen will always stay up until the first AFNI controller window is\n" ,
00509 "ready for use. If the time from program start to this ready condition\n" ,
00510 "is less than AFNI_SPLASHTIME, the splash screen will stay up until\n" ,
00511 "AFNI_SPLASHTIME has elapsed; otherwise, the splash screen will be\n" ,
00512 "removed as soon as AFNI is ready to go. By setting AFNI_SPLASHTIME\n" ,
00513 "to 0.0, you can have the splash screen removed as soon as possible\n" ,
00514 "(and the fade-out feature will be disabled).\n" ,
00515 "\n" ,
00516 "--------------------------------\n" ,
00517 "Variable: AFNI_FIM_PERCENT_LIMIT (editable)\n" ,
00518 "--------------------------------\n" ,
00519 "This sets an upper limit on the % Change that the FIM+ computation\n" ,
00520 "will compute. For example\n" ,
00521 "\n" ,
00522 " setenv AFNI_FIM_PERCENT_LIMIT 50\n" ,
00523 "\n" ,
00524 "means that computed values over 50% will be set to 50%, and values\n" ,
00525 "below -50% will be set to -50%. This can be useful to avoid scaling\n" ,
00526 "problems that arise when some spurious voxels with tiny baselines have\n" ,
00527 "huge percent changes. This limit applies to all 3 possible percentages\n" ,
00528 "that FIM and FIM+ can compute: % from baseline, % from average, and\n" ,
00529 "% from top.\n" ,
00530 "\n" ,
00531 "---------------------------\n" ,
00532 "Variable: AFNI_NOTES_DLINES\n" ,
00533 "---------------------------\n" ,
00534 "This sets the upper limit on the number of lines displayed in the\n" ,
00535 "Notes plugin, for each note. If not present, the limit is 9 lines\n" ,
00536 "shown per note at once. To see a note longer than this limit, you'll\n" ,
00537 "have to use the vertical scrollbar.\n" ,
00538 "\n" ,
00539 "-----------------------\n" ,
00540 "Variable: AFNI_FIM_MASK\n" ,
00541 "-----------------------\n" ,
00542 "This chooses the default subset of values computed with the FIM+\n" ,
00543 "button in a graph window. The mask should be the sum of the desired\n" ,
00544 "values from this list:\n" ,
00545 "\n" ,
00546 " 1 = Fit Coef\n" ,
00547 " 2 = Best Index\n" ,
00548 " 4 = % Change\n" ,
00549 " 8 = Baseline\n" ,
00550 " 16 = Correlation\n" ,
00551 " 32 = % From Ave\n" ,
00552 " 64 = Average\n" ,
00553 " 128 = % From Top\n" ,
00554 " 256 = Topline\n" ,
00555 " 512 = Sigma Resid\n" ,
00556 "\n" ,
00557 "If you don't set this variable, the default mask is 23 = 1+2+4+16.\n" ,
00558 "\n" ,
00559 "-----------------------------------\n" ,
00560 "Variable: AFNI_NO_BYTEORDER_WARNING\n" ,
00561 "-----------------------------------\n" ,
00562 "If this YES/NO variable is set to YES, then AFNI program will not\n" ,
00563 "warn you when reading in a dataset that does not contain a byte\n" ,
00564 "order flag. The default is to issue such a warning. Only older\n" ,
00565 "versions of AFNI create datasets that don't have the byte order\n" ,
00566 "flag. (See also the variable AFNI_BYTEORDER, described far above.)\n" ,
00567 "The purpose of this warning is to alert you to possible problems\n" ,
00568 "when you move datasets between computers with different CPU types.\n" ,
00569 "\n" ,
00570 "--------------------------\n" ,
00571 "Variable: AFNI_PCOR_DENEPS\n" ,
00572 "--------------------------\n" ,
00573 "The correlation coefficient calculated in FIM is calculated as the\n" ,
00574 "ratio of two quantities. If the denominator is negative or zero,\n" ,
00575 "then this value is meaningless and may even cause the program to\n" ,
00576 "crash. Mathematically, the denominator cannot be zero or negative,\n" ,
00577 "but this could arise due to finite precision arithmetic on the computer\n" ,
00578 "(i.e., roundoff error accumulation). To avoid this problem, the routine\n" ,
00579 "that computes the correlation coefficient compares the denominator to a\n" ,
00580 "value (called DENEPS) - if the denominator is less than DENEPS, then\n" ,
00581 "the correlation coefficient for that voxel is set to zero.\n" ,
00582 "\n" ,
00583 "The denominator that is being computed is proportional to the variance\n" ,
00584 "of the time series. If the voxel time series data is very small, then\n" ,
00585 "the variance will be really small - so much so that the DENEPS test\n" ,
00586 "will be failed, even though it shouldn't be. This problem has arisen\n" ,
00587 "when people input time series whose typical value is 0.001 or smaller.\n" ,
00588 "It never occurred to me that people would input data this small to the\n" ,
00589 "AFNI FIM routines. To get around this difficulty, set this environment\n" ,
00590 "variable to a value for DENEPS; for example\n" ,
00591 " setenv AFNI_PCOR_DENEPS 0.0\n" ,
00592 "will turn off the checking entirely. Or you could do\n" ,
00593 " setenv AFNI_PCOR_DENEPS 1.e-10\n" ,
00594 "\n" ,
00595 "-----------------------------\n" ,
00596 "Variable: AFNI_ENFORCE_ASPECT (editable)\n" ,
00597 "-----------------------------\n" ,
00598 "Some Linux window managers do no enforce the aspect ratio (width to height\n" ,
00599 "proportion) request that the image display module makes. This means that\n" ,
00600 "image windows can become undesirably distorted when manually resized.\n" ,
00601 "Setting this YES/NO variable to YES will make AFNI itself enforce the\n" ,
00602 "aspect ratio whenever an image window is resized.\n" ,
00603 "\n" ,
00604 "----------------------------------------\n" ,
00605 "Variables: AFNI_<plug_filename>_butcolor\n" ,
00606 "----------------------------------------\n" ,
00607 "These variables (one for each AFNI plugin) let you set the menu button colors\n" ,
00608 "for the Plugins menu item. For example\n" ,
00609 " setenv AFNI_plug_power_butcolor red3\n" ,
00610 "will make the \"Power Spectrum\" button appear in a dark red color. The format\n" ,
00611 "of the variable is exemplified above: the <plug_filename> is replaced by the\n" ,
00612 "filename of the plugin (after removing the suffix). Note that it is possible\n" ,
00613 "for the plugin author to hardcode the menu button for his/her plugin, in\n" ,
00614 "which case the corresponding environment variable will have no effect.\n" ,
00615 "\n" ,
00616 "Colors are specified as described in file README.setup. If you are using\n" ,
00617 "an X11 PseudoColor visual, then you should be economical with color usage!\n" ,
00618 "\n" ,
00619 "The purpose of this feature is to let you highlight the plugins that you\n" ,
00620 "use most frequently. The size of the of plugin menu is growing, and it\n" ,
00621 "is easy to misplace what you most use in the list.\n" ,
00622 "\n" ,
00623 "-----------------------------\n" ,
00624 "Variable: AFNI_MARKERS_NOQUAL (editable)\n" ,
00625 "-----------------------------\n" ,
00626 "If this YES/NO variable is set to YES, then the interactive AFNI program\n" ,
00627 "behaves as if the \"-noqual\" command line option had been included. This\n" ,
00628 "feature was added at the request of Dr. Michael S. Beauchamp, who has a\n" ,
00629 "very rare neurological disorder called \"noqaulagnosia\".\n" ,
00630 "\n" ,
00631 "----------------------\n" ,
00632 "Variable: AFNI_OPTIONS\n" ,
00633 "----------------------\n" ,
00634 "In the spirit of the previous variable, this variable can be used to set\n" ,
00635 "up command line options that will always be passed to the interactive\n" ,
00636 "AFNI program. If more than one option is needed, then they should be\n" ,
00637 "separated by spaces, and the whole value of the variable will need to be\n" ,
00638 "placed in quotes. For example\n" ,
00639 "\n" ,
00640 " setenv AFNI_OPTIONS \"-noqual -ncolors 60\"\n" ,
00641 "\n" ,
00642 "Note that the AFNI command line option \"-nomall\" cannot be specified this\n" ,
00643 "way (cf. the discussion under variable AFNI_NO_MCW_MALLOC).\n" ,
00644 "\n" ,
00645 "------------------------------\n" ,
00646 "Variable: AFNI_NO_SIDES_LABELS (editable)\n" ,
00647 "------------------------------\n" ,
00648 "As of 01 Dec 1999, the interactive AFNI program now displays a label\n" ,
00649 "beneath each image window showing which side of the image is on the left\n" ,
00650 "edge of the window. This label is based on the anatomical directions\n" ,
00651 "encoded in the anatomical dataset .HEAD file, usually when to3d was used\n" ,
00652 "to create the file. If you do NOT want these labels displayed (why not?),\n" ,
00653 "set this YES/NO environment variable to YES.\n" ,
00654 "\n" ,
00655 "----------------------------------\n" ,
00656 "Variable: AFNI_NO_ADOPTION_WARNING\n" ,
00657 "----------------------------------\n" ,
00658 "AFNI now can print a warning when it forces a dataset to have an anatomy\n" ,
00659 "parent dataset (the \"forced adoption\" function). This happens when\n" ,
00660 "there a dataset does not have an anatomy parent encoded into its .HEAD\n" ,
00661 "file (either via to3d or 3drefit), and there is more than one anatomical\n" ,
00662 "dataset in the directory that has Talairach transformation markers\n" ,
00663 "attached. If you wish to enable this warning, set this YES/NO variable\n" ,
00664 "to NO. For more information on this subject, please see\n" ,
00665 " http://afni.nimh.nih.gov/afni/afni_faq.shtml#AnatParent .\n" ,
00666 "\n" ,
00667 "-----------------------------------\n" ,
00668 "Variable: AFNI_NO_NEGATIVES_WARNING\n" ,
00669 "-----------------------------------\n" ,
00670 "If this YES/NO variable is set to YES, then to3d will skip the usual\n" ,
00671 "warning that it pops up in a message window when it discovers negative\n" ,
00672 "values in the input short images. (The warning will still be printed\n" ,
00673 "to stdout.)\n" ,
00674 "\n" ,
00675 "----------------------\n" ,
00676 "Variable: AFNI_NO_XDBE\n" ,
00677 "----------------------\n" ,
00678 "If this YES/NO variable is set to YES, then the X11 Double Buffer\n" ,
00679 "Extension (XDBE) will not be used, even if the X11 server supports it.\n" ,
00680 "This is needed when the X11 server says that it supports it, but actually\n" ,
00681 "does not implement it correctly - this is a problem on the Xsgi server\n" ,
00682 "running under IRIX 6.5.3 on R4400 machines.\n" ,
00683 "\n" ,
00684 "------------------------------\n" ,
00685 "Variable: AFNI_VIEW_ANAT_BRICK (editable)\n" ,
00686 " AFNI_VIEW_FUNC_BRICK (editable)\n" ,
00687 "------------------------------\n" ,
00688 "One of the (very few) confusing parts of AFNI is the \"warp-on-demand\"\n" ,
00689 "viewing of transformed datasets (e.g., in the +tlrc coordinate system).\n" ,
00690 "This allows you to look at slices taken from transformed volumes without\n" ,
00691 "actually computing and storing the entire transformed dataset. This\n" ,
00692 "viewing mode is controlled by from the \"Define Datamode\" control panel.\n" ,
00693 "When an anatomical dataset has a +tlrc.BRIK file, then you can choose\n" ,
00694 "between \"View Anat Data Brick\" and \"Warp Anat on Demand\"; when there\n" ,
00695 "is no +tlrc.BRIK file for the dataset, then only \"Warp Anat on Demand\"\n" ,
00696 "is possible.\n" ,
00697 "\n" ,
00698 "If you switch the Talairach view when the current anat dataset does\n" ,
00699 "not have a +tlrc.BRIK file, then the \"Warp Anat on Demand\" mode will\n" ,
00700 "be turned on. If you then switch to a dataset that does have a\n" ,
00701 "+tlrc.BRIK file, \"Warp Anat on Demand\" will still be turned on,\n" ,
00702 "although the \"View Anat Data Brick\" option will be enabled.\n" ,
00703 "\n" ,
00704 "If you set the YES/NO variable AFNI_VIEW_ANAT_BRICK to YES,\n" ,
00705 "then \"View Anat Data Brick\" will be turned on whenever possible after\n" ,
00706 "switching datasets. Similarly, setting AFNI_VIEW_FUNC_BRICK to YES\n" ,
00707 "will engage \"View Func Data Brick\" whenever possible (when the BRIK\n" ,
00708 "file exists and its grid spacing matches the anatomical grid spacing).\n" ,
00709 "Note that switching any dataset (func or anat) triggers the same\n" ,
00710 "routine, and will set either or both \"View Brick\" modes on. When\n" ,
00711 "these environment variables are present, the only way to switch to\n" ,
00712 "\"Warp\" mode when \"View Brick\" mode is possible is to do it manually\n" ,
00713 "(by clicking on the toggle button) when you want this.\n" ,
00714 "\n" ,
00715 "When you use one of the drawing plugins (\"Draw Dataset\" or \"Gyrus Finder\"),\n" ,
00716 "you must operate directly on the dataset BRIK. For this reason, it is\n" ,
00717 "important to be in \"View Data Brick\" mode on these occasions. Setting\n" ,
00718 "these variables is one way to ensure that this will happen whenever\n" ,
00719 "possible.\n" ,
00720 "\n" ,
00721 "When AFNI is in \"Warp Anat on Demand\" mode, the word \"{warp}\" will\n" ,
00722 "appear in the windows' titlebars. This provides a reminder of the\n" ,
00723 "viewing mode you are using (warped from a brick, or data directly\n" ,
00724 "extracted from a brick), since the \"Define Datamode\" control panel\n" ,
00725 "will not always be open.\n" ,
00726 "\n" ,
00727 "08 Aug 2003: I have modified the way these variables are treated in\n" ,
00728 "AFNI so that they now default to the \"YES\" behavior. If you don't\n" ,
00729 "want this, you have to explicitly set them to \"NO\" from this day forth.\n" ,
00730 "\n" ,
00731 "----------------\n" ,
00732 "Variable: TMPDIR\n" ,
00733 "----------------\n" ,
00734 "This variable specifies the directory where temporary files are to be\n" ,
00735 "written. It is not unique to AFNI, but is used by many Unix programs.\n" ,
00736 "You must have permission to write into this directory. If you want to\n" ,
00737 "use the current directory, setting TMPDIR to \".\" would work. If TMPDIR\n" ,
00738 "is not defined, directory /tmp will be used. On some systems, this\n" ,
00739 "directory may not have enough space for the creation of large temporary\n" ,
00740 "datasets. On most Unix systems, you can tell the size of various disk\n" ,
00741 "partitions using a command like \"df -k\" (on HPUX, \"bdf\" works).\n" ,
00742 "\n" ,
00743 "----------------------------\n" ,
00744 "Variable: AFNI_GRAYSCALE_BOT\n" ,
00745 "----------------------------\n" ,
00746 "This variable sets the darkest level shown in a grayscale image window.\n" ,
00747 "The default value is 55 (a leftover from Andrzej Jesmanowicz). You can\n" ,
00748 "set this value to anything from 0 to 254.\n" ,
00749 "\n" ,
00750 "----------------------------\n" ,
00751 "Variable: AFNI_SYSTEM_AFNIRC\n" ,
00752 "----------------------------\n" ,
00753 "If this variable is set, it is the name of a file to be read like the\n" ,
00754 "user's .afnirc file (see README.setup). The purpose is to allow a\n" ,
00755 "system-wide setup file to be used. To do this, you would create such\n" ,
00756 "a file in a useful place - perhaps where you store the AFNI binaries.\n" ,
00757 "Then each user account should have the equivalent of\n" ,
00758 "\n" ,
00759 " setenv AFNI_SYSTEM_AFNIRC /place/where/setup/is/stored/.afnirc\n" ,
00760 "\n" ,
00761 "defined in its .cshrc (.bashrc, etc.) file. Note that it doesn't make\n" ,
00762 "sense to define this variable in the user's .afnirc file, since that\n" ,
00763 "file won't be read until AFTER this file is read. Also note that use\n" ,
00764 "of the -skip_afnirc option will cause both the system and user setup\n" ,
00765 "files to be skipped.\n" ,
00766 "\n" ,
00767 "------------------------\n" ,
00768 "Variable: AFNI_PBAR_IMXY (editable)\n" ,
00769 "------------------------\n" ,
00770 "This variable determines the size of the image saved when the\n" ,
00771 "\"Save to PPM\" button is selected for a color pbar. It should be\n" ,
00772 "in the format\n" ,
00773 " setenv AFNI_PBAR_IMXY 20x256\n" ,
00774 "which means to set the x-size (horizontal) to 20 pixels and the\n" ,
00775 "y-size (vertical) to 256 pixels. These values are the default,\n" ,
00776 "by the way.\n" ,
00777 "\n" ,
00778 "--------------------------\n" ,
00779 "Variable: AFNI_LAYOUT_FILE\n" ,
00780 "--------------------------\n" ,
00781 "If defined, this variable is the name of a file to read at startup\n" ,
00782 "to define the \"layout\" of AFNI windows at the program start. If\n" ,
00783 "this name starts with a '/' character, then it is an absolute path;\n" ,
00784 "otherwise, it is taken to be a path relative to the user's home\n" ,
00785 "directory ($HOME). If the AFNI command line switch \"-layout\" is\n" ,
00786 "used, it will override this specification.\n" ,
00787 "\n" ,
00788 "The simplest way to produce a layout file is to use the \"Save Layout\"\n" ,
00789 "button on the Datamode->Misc menu. You can then edit this file;\n" ,
00790 "the format should be fairly self-explanatory. The structure of the\n" ,
00791 "file is similar to the .afnirc file (cf. README.setup). In fact,\n" ,
00792 "the layout file can be included into .afnirc (since it is just another\n" ,
00793 "*** section) and then setting AFNI_LAYOUT_FILE = .afnirc in the\n" ,
00794 "***ENVIRONMENT section should work.\n" ,
00795 "\n" ,
00796 "A sample layout file:\n" ,
00797 "\n" ,
00798 "***LAYOUT\n" ,
00799 " A geom=+73+1106 // start controller A\n" ,
00800 " A.sagittalimage geom=320x320+59+159 ifrac=0.8 // and Sagittal image\n" ,
00801 " A.sagittalgraph geom=570x440+490+147 matrix=9 // and Sagittal graph\n" ,
00802 " B // start controller B\n" ,
00803 " B.plugin.ROI_Average // start a plugin\n" ,
00804 "\n" ,
00805 "Each window to be opened has a separate command line in this file.\n" ,
00806 "The \"geom=\" qualifiers specify the size and position of the windows.\n" ,
00807 "For images, \"ifrac=\" can be used to specify the fraction of the window\n" ,
00808 "occupied by the image (if \"ifrac=1.0\", then no control widgets will be\n" ,
00809 "visible). For graphs, \"matrix=\" can be used to control the initial\n" ,
00810 "number of sub-graphs displayed. For plugins, the label on the button\n" ,
00811 "that starts the plugin is used after the \".plugin.\" string (blanks\n" ,
00812 "should be filled with underscores \"_\"). In the example above, the last\n" ,
00813 "two windows to be opened do not have a \"geom=\" qualifier, so their\n" ,
00814 "placement will be chosen by the window manager.\n" ,
00815 "\n" ,
00816 "If you add \"slow\" after the \"***LAYOUT\", then each window operation\n" ,
00817 "will be paused for 1 second to let you watch the layout operations\n" ,
00818 "proceed gradually. Otherwise, they will be executed as fast as\n" ,
00819 "possible (which still may not be all that fast).\n" ,
00820 "\n" ,
00821 "Using layouts with a window manager that requires user placement\n" ,
00822 "of new windows (e.g., twm) is a futile and frustrating exercise.\n" ,
00823 "\n" ,
00824 "-------------------------\n" ,
00825 "Variable: AFNI_tsplotgeom\n" ,
00826 "-------------------------\n" ,
00827 "Related to the above, if you set this environment variable (in the\n" ,
00828 "***ENVIRONMENT section, not in the ***LAYOUT section), it is used\n" ,
00829 "to set the geometry of the plotting windows used for time series\n" ,
00830 "plots, histograms, etc. -- all the graphs except the dataset plots.\n" ,
00831 "Its format should be something like \"550x350\"; this example sets\n" ,
00832 "the width to 550 pixels and the height to 350 pixels. If you don't\n" ,
00833 "set this, the default is \"200x200\", which is quite small on a high\n" ,
00834 "resolution display.\n" ,
00835 "\n" ,
00836 "--------------------------\n" ,
00837 "Variables: AFNI_REALTIME_*\n" ,
00838 "--------------------------\n" ,
00839 "This set of variables allows you to control the initial setup of the\n" ,
00840 "realtime data acquisition plugin (menu item \"RT Options\"). Normally,\n" ,
00841 "this plugin is active only if AFNI is started with the \"-rt\" command\n" ,
00842 "line option. (It will consume CPU time continually as it polls for\n" ,
00843 "an incoming data connection, which is why you don't want it running\n" ,
00844 "by default.) The following variables can be used to initialize the\n" ,
00845 "plugin's options:\n" ,
00846 "\n" ,
00847 "AFNI_REALTIME_Activate = This is a YES/NO variable, and allows you\n" ,
00848 " to have the realtime plugin active without\n" ,
00849 " using the \"-rt\" command line option. If\n" ,
00850 " this variable is set to YES, then you can\n" ,
00851 " disable the realtime plugin with \"-nort\".\n" ,
00852 "\n" ,
00853 "The variables below are used to set the initial status of the widgets\n" ,
00854 "in the realtime plugin's control window. Each one has the same name as\n" ,
00855 "the labels in the control window, with blanks replaced by underscores.\n" ,
00856 "The values to set for these variables are exact copies of the inputs\n" ,
00857 "you would specify interactively (again, with blanks replaced by\n" ,
00858 "underscores). For details as to the meaning of these options, see\n" ,
00859 "the plugin's Help window.\n" ,
00860 "\n" ,
00861 "AFNI_REALTIME_Images_Only = \"No\" or \"Yes\"\n" ,
00862 "AFNI_REALTIME_Root = name for datasets to be created\n" ,
00863 "AFNI_REALTIME_Update = an integer from 0 to 19\n" ,
00864 "AFNI_REALTIME_Function = \"None\" or \"FIM\" (cf. AFNI_FIM_IDEAL below)\n" ,
00865 "AFNI_REALTIME_Verbose = \"No\", \"Yes\", or \"Very\"\n" ,
00866 "AFNI_REALTIME_Registration = \"None\", \"2D:_realtime\", \"2D:_at_end\",\n" ,
00867 " \"3D:_realtime\", \"3D:_at_end\",\n" ,
00868 " or \"3D:_estimate\"\n" ,
00869 "AFNI_REALTIME_Base_Image = an integer from 0 to 59\n" ,
00870 "AFNI_REALTIME_Resampling = \"Cubic\", \"Quintic\", \"Heptic\", \"Fourier\",\n" ,
00871 " or \"Hept+Four\"\n" ,
00872 "AFNI_REALTIME_Graph = \"No\", \"Yes\", or \"Realtime\"\n" ,
00873 "AFNI_REALTIME_NR = an integer from 5 to 9999\n" ,
00874 "AFNI_REALTIME_YR = a floating point number from 0.1 to 10.0\n" ,
00875 "\n" ,
00876 "The following internal controls can only be set using these environment\n" ,
00877 "variables (there is no GUI to set these values):\n" ,
00878 "\n" ,
00879 "AFNI_REALTIME_volreg_maxite = an integer >= 1 [default = 9]\n" ,
00880 "AFNI_REALTIME_volreg_maxite_est = an integer >= 1 [default = 1]\n" ,
00881 "AFNI_REALTIME_volreg_graphgeom = something like 320x320+59+159\n" ,
00882 "\n" ,
00883 "AFNI_REALTIME_CHILDWAIT = max wait time (in sec) for child info\n" ,
00884 " process [default = 66.6]; not needed if\n" ,
00885 " child info process is not used\n" ,
00886 "\n" ,
00887 "AFNI_REALTIME_WRITEWAIT = if the image data pauses for this number\n" ,
00888 " of seconds, then the datasets being constructed\n" ,
00889 " will be written to disk [default=37.954];\n" ,
00890 " since this output may take several seconds,\n" ,
00891 " you may need to adjust this if you are in\n" ,
00892 " fact doing imaging with a very long TR.\n" ,
00893 " Note that after this wait, the plugin can\n" ,
00894 " still receive image data -- even if the image\n" ,
00895 " source program is silent for a very long time,\n" ,
00896 " AFNI will still be waiting patiently for data.\n" ,
00897 "\n" ,
00898 "AFNI_GRAPH_AUTOGRID = By default, if the number of time points in an\n" ,
00899 " AFNI graph viewer changes, the density of\n" ,
00900 " vertical grid lines changes. If you don't\n" ,
00901 " want this to happen, set this variable to NO.\n" ,
00902 "\n" ,
00903 "For more information about how the realtime plugin works, read the file\n" ,
00904 "README.realtime.\n" ,
00905 "\n" ,
00906 "------------------------\n" ,
00907 "Variable: AFNI_FIM_IDEAL\n" ,
00908 "------------------------\n" ,
00909 "This variable specifies the filename of the initial FIM ideal timeseries.\n" ,
00910 "The main use of this would be to be able to initialize the Realtime\n" ,
00911 "plugin without direct user intervention.\n" ,
00912 "\n" ,
00913 "----------------------------------\n" ,
00914 "Variable: AFNI_PLUGINS_ALPHABETIZE\n" ,
00915 "----------------------------------\n" ,
00916 "If this YES/NO variable is set to NO, then the plugin buttons will\n" ,
00917 "not be alphabetized on the menu, and they will appear in the\n" ,
00918 "order which AFNI chooses. Otherwise, the plugin menu buttons will\n" ,
00919 "be alphabetized by default. Alphabetizing is done without regard to\n" ,
00920 "case (using the C library routine strcasecmp).\n" ,
00921 "\n" ,
00922 "----------------------------\n" ,
00923 "Variable: AFNI_VOLREG_EDGING\n" ,
00924 "----------------------------\n" ,
00925 "This variable affects the operation of 3dvolreg, the volume registration\n" ,
00926 "plugin, and the 3D registration code in the realtime acquisition plugin.\n" ,
00927 "It determines the size of the region around the edges of the base volume\n" ,
00928 "where the default weight will be set to zero. Call the value of this\n" ,
00929 "variable 'ee'. If 'ee' is a plain number (e.g., 5), then it is a voxel\n" ,
00930 "count, giving the thickness along each face of the 3D brick. If 'ee' is\n" ,
00931 "of the form '5%', then it is a fraction of of each brick size. For\n" ,
00932 "example, '5%' of a 256x256x124 volume means that 13 voxels on each side\n" ,
00933 "of the xy-axes will get zero weight, and 6 along the z-axis. '5%' is\n" ,
00934 "the default value used by the 3D registration routines (in mri_3dalign.c)\n" ,
00935 "if no other value is specified.\n" ,
00936 "\n" ,
00937 "--------------------\n" ,
00938 "Variable: AFNI_TRACE\n" ,
00939 "--------------------\n" ,
00940 "This variable controls the initial setting of the tracing (debugging)\n" ,
00941 "code when AFNI programs startup. If it is set to 'y', then tracing\n" ,
00942 "is turned on and set to the LOW mode (like -trace in AFNI). If it is\n" ,
00943 "set to 'Y', then tracing is turned on and set to the HIGH mode (like\n" ,
00944 "-TRACE in AFNI). Anything else, and tracing is turned off.\n" ,
00945 "\n" ,
00946 "N.B.: You can't set this variable in .afnirc and expect it to have\n" ,
00947 " any effect (and why would you want to?), since it is read from\n" ,
00948 " the environment BEFORE the .afnirc file is read in.\n" ,
00949 "\n" ,
00950 "N.B.: At this moment (26 Jan 2001), only the AFNI program itself is\n" ,
00951 " configured for tracing. As time goes on, the entire AFNI\n" ,
00952 " programming library and suite of programs will be revamped for\n" ,
00953 " this purpose. The goal is to make it easier to find bugs, and\n" ,
00954 " localize crashes.\n" ,
00955 "\n" ,
00956 "------------------------\n" ,
00957 "Variable: AFNI_ROTA_ZPAD\n" ,
00958 "------------------------\n" ,
00959 "This variable controls the amount of zero-padding used during 3D rotations\n" ,
00960 "in 3drotate, 3dvolreg, etc. It provides a default value for the \"-zpad\"\n" ,
00961 "options of these programs. If zero-padding is used, then this many voxels\n" ,
00962 "are padded out on each edge (all 6 faces) of a 3D brick before rotation.\n" ,
00963 "After the rotation, these perimeter values (whatever they might be) will\n" ,
00964 "be stripped off. If \"-zpad\" is used on the command line, it overrides\n" ,
00965 "this value. Zero padding during rotation is useful to avoid edge effects,\n" ,
00966 "the worst of which is the loss of data off the edge of the volume during\n" ,
00967 "the 4 shearing stages.\n" ,
00968 "\n" ,
00969 "------------------------\n" ,
00970 "Variable: AFNI_TO3D_ZPAD\n" ,
00971 "------------------------\n" ,
00972 "This variable sets the number of slices added on each z-face in datasets\n" ,
00973 "created by program to3d. It provides a default value for the \"-zpad\" option\n" ,
00974 "of that program. It can be set to an integer, meaning a slice count, or\n" ,
00975 "a number of millimeters, meaning a minimum distance to pad:\n" ,
00976 " setenv AFNI_TO3D_ZPAD 2\n" ,
00977 " setenv AFNI_TO3D_ZPAD 16mm\n" ,
00978 "If \"-zpad\" is used on the to3d command line, it overrides this value.\n" ,
00979 "If neither is present, no zero padding is used. Note well that this\n" ,
00980 "padding is only in the z-direction, unlike that of AFNI_ROTA_ZPAD.\n" ,
00981 "\n" ,
00982 "----------------------------\n" ,
00983 "Variable: AFNI_IMAGE_MINFRAC (editable)\n" ,
00984 "----------------------------\n" ,
00985 "This variable sets the minimum size of an image window when it is first\n" ,
00986 "opened, in terms of a fraction of the overall screen area. By default,\n" ,
00987 "this value is set to 0.02; you can override this by (for example)\n" ,
00988 " setenv AFNI_IMAGE_MINFRAC 0.05\n" ,
00989 "If you set this value to 0.0, then there will be no minimum. This is\n" ,
00990 "the old behavior, where the initial window size is always 1 screen pixel\n" ,
00991 "per data pixel, and can lead to image windows that are hard to resize or\n" ,
00992 "otherwise use (when the dataset is small). The largest value I recommend\n" ,
00993 "for AFNI_IMAGE_MINFRAC is 0.1; however, you can set it to as large as 0.9\n" ,
00994 "if you are completely crazy, but I'm not responsible for the results --\n" ,
00995 "don't even think of complaining or commenting to me about problems that\n" ,
00996 "arise if you try this!\n" ,
00997 "\n" ,
00998 "----------------------------\n" ,
00999 "Variable: AFNI_IMAGE_MAXFRAC\n" ,
01000 "----------------------------\n" ,
01001 "This variable sets the maximum size of an image window, as a fraction of\n" ,
01002 "the width and height of the screen. The default value is 0.9. This lets\n" ,
01003 "you prevent image windows from auto-resizing to be too big when you\n" ,
01004 "change datasets. Note that if you have turned on AFNI_ENFORCE_ASPECT, then\n" ,
01005 "this feature will prevent you from resizing a window to be larger than\n" ,
01006 "the AFNI_IMAGE_MAXFRAC fraction of the screen dimensions.\n" ,
01007 "\n" ,
01008 "-----------------------\n" ,
01009 "Variable: AFNI_AUTOGZIP (cf. AFNI_COMPRESSOR) (editable)\n" ,
01010 "-----------------------\n" ,
01011 "If this YES/NO variable is set to YES, then when AFNI programs write a\n" ,
01012 "dataset .BRIK file to disk, they will test to see if the data is easily\n" ,
01013 "compressible (at least 80%). If so, then the GZIP compression will be\n" ,
01014 "used. (For this to work, the gzip program must be in your path.) This\n" ,
01015 "can be useful if you are dealing with mask datasets, which are usually\n" ,
01016 "highly compressible, but don't want the overhead of trying to compress\n" ,
01017 "and decompress arbitrary MRI datasets.\n" ,
01018 "\n" ,
01019 "A command line method to carry out compression of datasets that will\n" ,
01020 "compress well is to use a csh script like the following:\n" ,
01021 "\n" ,
01022 " #!/bin/csh\n" ,
01023 " foreach fred ( `find . -name \\*.BRIK -print` )\n" ,
01024 " ent16 -%50 < $fred\n" ,
01025 " if( $status == 1 ) gzip -1v $fred\n" ,
01026 " end\n" ,
01027 "\n" ,
01028 "This will only gzip .BRIK files that the program ent16 estimates will\n" ,
01029 "compress by at least 50%. Note that ent16's estimate of compression\n" ,
01030 "may be high or low relative to what gzip actually does.\n" ,
01031 "\n" ,
01032 "------------------------------\n" ,
01033 "Variable: AFNI_DONT_MOVE_MENUS (editable)\n" ,
01034 "------------------------------\n" ,
01035 "If this YES/NO variable is set to YES, then the functions that try\n" ,
01036 "to move popup menus to \"good\" locations on screens will be skipped.\n" ,
01037 "This seems to be necessary on some Solaris systems, where the menus\n" ,
01038 "can end up being moved to bizarre locations.\n" ,
01039 "\n" ,
01040 "----------------------------\n" ,
01041 "Variable: AFNI_MINC_DATASETS\n" ,
01042 "----------------------------\n" ,
01043 "If this YES/NO variable is not set to NO, then MINC-format files\n" ,
01044 "with name suffix .mnc will be read into the interactive AFNI\n" ,
01045 "program at startup, along with standard .HEAD/.BRIK datasets.\n" ,
01046 "That is, you have to set this variable explicitly to NO if you\n" ,
01047 "don't want MINC-format files to be automatically recognized by\n" ,
01048 "the interactive AFNI program. This variable does not affect\n" ,
01049 "the ability of command line programs (3dSomething) to read\n" ,
01050 ".mnc input files.\n" ,
01051 "\n" ,
01052 "----------------------------\n" ,
01053 "Variable: AFNI_MINC_FLOATIZE\n" ,
01054 "----------------------------\n" ,
01055 "If this YES/NO variable is set to YES, then when MINC-format files\n" ,
01056 "are read in as datasets, their values will be scaled to floats.\n" ,
01057 "Otherwise, their values will be scaled to the same data type as\n" ,
01058 "stored in the file. In some cases, the latter behavior is not\n" ,
01059 "good; for example, if a byte-valued file (intrinsic range 0..255)\n" ,
01060 "is scaled to the range 0..0.5 in the MINC header, then after\n" ,
01061 "conversion back to bytes, the resulting AFNI dataset values will\n" ,
01062 "all be zero. Setting AFNI_MINC_FLOATIZE to YES will cause the\n" ,
01063 "scaled values to be stored as floats.\n" ,
01064 "\n" ,
01065 "------------------------------\n" ,
01066 "Variable: AFNI_MINC_SLICESCALE\n" ,
01067 "------------------------------\n" ,
01068 "If this YES/NO variable is set to NO, then AFNI will not use the\n" ,
01069 "image-min and image-max scaling when reading data from MINC files.\n" ,
01070 "Normally, you want this scaling, since MINC files are scaled separately\n" ,
01071 "in each slice. However, if the image-min and image-max values in the\n" ,
01072 "MINC file are damaged, then you can turn off the scaling this way.\n" ,
01073 "\n" ,
01074 "----------------------------\n" ,
01075 "Variable: AFNI_ANALYZE_SCALE\n" ,
01076 "----------------------------\n" ,
01077 "If this YES/NO variable is set to NO, then the \"funused1\" entry\n" ,
01078 "in the Mayo Analyze .hdr file will not be used as a scale factor\n" ,
01079 "for the images contained in the corresponding .img file. Otherwise,\n" ,
01080 "if funused1 is positive and not equal to 1.0, all the image data\n" ,
01081 "in the .img file will be scaled by this value.\n" ,
01082 "\n" ,
01083 "-------------------------------\n" ,
01084 "Variable: AFNI_ANALYZE_FLOATIZE\n" ,
01085 "-------------------------------\n" ,
01086 "If this YES/NO variable is set to YES, then Mayo Analyze files\n" ,
01087 "will be scaled to floats on input. Otherwise, they will be read\n" ,
01088 "in the format in which they are stored in the .img file. Conversion\n" ,
01089 "to floats can be useful if the scaling factor is such that the image\n" ,
01090 "native format can't hold the scaled values; for example, if short\n" ,
01091 "values in the image range from -1000..1000 and the scale factor\n" ,
01092 "is 0.0001, then the scaled values range from -0.1..0.1, which would\n" ,
01093 "be truncated to 0 in the scaled image if it is not \"floatized\".\n" ,
01094 "(Conversion to floats will only be done to byte, short, and int\n" ,
01095 "image types.)\n" ,
01096 "\n" ,
01097 "---------------------------------\n" ,
01098 "Variable: AFNI_ANALYZE_ORIGINATOR\n" ,
01099 "---------------------------------\n" ,
01100 "If this YES/NO variable is set to YES, then AFNI will attempt\n" ,
01101 "to read and use the ORIGINATOR field in a Mayo Analyze file\n" ,
01102 "to set the origin of the pixel space in AFNI. This origin\n" ,
01103 "can be used directly by several programs--the main AFNI viewer,\n" ,
01104 "and all of the 3dxxxx programs, including especially 3dcopy,\n" ,
01105 "which is the preferred way to convert an Analyze format file\n" ,
01106 "to an AFNI native file.\n" ,
01107 "This variable will also force 3dAFNItoANALYZE to write the\n" ,
01108 "ORIGINATOR field into the output Analyze file based on the\n" ,
01109 "input AFNI file's origin information.\n" ,
01110 "The ORIGINATOR field should be compatible with SPM in most\n" ,
01111 "cases, but please verify this.\n" ,
01112 "\n" ,
01113 "--------------------------\n" ,
01114 "Variable: AFNI_START_SMALL\n" ,
01115 "--------------------------\n" ,
01116 "If this YES/NO variable is set to YES, then when AFNI starts, it will\n" ,
01117 "look for the smallest datasets in the first session, and choose these\n" ,
01118 "as its starting point. This can be useful if you also use the layout\n" ,
01119 "feature to pop open an image window on startup; in that case, if the\n" ,
01120 "default starting dataset (the first alphabetical) is huge, you won't\n" ,
01121 "see anything while the program reads all of into memory before displaying\n" ,
01122 "the first image.\n" ,
01123 "\n" ,
01124 "---------------------------\n" ,
01125 "Variable: AFNI_MENU_COLSIZE\n" ,
01126 "---------------------------\n" ,
01127 "This numerical variable sets the maximum number of entries in a popup\n" ,
01128 "menu column (e.g., like the sub-brick menus for bucket datasets). The\n" ,
01129 "default value is 20, but you may want to make this larger (say 40). When\n" ,
01130 "you have a menu with a huge number of entries, the menu can become so\n" ,
01131 "wide that it doesn't fit on the screen. Letting the columns be longer\n" ,
01132 "will make the menus be narrower across the screen.\n" ,
01133 "\n" ,
01134 "Another way to get a handle on such huge menus is to Button-3 (right)\n" ,
01135 "click on the label to the left of the menu. This will popup a one-\n" ,
01136 "column scrollable list chooser that is equivalent to the menu. In this\n" ,
01137 "way, it is still possible to use menus that have hundreds of entries.\n" ,
01138 "The maximum number of entries shown at one time in a scrollable list\n" ,
01139 "chooser is given by variable AFNI_chooser_listmax if it exists, otherwise\n" ,
01140 "by AFNI_MENU_COLSIZE.\n" ,
01141 "\n" ,
01142 "-----------------------------\n" ,
01143 "Variable: AFNI_GLOBAL_SESSION\n" ,
01144 "-----------------------------\n" ,
01145 "This variable, if it exists, is the name of a directory that contains\n" ,
01146 "\"global\" datasets - ones that you want to be visible in each \"Switch Underlay\"\n" ,
01147 "or \"Switch Overlay\" menu. Pointers to the datasets read from this directory\n" ,
01148 "will be appended to the dataset list for each directory read from the\n" ,
01149 "command line. In the \"Switch\" choosers, these datasets are marked with\n" ,
01150 "the character 'G' at the right, and they appear last in the list.\n" ,
01151 "\n" ,
01152 "It really only makes sense to put +tlrc datasets in the global session\n" ,
01153 "directory, since only they can be presumed to be aligned with other datasets.\n" ,
01154 "Also, it is probably best if you make sure each global anatomical dataset\n" ,
01155 "has itself as the anatomy parent; this can be enforced by issuing the command\n" ,
01156 " 3drefit -apar SELF *.HEAD\n" ,
01157 "in the global session directory.\n" ,
01158 "\n" ,
01159 "When you Switch Sessions and are viewing a global dataset, it is likely that\n" ,
01160 "you will NOT be viewing the same dataset after the Switch Session. You will\n" ,
01161 "have to then Switch Underlay and/or Switch Overlay to get back to the same\n" ,
01162 "global dataset(s).\n" ,
01163 "\n" ,
01164 "If you start AFNI and there are no datasets in the sessions given on the\n" ,
01165 "command line, then the directory specified by this variable becomes the\n" ,
01166 "default session. If there are no datasets there, either, then AFNI makes\n" ,
01167 "up a dummy dataset (AFNI cannot operate without at least one dataset).\n" ,
01168 "\n" ,
01169 "------------------------------\n" ,
01170 "Variable: AFNI_DISP_SCROLLBARS (editable)\n" ,
01171 "------------------------------\n" ,
01172 "If this YES/NO variable is set to YES, then the 'Disp' control window\n" ,
01173 "(on the image viewers) will have scrollbars attached. This window has\n" ,
01174 "grown larger over the years, and for some people with pitifully small\n" ,
01175 "displays (e.g., laptops), it is now taller than their screens. If\n" ,
01176 "activated, this option will prevent the Disp window from being so tall\n" ,
01177 "and will attach scrollbars so you can access all of its contents.\n" ,
01178 "\n" ,
01179 "Note: If you change this value interactively, via Edit Environment, the\n" ,
01180 "change will only affect Disp windows opened after you 'Set' the variable.\n" ,
01181 "That is, already opened Disp windows won't suddenly get scrollbars if\n" ,
01182 "you change this to YES.\n" ,
01183 "\n" ,
01184 "------------------------------\n" ,
01185 "Variable: AFNI_GRAPH_TEXTLIMIT (editable)\n" ,
01186 "------------------------------\n" ,
01187 "This numerical variable sets the upper limit on the number of rows shown\n" ,
01188 "in the Button-3 popup in a sub-graph. If the number of rows in the popup\n" ,
01189 "would be more than this value, a text window with scrollbars is used\n" ,
01190 "instead of a \"spring-loaded\" menu pane. If you set this value to 1, then\n" ,
01191 "the text window will always be used. Note that a text window does not\n" ,
01192 "automatically popdown, but must be explicitly dismissed by the user\n" ,
01193 "pressing the \"Quit\" button.\n" ,
01194 "\n" ,
01195 "-----------------------------\n" ,
01196 "Variable: AFNI_GRAPH_BASELINE\n" ,
01197 "-----------------------------\n" ,
01198 "This variable should be set to one of the strings \"Individual\", \"Common\",\n" ,
01199 "or \"Global\", corresponding to the choices on the Opt->Baseline menu in\n" ,
01200 "a graph window. (Actually, only the first letter of the string will be\n" ,
01201 "used.) This variable will determine the initial setting of the Baseline\n" ,
01202 "menu when a graph window opens.\n" ,
01203 "\n" ,
01204 "-------------------------------\n" ,
01205 "Variable: AFNI_GRAPH_GLOBALBASE\n" ,
01206 "-------------------------------\n" ,
01207 "Normally, the global baseline for a graph window is set to the smallest\n" ,
01208 "value found in the entire 3D+time dataset. This variable lets you specify\n" ,
01209 "a numerical value to be used for this purpose instead. Probably the most\n" ,
01210 "common setting (for those who want to use this feature at all, which means\n" ,
01211 "Mike Beauchamp) would be\n" ,
01212 " setenv AFNI_GRAPH_GLOBALBASE 0\n" ,
01213 "Of course, you can always change the global baseline from the Opt->Baseline\n" ,
01214 "menu.\n" ,
01215 "\n" ,
01216 "--------------------------\n" ,
01217 "Variable: AFNI_VALUE_LABEL (editable)\n" ,
01218 "--------------------------\n" ,
01219 "If this YES/NO variable is set to YES, then the data value label on the\n" ,
01220 "Define Overlay control panel will be turned on when only 1 or 2 image\n" ,
01221 "viewer windows are open. This will consume more CPU time and redrawing\n" ,
01222 "time than the default, which is that this label is only turned on when\n" ,
01223 "all 3 image viewer windows are open. If you are operating X11 remotely\n" ,
01224 "over a slow connection, this option should not be turned on.\n" ,
01225 "\n" ,
01226 "----------------------------\n" ,
01227 "Variable: AFNI_SUMA_BOXCOLOR (editable)\n" ,
01228 "----------------------------\n" ,
01229 "This string defines the color used for overlaying surface nodes transmitted\n" ,
01230 "from SUMA to AFNI. The default is an orangish-yellow. If you like yellow,\n" ,
01231 "then do\n" ,
01232 " setenv AFNI_SUMA_COLOR yellow\n" ,
01233 "If this is set to \"none\", then these lines won't be plotted.\n" ,
01234 "\n" ,
01235 "-----------------------------\n" ,
01236 "Variable: AFNI_SUMA_LINECOLOR (editable)\n" ,
01237 "-----------------------------\n" ,
01238 "This string defines the color used for overlaying the intersection of SUMA\n" ,
01239 "surface triangles with image slice planes. The default is white. If this\n" ,
01240 "is set to \"none\", then these lines won't be plotted.\n" ,
01241 "\n" ,
01242 "---------------------------\n" ,
01243 "Variable: AFNI_SUMA_BOXSIZE (editable)\n" ,
01244 "---------------------------\n" ,
01245 "This variable defines the size of the boxes drawn at each surface node\n" ,
01246 "transmitted from SUMA. The default is 0.25, which means that each box is\n" ,
01247 "plus and minus 1/4 of a voxel size about the node location. If you want a\n" ,
01248 "larger box, you could try\n" ,
01249 " setenv AFNI_SUMA_BOXSIZE 0.5\n" ,
01250 "\n" ,
01251 "----------------------------\n" ,
01252 "Variable: AFNI_SUMA_LINESIZE (editable)\n" ,
01253 "----------------------------\n" ,
01254 "This variable sets the thickness of the lines used when drawing a surface\n" ,
01255 "intersection overlay. The units are the width of the entire image;\n" ,
01256 "reasonable values are in the range 0..0.01; 0 means to draw the thinnest\n" ,
01257 "line possible. Since this is editable, you can experiment with it to\n" ,
01258 "see what looks good.\n" ,
01259 "\n" ,
01260 "-------------------------\n" ,
01261 "Variable: AFNI_NIML_START\n" ,
01262 "-------------------------\n" ,
01263 "If this YES/NO variable is set to YES, then NIML listening will be engaged\n" ,
01264 "from when AFNI starts. You can also enable NIML from the command line with\n" ,
01265 "the option \"-niml\", and from the Datamode->Misc menu item \"Start NIML\".\n" ,
01266 "\n" ,
01267 "NIML is the mechanism by which AFNI talks to other programs - it is the\n" ,
01268 "successor to plugouts. At this moment (Mar 2002), the only external NIML\n" ,
01269 "program is SUMA - the surface mapper.\n" ,
01270 "\n" ,
01271 "---------------------------\n" ,
01272 "Variable: AFNI_KEEP_PANNING (editable)\n" ,
01273 "---------------------------\n" ,
01274 "If this YES/NO variable is set to YES, then when the Zoom pan gets turned\n" ,
01275 "on in the AFNI image viewer, it will stay on until it is explicitly turned\n" ,
01276 "off. (The default behavior is to turn panning off after the user releases\n" ,
01277 "the mouse button.)\n" ,
01278 "\n" ,
01279 "-------------------------------\n" ,
01280 "Variable: AFNI_IMAGE_LABEL_MODE\n" ,
01281 "-------------------------------\n" ,
01282 "This integer determines the placement of the image coordinate labels drawn\n" ,
01283 "in the AFNI image viewer windows. The possible values are\n" ,
01284 " 0 = Labels are off\n" ,
01285 " 1 = Labels in upper left\n" ,
01286 " 2 = Labels in upper right\n" ,
01287 " 3 = Labels in lower left\n" ,
01288 " 4 = Labels in lower right\n" ,
01289 " 5 = Labels in upper middle\n" ,
01290 " 6 = Labels in lower middle\n" ,
01291 "You can also control the placement and size of the labels from the Button-3\n" ,
01292 "(right-click) popup menu attached to the intensity bar to the right of the\n" ,
01293 "image sub-window.\n" ,
01294 "\n" ,
01295 "-------------------------------\n" ,
01296 "Variable: AFNI_IMAGE_LABEL_SIZE\n" ,
01297 "-------------------------------\n" ,
01298 "This integer determines the size of the image coordinate labels:\n" ,
01299 " 0 = Small\n" ,
01300 " 1 = Medium\n" ,
01301 " 2 = Large\n" ,
01302 " 3 = Huge\n" ,
01303 " 4 = Enormous\n" ,
01304 "\n" ,
01305 "--------------------------------\n" ,
01306 "Variable: AFNI_IMAGE_LABEL_COLOR (editable)\n" ,
01307 "--------------------------------\n" ,
01308 "This variable controls the color of the image coordinate labels.\n" ,
01309 "\n" ,
01310 "----------------------------------\n" ,
01311 "Variable: AFNI_IMAGE_LABEL_SETBACK (editable)\n" ,
01312 "----------------------------------\n" ,
01313 "This variable, a floating point value between 0 and 0.1, determines how\n" ,
01314 "far from the edge an image coordinate label will be drawn. The units are\n" ,
01315 "fractions of the image width/height.\n" ,
01316 "\n" ,
01317 "------------------------------\n" ,
01318 "Variable: AFNI_CROSSHAIR_LINES (editable)\n" ,
01319 "------------------------------\n" ,
01320 "If this YES/NO variable is set to YES, then the image crosshairs will be\n" ,
01321 "drawn using lines rather than pixels. By default (this is the original\n" ,
01322 "AFNI way), crosshair lines are drawn the same way as functional overlays:\n" ,
01323 "by putting color pixels on top of the image. The new way draws lines on\n" ,
01324 "top of the image instead. The difference is quite visible when the image\n" ,
01325 "is zoomed; overlay by pixels shows the crosshair lines as fat blobs, but\n" ,
01326 "the lines are drawn as thin as possible, no matter what the image window\n" ,
01327 "size and zoom factor.\n" ,
01328 "\n" ,
01329 "Good points about crosshairs drawn with lines:\n" ,
01330 " - They are less obtrusive than pixel overlay, especially if you zoom\n" ,
01331 " or enlarge the image a lot\n" ,
01332 " - When doing a montage with Spacing=1, they'll look better in the\n" ,
01333 " orthogonal slices.\n" ,
01334 "Good points about crosshairs drawn with pixel overlay:\n" ,
01335 " - Pixel overlays can be rendered as translucent (on X11 TrueColor displays);\n" ,
01336 " geometrical overlays are always solid color.\n" ,
01337 "So you have to decide what you need most. You can change this item using\n" ,
01338 "the \"Edit Environment\" pseudo-plugin on the Datamode->Misc menu, so you\n" ,
01339 "can play with it interactively to get the features you want.\n" ,
01340 "\n" ,
01341 "----------------------------\n" ,
01342 "Variable: AFNI_CROP_ZOOMSAVE (editable)\n" ,
01343 "----------------------------\n" ,
01344 "When saving a zoomed image, the default is to save the entire zoomed image,\n" ,
01345 "not just the part you see. If this YES/NO variable is set to YES, then only\n" ,
01346 "the visible part will be saved.\n" ,
01347 "\n" ,
01348 "---------------------------\n" ,
01349 "Variables: AFNI_TLRC_BBOX_*\n" ,
01350 "---------------------------\n" ,
01351 "These variables let you choose the size of the \"Talairach Box\", into which\n" ,
01352 "+tlrc datasets are transformed. If defined, they should be positive values,\n" ,
01353 "in mm. The 5 variables (any or all of which may be used) are:\n" ,
01354 "\n" ,
01355 " AFNI_TLRC_BBOX_LAT = distance from midline to maximum left/right position\n" ,
01356 " [default=80]\n" ,
01357 " AFNI_TLRC_BBOX_ANT = distance from AC to most anterior point in box\n" ,
01358 " [default=80]\n" ,
01359 " AFNI_TLRC_BBOX_POS = distance from AC to most posterior point in box\n" ,
01360 " [default=110]\n" ,
01361 " AFNI_TLRC_BBOX_INF = distance from AC-PC line to most inferior point in box\n" ,
01362 " [default=55 for small box, 65 for big box]\n" ,
01363 " AFNI_TLRC_BBOX_SUP = distance from AC-PC line to most superior point in box\n" ,
01364 " [default=85]\n" ,
01365 "\n" ,
01366 "For example, \"setenv AFNI_TLRC_BBOX_INF 100\" lets you define the +tlrc box\n" ,
01367 "to extend 100 mm below the AC-PC line. Please note that virtually all the\n" ,
01368 "3d* analysis programs (3dANOVA, etc.) do voxel-by-voxel analyses. This fact\n" ,
01369 "means that you will be unable to compare datasets created in +tlrc coordinates\n" ,
01370 "with different box sizes. Also, you will be unable to overlay regions from\n" ,
01371 "the Talairach Daemon database onto odd-sized +tlrc datasets. Therefore, I\n" ,
01372 "recommend that these variables be used only when strictly needed, and with\n" ,
01373 "caution.\n" ,
01374 "\n" ,
01375 "-------------------------\n" ,
01376 "Variable: AFNI_TTRR_SETUP\n" ,
01377 "-------------------------\n" ,
01378 "Name of a file to be loaded to define Talairach Atlas Colors, when the Atlas\n" ,
01379 "Colors control panel is first created. Format is the same as a file created\n" ,
01380 "from this control panel's \"Save\" button. This filename should be an absolute\n" ,
01381 "path (e.g., /home/yourname/.afni_ttcolors), since otherwise it will be read\n" ,
01382 "relative to the directory in which you start AFNI.\n" ,
01383 "\n" ,
01384 "-----------------------------\n" ,
01385 "Variable: AFNI_LOAD_PRINTSIZE\n" ,
01386 "-----------------------------\n" ,
01387 "AFNI will print (to stderr) a warning that it is loading a large dataset from\n" ,
01388 "disk. This value determines the meaning of \"large\". For example, setting\n" ,
01389 "this variable to \"40M\" means that loading a dataset larger than 40 Megabytes\n" ,
01390 "will trigger the warning. If not given, the default value is 100 Megabytes.\n" ,
01391 "The purpose of the warning is just to let the user know that it may be several\n" ,
01392 "seconds before the dataset is loaded (e.g., before the images appear). If you\n" ,
01393 "don't want this warning at all, set this variable to the string \"0\".\n" ,
01394 "\n" ,
01395 "-------------------------------\n" ,
01396 "Variable: AFNI_ANALYZE_DATASETS\n" ,
01397 "-------------------------------\n" ,
01398 "If this YES/NO variable is not set to NO, then ANALYZE-format files with name\n" ,
01399 "suffix .hdr will be read into the interactive AFNI program at startup, along\n" ,
01400 "with standard .HEAD/.BRIK datasets. That is, you have to set this variable\n" ,
01401 "explicitly to NO if you don't want ANALYZE-format files to be automatically\n" ,
01402 "recognized by the interactive AFNI program. This variable does not affect\n" ,
01403 "the ability of command line programs (3dSomething) to read .hdr input files.\n" ,
01404 "\n" ,
01405 "-----------------------------\n" ,
01406 "Variable: AFNI_ANALYZE_ORIENT\n" ,
01407 "-----------------------------\n" ,
01408 "ANALYZE .hdr files do not contain reliable information about the orientation\n" ,
01409 "of the data volumes. By default, AFNI assumes that these datasets are\n" ,
01410 "oriented in LPI order. You can set this variable to a different default\n" ,
01411 "order. See AFNI_ORIENT for details on the 3 letter format for this.\n" ,
01412 "\n" ,
01413 "---------------------------------\n" ,
01414 "Variable: AFNI_ANALYZE_AUTOCENTER\n" ,
01415 "---------------------------------\n" ,
01416 "ANALYZE .hdr files do not contain information about the origin of coordinates.\n" ,
01417 "The default AFNI approach mirrors that of FSL - the outermost corner of the\n" ,
01418 "first voxel in the dataset is set to (0,0,0). If you set this variable\n" ,
01419 "(AFNI_ANALYZE_AUTOCENTER) to YES, then instead (0,0,0) will be set to the\n" ,
01420 "center of the 3D ANALYZE array. This is the default that would be applied\n" ,
01421 "if you read the ANALYZE array into program to3d.\n" ,
01422 "\n" ,
01423 "----------------------------\n" ,
01424 "Variable: AFNI_VERSION_CHECK\n" ,
01425 "----------------------------\n" ,
01426 "If this YES/NO variable is set to NO, then AFNI will not try to check if its\n" ,
01427 "version is up-to-date when it starts. Otherwise, it will try to check the\n" ,
01428 "program version with the AFNI web server.\n" ,
01429 "\n" ,
01430 "-----------------------------------\n" ,
01431 "Variable: AFNI_SLICE_SPACING_IS_GAP\n" ,
01432 "-----------------------------------\n" ,
01433 "This YES/NO variable is designed to patch a flaw in some DICOM files, where\n" ,
01434 "the \"Spacing Between Slices\" attribute is erroneously set to the gap between\n" ,
01435 "the slices, rather than the center-to-center slice distance specified in\n" ,
01436 "the DICOM standard. If this variable is set to YES, then the \"Slice Thickness\"\n" ,
01437 "attribute will always be added to \"Spacing Between Slices\" to get the z voxel\n" ,
01438 "size (assuming both attributes are present in the DICOM file).\n" ,
01439 "\n" ,
01440 "To check if a DICOM file has this problem, you can read it into to3d with\n" ,
01441 "the command \"to3d suspect_file_name\". A warning will be printed to the\n" ,
01442 "terminal window if attribute \"Spacing Between Slices\" is less than\n" ,
01443 "attribute \"Slice Thickness\". Another way to check is with a command like so\n" ,
01444 "\n" ,
01445 " dicom_hdr suspect_file_name | grep \"Slice\"\n" ,
01446 "\n" ,
01447 "then check if the \"Spacing Between Slices\" and \"Slice Thickness\" values are\n" ,
01448 "correct for the given acquisition. We have only seen this problem in GE\n" ,
01449 "generated DICOM files, but that doesn't mean it won't occur elsewhere.\n" ,
01450 "\n" ,
01451 "If this variable is set to NO, then this patchup will never be made.\n" ,
01452 "The z voxel size will be set to \"Spacing Between Slices\" if present,\n" ,
01453 "otherwise to \"Slice Thickness\". This may be needed for some Phillips pulse\n" ,
01454 "sequences, which can report \"Spacing Between Slices\" < \"Slice Thickness\".\n" ,
01455 "In such a case, if this variable is not set, the wrong z voxel size will\n" ,
01456 "be assigned!\n" ,
01457 "\n" ,
01458 "If this variable is not set at all, AND if \"Spacing Between Slices\" is less\n" ,
01459 "less than 0.99 times \"Slice Thickness\", it will be treated as a gap;\n" ,
01460 "that is, the z voxel size will again be set to \"Spacing Between Slices\" +\n" ,
01461 "\"Slice Thickness\" if \"Spacing Between Slices\" < 0.99*\"Slice Thickness\".\n" ,
01462 "Otherwise, the z voxel size will be set to the larger of\n" ,
01463 "\"Spacing Between Slices\" and \"Slice Thickness\".\n" ,
01464 "\n" ,
01465 "N.B.: \"YES\", \"NO\", and \"not set\" have 3 different sets of behavior!\n" ,
01466 " In the summary below, if a variable isn't set, treat it as zero:\n" ,
01467 "\n" ,
01468 " YES => dz = Thickness + Spacing\n" ,
01469 " NO => dz = Spacing if present, otherwise Thickness\n" ,
01470 " not set => if( Spacing > 0 && Spacing < 0.99*Thickness )\n" ,
01471 " dz = Thickness + Spacing\n" ,
01472 " else\n" ,
01473 " dz = MAX( Thickness , Spacing )\n" ,
01474 "\n" ,
01475 "If neither variable is set, then dz=1 mm, which is probably wrong.\n" ,
01476 "\n" ,
01477 "Sorry about this complexity, but the situation with various manufacturers\n" ,
01478 "is complicated, murky, and confusingly maddening.\n" ,
01479 "\n" ,
01480 "---------------------------------------------------\n" ,
01481 "Variables: AFNI_DICOM_RESCALE and AFNI_DICOM_WINDOW\n" ,
01482 "---------------------------------------------------\n" ,
01483 "DICOM image files can contain rescaling and windowing \"tags\". If present,\n" ,
01484 "these values indicate to affinely modify the values stored in the file.\n" ,
01485 "As far as I can tell, \"rescale\" means that the values should always be\n" ,
01486 "modified, whereas \"window\" means the values should be modified for display\n" ,
01487 "purposes. If both are present, the rescale comes before window. These\n" ,
01488 "two YES/NO environment variables control whether the AFNI image input\n" ,
01489 "functions (used in to3d) should apply the rescale and window tags.\n" ,
01490 "\n" ,
01491 "It is my impression from the laconic, terse, and opaque DICOM manual that\n" ,
01492 "window tags are intended for display purposes only, and that they aren't\n" ,
01493 "needed for signal processing. But you'll have to examine your own data to\n" ,
01494 "decide whether to use these options -- manufacturers seem to differ.\n" ,
01495 "Plus, I don't have that much experience with DICOM data from many different\n" ,
01496 "sources.\n" ,
01497 "\n" ,
01498 "-----------------------\n" ,
01499 "Variable: IDCODE_PREFIX\n" ,
01500 "-----------------------\n" ,
01501 "AFNI stores with each dataset a unique string, called an \"idcode\". An example\n" ,
01502 "is \"XYZ_MoNLqdNOwMNEYmKSBytfJg\". You can alter the first three characters of\n" ,
01503 "the idcode with this variable. For example,\n" ,
01504 " setenv IDCODE_PREFIX RWC\n" ,
01505 "sets the first 3 characters of newly generated idcodes to be the initials of\n" ,
01506 "AFNI's author. I find this a handy way to \"brand\" my datasets. Of course,\n" ,
01507 "there are only 17576 possible 3 letter combinations (140608 if you allow for\n" ,
01508 "case), so you should claim your prefix soon!!!\n" ,
01509 "\n" ,
01510 "Idcodes are used to store links between datasets. For example, when SUMA\n" ,
01511 "sends a surface to AFNI, it identifies the dataset to which the surface is\n" ,
01512 "to be associated with the dataset's idcode. Similarly, when AFNI sends a\n" ,
01513 "color overlay to SUMA, it uses the surface idcode to indicate which surface\n" ,
01514 "family the overlay is to be mapped onto.\n" ,
01515 "\n" ,
01516 "-------------------------\n" ,
01517 "Variable: AFNI_AGIF_DELAY\n" ,
01518 "-------------------------\n" ,
01519 "This is the time delay between frames when writing an animated GIF file from\n" ,
01520 "an image viewer window. The units are 100ths of seconds; the default value\n" ,
01521 "is 20 (= 5 frames per second).\n" ,
01522 "\n" ,
01523 "-----------------------------\n" ,
01524 "Variable: AFNI_MPEG_FRAMERATE\n" ,
01525 "-----------------------------\n" ,
01526 "This value sets the frame rate (per second) of the MPEG-1 output animation\n" ,
01527 "from the image viewer window. The legal values allowed by MPEG-1 are\n" ,
01528 "24, 25, 30, 50, and 60; 24 is the default.\n" ,
01529 "\n" ,
01530 "-----------------------------\n" ,
01531 "Variable: AFNI_STARTUP_SCRIPT\n" ,
01532 "-----------------------------\n" ,
01533 "If this is set, this is the name of an AFNI Script to run when AFNI first\n" ,
01534 "starts. (See the file README.driver for information about AFNI Scripts.)\n" ,
01535 "If this is not set, it defaults to \".afni.startup_script\". The program first\n" ,
01536 "tries to read this filename from the current working directory; if that fails,\n" ,
01537 "then it tries to read from your home directory. No error message is given\n" ,
01538 "if neither file can be read.\n" ,
01539 "\n" ,
01540 "You can save a file \".afni.startup_script\" that will recreate the window\n" ,
01541 "layout you currently have. Use the \"Datamode->Misc->Save Layout\" button\n" ,
01542 "and press \"Set\" on the popup control without entering any filename. Instead\n" ,
01543 "of a Layout file (cf. AFNI_LAYOUT_FILE above), you'll get a Script file.\n" ,
01544 "\n" ,
01545 "The capabilities of Script files are being expanded. Not all features of\n" ,
01546 "the AFNI window setup are currently save-able this way.\n" ,
01547 "\n" ,
01548 "You can load a Script file interactively during an AFNI run by using the\n" ,
01549 "button \"Datamode->Misc->Run Script\". As a 'secret' option, if you enter\n" ,
01550 "a line containing a blank in the the filename dialog, that line will be\n" ,
01551 "executed as a single command, rather than be used as a script filename.\n" ,
01552 "\n" ,
01553 "------------------------------\n" ,
01554 "Variable: AFNI_DEFAULT_OPACITY\n" ,
01555 "------------------------------\n" ,
01556 "This should be set to an integer from 1..9, and controls the default opacity\n" ,
01557 "setting for the color overlay in image viewer windows.\n" ,
01558 "\n" ,
01559 "-----------------------------\n" ,
01560 "Variable: AFNI_DEFAULT_IMSAVE\n" ,
01561 "-----------------------------\n" ,
01562 "This should be set to the suffix of the image format to which you want to save\n" ,
01563 "from an image viewer. The suffixes AFNI knows about (as of 23 Jan 2003) are\n" ,
01564 " ppm = Portable PixMap format = cat\n" ,
01565 " jpg = Joint Photographics Experts Group (JPEG) format = cjpeg\n" ,
01566 " gif = Compuserve Graphics Interchange File (GIF) format = ppmtogif\n" ,
01567 " tif = Tagged Image File Format (TIFF) = ppm2tiff or pnmtotiff\n" ,
01568 " bmp = Windows Bitmap (BMP) format = ppmtobmp\n" ,
01569 " eps = Encapsulated PostScript format = pnmtops\n" ,
01570 " pdf = Portable Document Format = epstopdf\n" ,
01571 " png = Portable Network Graphics format = pnmtopng\n" ,
01572 "The third column is the name of the external filter program that AFNI uses to\n" ,
01573 "write the format. If a filter is not present on your system, then that option\n" ,
01574 "is not available. Most of these filters are part of the netpbm package.\n" ,
01575 "\n" ,
01576 "-----------------------------\n" ,
01577 "Variables: AFNI_COLORSCALE_xx for xx=01, 02, ..., 99\n" ,
01578 "-----------------------------\n" ,
01579 "These variables let you name files to be read it at AFNI startup to define\n" ,
01580 "\"continuous\" colorscales for the \"**\" mode of the color pbar. These files\n" ,
01581 "will be looked for in the current directory when you start AFNI, or in your\n" ,
01582 "home directory (if they aren't in the current directory). A sample file:\n" ,
01583 "\n" ,
01584 " Yellow-Red-Blue\n" ,
01585 " 1.0 #ffff00\n" ,
01586 " 0.7 #ffaa00\n" ,
01587 " 0.5 #ff0000\n" ,
01588 " 0.3 #aa00aa\n" ,
01589 " 0.0 #0000ff\n" ,
01590 "\n" ,
01591 "The first line is the name of this colorscale, to go in the colorscale popup\n" ,
01592 "chooser. The succeeding lines each have a number and a color definition.\n" ,
01593 "The numbers should be decreasing, and indicate the location on the colorscale.\n" ,
01594 "The largest number corresponds to the top of the colorscale and the smallest\n" ,
01595 "to the bottom - intermediate numbers denote intermediate locations. The colors\n" ,
01596 "at each location are specified using X11 notation (cf. \"man XParseColor\").\n" ,
01597 "In this example, I'm using hexadecimal colors, in the form #rrggbb, where each\n" ,
01598 "hex pair ranges from 00 to ff. Another color format is \"rgbi:rf/gf/bf\",\n" ,
01599 "where each value rf,gf,bf is a number between 0.0 and 1.0 (inclusive); for\n" ,
01600 "example, yellow would be \"rgbi:1.0/1.0/0.0\".\n" ,
01601 "\n" ,
01602 "Colors are interpolated (linearly in RGB space) between the break locations\n" ,
01603 "given in the file. There are actually 128 color locations on a colorscale.\n" ,
01604 "\n" ,
01605 "An alternative format for the file is to omit the numbers indicating the\n" ,
01606 "break locations. In this case, the break locations will be taken to be\n" ,
01607 "equally spaced. For example:\n" ,
01608 "\n" ,
01609 " Yellow-Red-Blue\n" ,
01610 " #ffff00\n" ,
01611 " #ffaa00\n" ,
01612 " #ff0000\n" ,
01613 " #aa00aa\n" ,
01614 " #0000ff\n" ,
01615 "\n" ,
01616 "This example is not exactly the same as the other one, since the breakpoints\n" ,
01617 "are evenly spaced now (as if they had been given as 1.0, 0.75, 0.5, 0.25,\n" ,
01618 "and 0.0). With this format, if you want to manually specify all 128 colors,\n" ,
01619 "you can do so, 1 color per line, remembering that the first line of the file\n" ,
01620 "is taken to be the colorscale title (no blanks allowed in the title!).\n" ,
01621 "\n" ,
01622 "---------------------------------\n" ,
01623 "Variable: AFNI_COLORSCALE_DEFAULT\n" ,
01624 "---------------------------------\n" ,
01625 "If set, this is the name of the default colorscale to use in setup. As a\n" ,
01626 "special case, if you DO NOT want a colorscale to be setup by default at all,\n" ,
01627 "then set this variable to the string \"NO\".\n" ,
01628 "N.B.: This variable only applies if you are using AFNI with a TrueColor X11\n" ,
01629 "visual. If you are using a PseudoColor visual, then this variable is ignored!\n" ,
01630 "\n" ,
01631 "----------------------------\n" ,
01632 "Variable: AFNI_RESCAN_METHOD\n" ,
01633 "----------------------------\n" ,
01634 "On 28 Dec 2002, I modified the way that the \"Rescan\" operation in AFNI works\n" ,
01635 "when re-reading datasets from sessions. The old way would purge and replace\n" ,
01636 "all datasets; the new way just adds datasets that didn't exist before.\n" ,
01637 "There are some differences between these methods:\n" ,
01638 " \"Replace\" will detect changes to a dataset, so if you add a brick using\n" ,
01639 " 3dTcat -glueto (for example), this will be reflected in AFNI.\n" ,
01640 " \"Replace\" will cause troubles if you are using a dataset in a plugin;\n" ,
01641 " the two main examples are volume rendering and the drawing plugin.\n" ,
01642 " This problem will occur even if you didn't do anything to the dataset\n" ,
01643 " on disk, since the internal pointer to the dataset will have been\n" ,
01644 " changed by the rescan, but the plugins won't know that.\n" ,
01645 " \"Add\" will not detect changes to a dataset on disk, but it also won't\n" ,
01646 " affect the pointers to the existing datasets.\n" ,
01647 "You can choose to use the \"Replace\" method (the old style) by setting\n" ,
01648 "this environment variable to the string \"REPLACE\".\n" ,
01649 "\n" ,
01650 "---------------------------\n" ,
01651 "Variable: AFNI_OLD_PPMTOBMP\n" ,
01652 "---------------------------\n" ,
01653 "The old (before 21 Feb 2003) usage of netpbm program \"ppmtobmp\" was to\n" ,
01654 "write a color image quantized to 255 colors. The new usage is to write\n" ,
01655 "a 24-bit image, which is thus not color-quantized. If you want the old\n" ,
01656 "behavior, set this environment variable to YES. This setting (YES) will\n" ,
01657 "be necessary if you have an older version of ppmtobmp in your path, which\n" ,
01658 "doesn't support the \"-bpp\" option.\n" ,
01659 "\n" ,
01660 "------------------------------\n" ,
01661 "Variable: AFNI_1DPLOT_COLOR_xx\n" ,
01662 "------------------------------\n" ,
01663 "This variable lets you set the colors used in the 1dplot program (and other\n" ,
01664 "similar graphs). Here, \"xx\" is a number from \"01\" to \"19\". The value of\n" ,
01665 "the environment variable must be in the form \"rgbi:rf/gf/bf\", where each\n" ,
01666 "color intensity (rf, gf, bf) is a number between 0.0 and 1.0. For example,\n" ,
01667 "\"rgbi:1.0/1.0/0.0\" is yellow. By default, the first 4 colors are defined\n" ,
01668 "as the equivalents of\n" ,
01669 " setenv AFNI_1DPLOT_COLOR_01 rgbi:0.0/0.0/0.0\n" ,
01670 " setenv AFNI_1DPLOT_COLOR_02 rgbi:0.9/0.0/0.0\n" ,
01671 " setenv AFNI_1DPLOT_COLOR_03 rgbi:0.0/0.7/0.0\n" ,
01672 " setenv AFNI_1DPLOT_COLOR_04 rgbi:0.0/0.0/0.9\n" ,
01673 "which are black, red, green, and blue, respectively. You can alter these\n" ,
01674 "colors, or leave them unchanged and start defining colors at 05. The largest\n" ,
01675 "color number you define will be the last color index used; if more line colors\n" ,
01676 "are needed, they will cycle back to color 01. If you leave a gap in the\n" ,
01677 "numbering (e.g., you define color 07 but not 05 or 06), then the undefined\n" ,
01678 "colors will be black.\n" ,
01679 "\n" ,
01680 "---------------------------------\n" ,
01681 "Variable: AFNI_SIEMENS_INTERLEAVE\n" ,
01682 "---------------------------------\n" ,
01683 "The old (pre-DICOM) Siemens .ima image mosaic format sometimes stores the\n" ,
01684 "multi-slice EPI data in correct spatial order and sometimes in correct\n" ,
01685 "time acquisition order. In the latter case, the images are stored in\n" ,
01686 "a spatially-interleaved fashion. As far as I know, there is no way to\n" ,
01687 "tell this from the .ima file header itself. Therefore, if you have a\n" ,
01688 "problem with such files, set this variable to YES to un-interleave the\n" ,
01689 "images when to3d reads them. One way to tell if the images need to be\n" ,
01690 "un-interleaved is to do\n" ,
01691 " afni -im fred.ima\n" ,
01692 "then look at the images in an Axial image viewer. If the slices make up\n" ,
01693 "a single coherent volume, then they are NOT interleaved. If the slices\n" ,
01694 "look like they make up 2 separate brain volumes, then they need to be\n" ,
01695 "un-interleaved, and you need to set this variable to YES.\n" ,
01696 "\n" ,
01697 "-----------------------------\n" ,
01698 "Variable: AFNI_TRY_DICOM_LAST\n" ,
01699 "-----------------------------\n" ,
01700 "When to3d tries to read an image file, it guesses the format from the\n" ,
01701 "filename. However, this doesn't always work. In particular, DICOM files\n" ,
01702 "don't have any fixed filename suffix or prefix. If all else fails, to3d\n" ,
01703 "normally tries to read a file as a DICOM file, and as a last resort, as\n" ,
01704 "a flat binary file. However, if a file is NOT a DICOM file, the DICOM\n" ,
01705 "reading function will print out a lot of error messages, since there is\n" ,
01706 "also no standard internal marker in all DICOM files that identify them.\n" ,
01707 "Most people don't like all these messages (perhaps hundreds per file),\n" ,
01708 "even if the program then successfully reads their flat binary files.\n" ,
01709 "\n" ,
01710 "If this YES/NO variable is set to YES, then the normal last-resort order\n" ,
01711 "of reading described above is reversed. If to3d can't read the file any\n" ,
01712 "other way, it will try it as a flat binary file. If that fails, then\n" ,
01713 "DICOM will be the ultimate resort, instead of being the penultimate\n" ,
01714 "resort that it is by default. This may help elide some error messages.\n" ,
01715 "However, if you have a DICOM file that is exactly 131072 bytes long\n" ,
01716 "(for example), then it will be interpreted as a headerless 256x256 image\n" ,
01717 "of shorts, instead of whatever it really is. So only set this variable\n" ,
01718 "to YES if necessary!\n" ,
01719 "\n" ,
01720 "-----------------------------\n" ,
01721 "Variable: AFNI_THRESH_BIGSTEP\n" ,
01722 "-----------------------------\n" ,
01723 "The AFNI threshold sliders (in the Define Overlay control panels and the\n" ,
01724 "Render Dataset plugins) are divided into 10000 steps from bottom to top.\n" ,
01725 "If you click in the trough or use the PageUp/PageDown keys, the default\n" ,
01726 "action is to move the slider 10 of the steps at once. (The up and down\n" ,
01727 "arrow keys move 1 step at a time.) You can change this big step from the\n" ,
01728 "default of 10 to any value between 1 and 1000 by setting this environment\n" ,
01729 "variable; for example\n" ,
01730 " setenv AFNI_THRESH_BIGSTEP 100\n" ,
01731 "will move the slider 1% of its height per PageUp/PageDown key or mouse click.\n" ,
01732 "\n" ,
01733 "------------------------------\n" ,
01734 "Variable: AFNI_SNAPFILE_PREFIX\n" ,
01735 "------------------------------\n" ,
01736 "Image files saved with the \"snapfile\" (or \"record to file\") by default have\n" ,
01737 "filenames of the form \"S_000001.ppm\". The prefix \"S\" can be altered by\n" ,
01738 "setting this environment variable; for example,\n" ,
01739 " setenv AFNI_SNAPFILE_PREFIX Elvis\n" ,
01740 "will save snapfiles with names like \"Elvis_000666.ppm\". You can view snapfiles\n" ,
01741 "with the \"aiv\" (\"AFNI Image Viewer\") utility, the \"xv\" program, or many other\n" ,
01742 "Unix utilities.\n" ,
01743 "\n" ,
01744 "-------------------------------\n" ,
01745 "Variable: AFNI_STARTUP_WARNINGS\n" ,
01746 "-------------------------------\n" ,
01747 "When the interactive AFNI program starts, it may pop up warnings about the\n" ,
01748 "programming environment for which it was compiled. At this time, there are\n" ,
01749 "two such warning messages possible:\n" ,
01750 " LessTiff: AFNI will work with LessTif, but works better with Motif.\n" ,
01751 " Button-3: On Solaris 2.8, Button-3 popup menus don't work quite properly.\n" ,
01752 "If you are tired of seeing these messages, set AFNI_STARTUP_WARNINGS to NO.\n" ,
01753 "\n" ,
01754 "----------------------\n" ,
01755 "Variable: AFNI_1D_TIME\n" ,
01756 "----------------------\n" ,
01757 "If this YES/NO variable is set to YES, then when a multicolumn .1D file is\n" ,
01758 "read in as an AFNI dataset, the column variable is taken to be time, and\n" ,
01759 "a time-dependent dataset is created. The default is to create a bucket\n" ,
01760 "dataset.\n" ,
01761 "\n" ,
01762 "-------------------------\n" ,
01763 "Variable: AFNI_1D_TIME_TR\n" ,
01764 "-------------------------\n" ,
01765 "If this is set, and AFNI_1D_TIME is YES, then this determines the TR (in\n" ,
01766 "seconds) of a .1D file read in as an AFNI dataset.\n" ,
01767 "\n" ,
01768 "------------------------\n" ,
01769 "Variable: AFNI_3D_BINARY\n" ,
01770 "------------------------\n" ,
01771 "If this is set to YES, then .3D files are written by AFNI programs in\n" ,
01772 "binary, rather than the default text mode. Binary files will be more\n" ,
01773 "compact (usually) and faster to read in.\n" ,
01774 "\n" ,
01775 "--------------------------\n" ,
01776 "Variable: AFNI_MAX_OPTMENU (editable)\n" ,
01777 "--------------------------\n" ,
01778 "This variable (default=255) sets the maximum number of entries allowed\n" ,
01779 "in an AFNI \"option menu\" -- these are the buttons that popup a menu\n" ,
01780 "of values from which to choose, and which also let you popup a text\n" ,
01781 "list chooser by right-clicking in the menu's label. (Example: the\n" ,
01782 "sub-brick option menus \"Anat\", \"Func\", \"Thr\" on the \"Define Overlay\"\n" ,
01783 "control panel.)\n" ,
01784 "\n" ,
01785 "Some computer systems may crash when an option menu gets too big.\n" ,
01786 "That's why there is a default limit in AFNI of 255 entries. However,\n" ,
01787 "if you have a bucket dataset with more than 255 sub-bricks, this makes\n" ,
01788 "it impossible to view the later data volumes. If this problem arises,\n" ,
01789 "you can try setting this environment variable to a larger limit (e.g.,\n" ,
01790 "99999 would take care of all currently imaginable cases).\n" ,
01791 "\n" ,
01792 "---------------------------------\n" ,
01793 "Variable: AFNI_VALUE_LABEL_DTABLE\n" ,
01794 "---------------------------------\n" ,
01795 "This variable sets a filename that holds a default value-label table\n" ,
01796 "for the Draw Dataset plugin. A sample file is shown below:\n" ,
01797 "\n" ,
01798 " <VALUE_LABEL_DTABLE\n" ,
01799 " ni_type=\"2*String\"\n" ,
01800 " ni_dimen=\"3\" >\n" ,
01801 " \"1\" \"elvis\"\n" ,
01802 " \"2\" \"presley\"\n" ,
01803 " \"3\" \"memphis\"\n" ,
01804 " </VALUE_LABEL_DTABLE>\n" ,
01805 "\n" ,
01806 "The 'ni_dimen' attribute is the number of value-label pairs; in the\n" ,
01807 " above example it is 3.\n" ,
01808 "Each value-label pair is shown on a separate line. The values and\n" ,
01809 " labels are strings, enclosed in quote characters. There should be\n" ,
01810 " exactly as many value-label pairs as specified in 'ni_dimen'.\n" ,
01811 "If you really want to put a double quote character \" in a label,\n" ,
01812 " you can enclose the label in single forward quotes ' instead.\n" ,
01813 "When you 'Save' a drawn dataset from the Draw Dataset plugin, the\n" ,
01814 " .HEAD file attribute VALUE_LABEL_DTABLE will contain a table in\n" ,
01815 " exactly this XML-based format.\n" ,
01816 "\n" ,
01817 "-------------------------------\n" ,
01818 "Variable: AFNI_STROKE_THRESHOLD (editable)\n" ,
01819 "-------------------------------\n" ,
01820 "If you press Button-1 in an image window, and then move it left or\n" ,
01821 "right (\"stroke it\") before releasing the button, the grayscale mapping\n" ,
01822 "changes in the same way as if you pressed the 'c' button up and the 'b'\n" ,
01823 "button down. This variable sets the threshold for the stroking movement\n" ,
01824 "size in pixels; a movement of this number of pixels rightwards corresponds\n" ,
01825 "to one press of 'c' up and 'b' down, while a leftwards movement is like\n" ,
01826 "one press of 'c' down and 'b' up. Larger movements make larger adjustments.\n" ,
01827 "\n" ,
01828 "A larger threshold makes the stroking less sensitive; a smaller threshold\n" ,
01829 "makes it more sensitive. The value you choose will depend on your personal\n" ,
01830 "taste. The default is 32 pixels, which is the flavor I prefer. If you set\n" ,
01831 "this variable to 0, then the stroking function is disabled.\n" ,
01832 "\n" ,
01833 "-------------------------------\n" ,
01834 "Variable: AFNI_STROKE_AUTOPLOT (editable)\n" ,
01835 "-------------------------------\n" ,
01836 "If this variable is set to YES, then the graymap-versus-data value plot\n" ,
01837 "(manually controlled by \"Display Graymap Plot\") is automatically popped\n" ,
01838 "up when the grayscale mapping is altered by using the stroking feature\n" ,
01839 "described above. When the stroke is finished, the plot will pop down.\n" ,
01840 "N.B.: when the 'Draw Dataset' plugin is active, this option is disabled\n" ,
01841 "temporarily.\n" ,
01842 "\n" ,
01843 "-----------------------------\n" ,
01844 "Variable: AFNI_IMAGE_MINTOMAX (editable)\n" ,
01845 "-----------------------------\n" ,
01846 "If this variable is set to YES, then image viewer windows will be set\n" ,
01847 "to the \"Min-to-Max\" state rather than the default \"2%-to-98%\" state\n" ,
01848 "when they are opened. If you set this in the \"Edit Environment\"\n" ,
01849 "control, it only affects image viewer windows opened after that point.\n" ,
01850 "\n" ,
01851 "--------------------------------\n" ,
01852 "Variable: AFNI_IMAGE_GLOBALRANGE (editable)\n" ,
01853 "--------------------------------\n" ,
01854 "If this variable is set to YES, then the image viewer windows will be\n" ,
01855 "set to scale the bottom gray level to the minimum value in the 3D\n" ,
01856 "volume and the top gray level to the maximum value in the 3D volume.\n" ,
01857 "This setting overrides the \"Min-to-Max\" and \"2%-to-98%\" settings in\n" ,
01858 "the \"Disp\" control panel. This setting also applies to all image\n" ,
01859 "viewers. If you set this in the \"Edit Environment\" control, it will\n" ,
01860 "apply to all open image viewers immediately, as well as to any image\n" ,
01861 "viewers opened later.\n" ,
01862 "\n" ,
01863 "----------------------------\n" ,
01864 "Variable: AFNI_DRAW_UNDOSIZE (editable)\n" ,
01865 "----------------------------\n" ,
01866 "This variable sets the size (in units of Megabytes) of the Undo/Redo\n" ,
01867 "buffer in the Draw Dataset plugin. The default value is 6. If you\n" ,
01868 "are short on memory, you could set this to 1. If you are running out\n" ,
01869 "of undo levels, you could set this to a larger value; however, this\n" ,
01870 "would only be needed if you are drawing huge 3D swaths of data at a\n" ,
01871 "time (e.g., using the 3D sphere option with a large radius).\n" ,
01872 "\n" ,
01873 "---------------------\n" ,
01874 "Variable: AFNI_SPEECH (editable)\n" ,
01875 "---------------------\n" ,
01876 "If this YES/NO variable is set to NO, then the AFNI speech synthesis\n" ,
01877 "is disabled. At the current time (Nov 2003), only the Mac OS X 10.3\n" ,
01878 "version of AFNI uses speech synthesis in any way. And that's just\n" ,
01879 "for fun.\n" ,
01880 "\n" ,
01881 "------------------------------\n" ,
01882 "Variable: AFNI_IMAGE_ZEROCOLOR\n" ,
01883 "------------------------------\n" ,
01884 "This variable, if set to the string name of one of the colors in the\n" ,
01885 "color chooser menus (e.g., \"Black\"), will result in voxels whose value\n" ,
01886 "is 0 being set to this color in the slice viewing windows (except when\n" ,
01887 "viewing RGB images). The main function is to avoid having to use the\n" ,
01888 "\"Choose Zero Color\" menu all the time, especially when you use the \"Swap\"\n" ,
01889 "feature to invert the grayscale map (e.g., to make a T2 weighted image\n" ,
01890 "look sort of like a T1 weighted image).\n" ,
01891 "\n" ,
01892 "----------------------------\n" ,
01893 "Variable: AFNI_MPEG_DATASETS\n" ,
01894 "----------------------------\n" ,
01895 "This variable can be used to allow MPEG files to be read in as AFNI datasets.\n" ,
01896 "Such datasets are inherently 3 dimensional. How they will be organized inside\n" ,
01897 "AFNI depends on the setting of this variable. The options are:\n" ,
01898 " SPACE = the frame sequence number will be the z-axis\n" ,
01899 " TIME = the frame sequence number will be the time axis\n" ,
01900 " NO = MPEG files won't be read as AFNI datasets\n" ,
01901 " (they can still be read as images into to3d, aiv, etc.)\n" ,
01902 "If this variable is NOT set to anything, then it is the same as SPACE.\n" ,
01903 "\n" ,
01904 "MPEG filenames input to AFNI programs (as sources of images or as datasets)\n" ,
01905 "must end in \".mpg\", \".MPG\", \".mpeg\", or \".MPEG\". MPEG datasets will be read\n" ,
01906 "so that the individal images are displayed in an Axial image window.\n" ,
01907 "\n" ,
01908 "---------------------------\n" ,
01909 "Variable: AFNI_MPEG_GRAYIZE\n" ,
01910 "---------------------------\n" ,
01911 "If this YES/NO variable is set to YES, then MPEG files read into AFNI,\n" ,
01912 "to3d, or aiv will be converted to grayscale, even if the images in\n" ,
01913 "the movie are in color.\n" ,
01914 "\n" ,
01915 "--------------------------\n" ,
01916 "Variable: AFNI_VIDEO_DELAY (editable)\n" ,
01917 "--------------------------\n" ,
01918 "This is the number of milliseconds the AFNI waits between drawing new\n" ,
01919 "images when the 'V' or 'v' keys are pressed in an image (or graph)\n" ,
01920 "window. The default value is 1, which is faster than video can be\n" ,
01921 "displayed anyway. Set this to a larger value (e.g, 100) to slow down\n" ,
01922 "the image redraw rate.\n" ,
01923 "\n" ,
01924 "----------------------------\n" ,
01925 "Variable: AFNI_IMAGE_ENTROPY (editable)\n" ,
01926 "----------------------------\n" ,
01927 "If this numeric variable is set, this is the entropy of an image below\n" ,
01928 "which the 2%-98% image scaling will be disabled, and min-to-max will\n" ,
01929 "be used instead. The units are bits/byte; a useful threshold seems to\n" ,
01930 "be in the range (0.2,0.5). For images that only have a few values\n" ,
01931 "different from 0, the 2%-98% scaling can produce weird artifacts. Such\n" ,
01932 "images will also have a very low entropy. Since this variable can be\n" ,
01933 "changed interactively from the Edit Environment controls, you can play\n" ,
01934 "with it to see how it affects your images.\n" ,
01935 "\n" ,
01936 "----------------------------\n" ,
01937 "Variable: AFNI_LOGO16 (etc.)\n" ,
01938 "----------------------------\n" ,
01939 "If this variable is set to YES, then the 'AFNI' background logo used in\n" ,
01940 "the controller and image windows will be enabled. By default, it is off.\n" ,
01941 "You can control the colors of this logo by the following variables:\n" ,
01942 " AFNI_LOGO16_FOREGROUND_x\n" ,
01943 " AFNI_LOGO16_BACKGROUND_x\n" ,
01944 "where 'x' is 'A', 'B', 'C', etc., for the various controller labels.\n" ,
01945 "If AFNI_LOGO16_BACKGROUND_x isn't set, then AFNI_LOGO16_BACKGROUND\n" ,
01946 "(with no suffix) is checked as an alternate. The values of these\n" ,
01947 "variables should be the names of one of the labels on the color chooser\n" ,
01948 "menus (e.g., the \"Xhairs Color\" menu). You can use these variables to\n" ,
01949 "make the windows for the various controllers somewhat distinct in\n" ,
01950 "appearance. If these color variables are not set at all, then AFNI\n" ,
01951 "uses some colors of my choosing for this purpose.\n" ,
01952 "\n" ,
01953 "--------------------------\n" ,
01954 "Variable: AFNI_THRESH_LOCK (editable)\n" ,
01955 "--------------------------\n" ,
01956 "This variable can be used to lock the Define Overlay threshold sliders\n" ,
01957 "together. There are three possibilities:\n" ,
01958 " NO (the default) => each controller's slider is independent\n" ,
01959 " VALUE => the numerical value on each slider will be the same\n" ,
01960 " P-VALUE => the p-value for each slider will be the same\n" ,
01961 "This locking only applies to AFNI controllers that are Lock-ed together\n" ,
01962 "(cf. AFNI_ALWAYS_LOCK and the Define Datamode->Lock menu). If p-values\n" ,
01963 "are locked, this lock will also only apply to controllers whose current\n" ,
01964 "Threshold sub-brick has a known statistical distribution.\n" ,
01965 "\n" ,
01966 "When you drag a locked threshold slider, the other one will only change\n" ,
01967 "when you release the mouse button -- they won't slide in tandem, but will\n" ,
01968 "just jump to the final value.\n" ,
01969 "\n" ,
01970 "------------------------\n" ,
01971 "Variable: AFNI_PBAR_LOCK (editable)\n" ,
01972 "------------------------\n" ,
01973 "If this variable is set to YES, then the Define Overlay color bars\n" ,
01974 "(the \"pbars\") of AFNI controllers that are Lock-ed together will be\n" ,
01975 "coordinated. Changes to one locked pbar will be reflected in the\n" ,
01976 "others immediately.\n" ,
01977 "\n" ,
01978 "----------------------------\n" ,
01979 "Variable: AFNI_IMAGE_ZOOM_NN (editable)\n" ,
01980 "----------------------------\n" ,
01981 "If this variable is set to YES, then image viewer windows will use\n" ,
01982 "nearest neighbor interpolation for zooming. The default is linear\n" ,
01983 "interpolation, which produces smoother-looking images. However, some\n" ,
01984 "people want to see the actual data values represented in the window,\n" ,
01985 "not some fancy-schmancy interpolated values designed to look good but\n" ,
01986 "in fact making a mockery of a sham of a mockery of a travesty of two\n" ,
01987 "mockeries of a sham of reality.\n" ,
01988 "\n" ,
01989 "------------------------------\n" ,
01990 "Variable: AFNI_DISABLE_CURSORS\n" ,
01991 "------------------------------\n" ,
01992 "If this variable is set to YES, then AFNI will not try to change the X11\n" ,
01993 "cursor shape. This feature is available because it seems that sometimes\n" ,
01994 "particular X11 installations choices of cursor and AFNI's choices don't\n" ,
01995 "work together well. If you have unpleasant cursors in AFNI (e.g., an X),\n" ,
01996 "try setting this variable to YES.\n" ,
01997 "\n" ,
01998 "-----------------------------\n" ,
01999 "Variable: AFNI_SLAVE_FUNCTIME (editable)\n" ,
02000 "-----------------------------\n" ,
02001 "When the underlay and overlay datasets both are time-dependent, switching\n" ,
02002 "the time index will change both the underlay and overlay sub-bricks. If\n" ,
02003 "you want the time index control to change ONLY the underlay sub-brick,\n" ,
02004 "then set this variable to NO.\n" ,
02005 "\n" ,
02006 "----------------------------\n" ,
02007 "Variable: AFNI_SLAVE_THRTIME (editable)\n" ,
02008 "----------------------------\n" ,
02009 "When the underlay and overlay datasets both are time-dependent, switching\n" ,
02010 "the time index will change both the underlay and overlay sub-bricks, but\n" ,
02011 "NOT the threshold sub-brick. If you want the time index control to change\n" ,
02012 "the threshold sub-brick, then set this variable to YES.\n" ,
02013 "\n" ,
02014 "----------------------------\n" ,
02015 "Variable: AFNI_CLICK_MESSAGE\n" ,
02016 "----------------------------\n" ,
02017 "If this veriable is set to NO, then the string\n" ,
02018 " [---------------]\n" ,
02019 " [ Click in Text ]\n" ,
02020 " [ to Pop Down!! ]\n" ,
02021 "will NOT be appended to the very first popup message window that AFNI\n" ,
02022 "creates. This message was added because some people do not realize\n" ,
02023 "that the way to get rid of these popups (before they vanish on their\n" ,
02024 "own after 30 seconds) is to click in them. You know who you are.\n" ,
02025 "However, if you are advanced enough to read this file, then you probably\n" ,
02026 "aren't one of THEM.\n" ,
02027 "\n" ,
02028 "------------------------------------\n" ,
02029 "Variable: AFNI_REALTIME_MP_HOST_PORT (editable)\n" ,
02030 "------------------------------------\n" ,
02031 "When this variable is set, the realtime plugin will attempt to open a tcp\n" ,
02032 "socket to the corresponding host and port, and will send the six registration\n" ,
02033 "correction parameters for each 3D volume received by the plugin. This applies\n" ,
02034 "only to the case of graphing 3D registration. The socket will be opened at\n" ,
02035 "the start of each run, and will be closed at the end. A simple example of\n" ,
02036 "what to set this variable to is localhost:53214. See 'serial_helper -help'\n" ,
02037 "for more details.\n" ,
02038 "\n" ,
02039 "-----------------------------\n" ,
02040 "Variable: AFNI_X11_REDECORATE (editable)\n" ,
02041 "-----------------------------\n" ,
02042 "By default, AFNI tries to change some of the \"decorations\" (control buttons)\n" ,
02043 "on some of the windows it creates (e.g., removing resize handles). If you\n" ,
02044 "don't want this to happen, set this variable to NO. This variable only\n" ,
02045 "has an effect on windows created AFTER it is set, so if you change this\n" ,
02046 "interactively in the Edit Environment plugin, it will not affect existing\n" ,
02047 "windows. Normally, you would want to set this in your .afnirc file.\n" ,
02048 "\n" ,
02049 "-------------------------------\n" ,
02050 "Variable: AFNI_IMAGE_SAVESQUARE\n" ,
02051 "-------------------------------\n" ,
02052 "YES/NO: Forces images (from the image view \"Save\" button) to be saved with\n" ,
02053 "square pixels, even if they are stored with nonsquare pixels.\n" ,
02054 "\n" ,
02055 "-------------------------------\n" ,
02056 "Variable: AFNI_BUCKET_LABELSIZE\n" ,
02057 "-------------------------------\n" ,
02058 "THIS VARIABLE HAS BEEN REMOVED FROM AFNI.\n" ,
02059 "\n" ,
02060 "Formerly, it was used to set the width of the \"ULay\", \"OLay\", and \"Thr\" menu\n" ,
02061 "choosers on the \"Define Overlay\" control panel. As of 03 May 2005, AFNI now\n" ,
02062 "calculates the default width based on the longest sub-brick label input\n" ,
02063 "for each dataset.\n" ,
02064 "\n" ,
02065 "-------------------------\n" ,
02066 "Variable: AFNI_MAX_1DSIZE\n" ,
02067 "-------------------------\n" ,
02068 "Sets the maximum size (in bytes) of each 1D file that will be automatically\n" ,
02069 "loaded when AFNI starts. The default is 123 Kbytes. The intention is to\n" ,
02070 "prevent loading of very large files that are not intended to be used for\n" ,
02071 "graphing/FIMming purposes.\n" ,
02072 "\n" ,
02073 "---------------------------\n" ,
02074 "Variable: AFNI_TITLE_LABEL2 (editable)\n" ,
02075 "---------------------------\n" ,
02076 "If this YES/NO variable is YES, then the AFNI window titlebars will show\n" ,
02077 "the 'label2' field from the AFNI dataset .HEAD file, rather than the\n" ,
02078 "dataset filename. If the label2 field is set to a nontrivial value,\n" ,
02079 "that is. You can set the label2 field with the 3drefit command.\n" ,
02080 "\n" ,
02081 "-------------------------------\n" ,
02082 "Variable: AFNI_SHOW_SURF_POPUPS\n" ,
02083 "-------------------------------\n" ,
02084 "If this YES/NO variable is set to YES, then when AFNI receives surface\n" ,
02085 "nodes, triangles or normals from suma, a popup message will be displayed.\n" ,
02086 "Otherwise, the message will be send to stderr (on the terminal window).\n" ,
02087 "\n" ,
02088 "-------------------------------\n" ,
02089 "Variable: AFNI_KILL_SURF_POPUPS\n" ,
02090 "-------------------------------\n" ,
02091 "If this YES/NO variable is set to YES, then when AFNI receives surface\n" ,
02092 "nodes, triangles or normals from suma, no messages will be displayed,\n" ,
02093 "either in a popup or stderr. Note that if errors occur, popups will\n" ,
02094 "still be shown; this just turns off the normal information messages.\n" ,
02095 "N.B.: If AFNI_SHOW_SURF_POPUPS is YES, then it wins over\n" ,
02096 " AFNI_KILL_SURF_POPUPS being YES. If neither is set, then\n" ,
02097 " messages are displayed to stderr.\n" ,
02098 "\n" ,
02099 "-----------------------------\n" ,
02100 "Variable: AFNI_EDGIZE_OVERLAY (editable)\n" ,
02101 "-----------------------------\n" ,
02102 "If set to YES, then the color overlays in the image windows will only\n" ,
02103 "have their edge pixels displayed. That is, each 'blob' will be hollowed\n" ,
02104 "out, leaving only its edges. If you do this, you probably want to make\n" ,
02105 "the color overlay opaque, so that the results are easily seen.\n" ,
02106 "\n" ,
02107 "--------------------------\n" ,
02108 "Variable: AFNI_NIFTI_DEBUG (editable)\n" ,
02109 "--------------------------\n" ,
02110 "This integral variable determines the debug level used by the nifti_io\n" ,
02111 "library functions. If set to 0, only errors are reported by the library.\n" ,
02112 "The maximum debug level used is currently 4. Note that if this is changed\n" ,
02113 "from within AFNI, a 'Rescan: This' operation should probably be performed,\n" ,
02114 "which will force a re-reading of the datasets and so force an elicitation\n" ,
02115 "of the NIfTI debug messages (for .nii files, that is).\n" ,
02116 "\n" ,
02117 "-------------------------\n" ,
02118 "Variable AFNI_NIFTI_NOEXT\n" ,
02119 "-------------------------\n" ,
02120 "When writing a '.nii' (or '.nii.gz') file from an AFNI program, normally\n" ,
02121 "a NIfTI-1.1 extension field with some extra AFNI header information is\n" ,
02122 "written into the output file. If you set this variable to YES, then\n" ,
02123 "this extension is not written, which will make the output be a 'pure'\n" ,
02124 "NIfTI-1.1 file. Only use this if absolutely necessary. You can also\n" ,
02125 "use the 'nifti_tool' program to strip extension data from a NIfTI-1.1\n" ,
02126 "dataset file.\n" ,
02127 "\n" ,
02128 "---------------------------\n" ,
02129 "Variable: AFNI_OVERLAY_ZERO (editable)\n" ,
02130 "---------------------------\n" ,
02131 "If set to YES, this variable indicates that voxels in the overlay dataset\n" ,
02132 "that have the numerical value of 0 will get colored when the Inten color\n" ,
02133 "scale on the Define Datamode panel indicates that 0 has a color that isn't\n" ,
02134 "\"none\". The default way that AFNI works is NOT to colorize voxels that\n" ,
02135 "are 0, even if they should otherwise get a color.\n" ,
02136 "\n" ,
02137 "---------------------------\n" ,
02138 "Variable: NIML_TRUSTHOST_xx\n" ,
02139 "---------------------------\n" ,
02140 "These environment variables ('xx' = '01', '02', ..., '99') set the names\n" ,
02141 "and/or addresses of external computer hosts to trust with NIML TCP/IP\n" ,
02142 "connections, which are how AFNI and SUMA communicate. Should only be\n" ,
02143 "necessary to use these if you are using AFNI and SUMA on different\n" ,
02144 "machines. Connections from machines not on the trusted list will be\n" ,
02145 "rejected, for the sake of security. The 'localhost' or 127.0.0.1 address\n" ,
02146 "and local class B network 192.168.0.* addresses are always trusted.\n" ,
02147 "\n" ,
02148 "---------------------------\n" ,
02149 "Variable: AFNI_DONT_LOGFILE\n" ,
02150 "---------------------------\n" ,
02151 "Most AFNI programs write a copy of their command line to a file in your\n" ,
02152 "home directory named \".afni.log\". If you do NOT want the log to be\n" ,
02153 "kept, set this environment variable to YES. The purpose of the log\n" ,
02154 "is for you to be able to look back and see what AFNI commands you used\n" ,
02155 "in the past. However, if you are doing a vast number of commands inside\n" ,
02156 "a script, the log file might eventually become gigantic (the Kevin Murphy\n" ,
02157 "effect).\n" ,
02158 "\n" ,
02159 "-------------------------\n" ,
02160 "Variable: AFNI_WRITE_NIML\n" ,
02161 "-------------------------\n" ,
02162 "If this variable is set to YES, then AFNI .HEAD files will be written in\n" ,
02163 "the new NIML (XML subset) format, rather than the 'classic' format. The\n" ,
02164 "volumetric image data is still in the pure binary .BRIK file, not XML-ified\n" ,
02165 "in any way. At present (Jun 2005) this format is experimental, but will\n" ,
02166 "someday soon become the default.\n" ,
02167 "\n" ,
02168 "=============================================\n" ,
02169 "| Robert W Cox, PhD |\n" ,
02170 "| Scientific and Statistical Computing Core |\n" ,
02171 "| National Institute of Mental Health |\n" ,
02172 "| National Institutes of Health |\n" ,
02173 "| Department of Health & Human Services |\n" ,
02174 "| United States of America |\n" ,
02175 "| Earth, United Federation of Planets |\n" ,
02176 "=============================================\n" ,
02177 "\n" ,
02178 "############################################################################\n" ,
02179 "##### Variables that Specifically Affect the Operation of 3dDeconvolve #####\n" ,
02180 "############################################################################\n" ,
02181 "\n" ,
02182 "----------------------------------\n" ,
02183 "Variable: AFNI_3dDeconvolve_extend\n" ,
02184 "----------------------------------\n" ,
02185 "If you input a stimulus time series (via the -stim_file option) to\n" ,
02186 "3dDeconvolve that is shorter than needed for the regression analysis, the\n" ,
02187 "program will normally print a warning message and extend the time series\n" ,
02188 "with zero values to the needed length. If you would rather have the program\n" ,
02189 "stop if it detects this problem (the behavior before 22 Oct 2003), then set\n" ,
02190 "this environment variable to NO.\n" ,
02191 "\n" ,
02192 "---------------------------------\n" ,
02193 "Variable: AFNI_3dDeconvolve_nodup\n" ,
02194 "---------------------------------\n" ,
02195 "If this variable is set to YES, then if the 3dDeconvolve program detects\n" ,
02196 "duplicate input stimulus filenames or duplicate regressors, the program\n" ,
02197 "will fail (with an error message) rather than attempt to continue.\n" ,
02198 "\n" ,
02199 "-----------------------------------------\n" ,
02200 "Variable: AFNI_3dDeconvolve_nodata_extras\n" ,
02201 "-----------------------------------------\n" ,
02202 "When using the -nodata option in 3dDeconvolve, the default printout gives\n" ,
02203 "the 'normalized standard deviation' for each stimulus parameter. If you\n" ,
02204 "set this variable to YES, then the printout will include the -polort\n" ,
02205 "baseline parameters as well, and also the L2 norm of each column in\n" ,
02206 "the regression matrix.\n" ,
02207 "\n" ,
02208 "--------------------------\n" ,
02209 "Variable: AFNI_XJPEG_COLOR\n" ,
02210 "--------------------------\n" ,
02211 "Determines the color of the lines drawn between the column boxes in the\n" ,
02212 "output from the -xjpeg option to 3dDeconvolve. The color format is\n" ,
02213 "\"rgbi:rf/gf/bf\", where each value rf,gf,bf is a number between 0.0 and 1.0\n" ,
02214 "(inclusive); for example, yellow would be \"rgbi:1.0/1.0/0.0\". As a\n" ,
02215 "special case, if this value is the string \"none\" or \"NONE\", then these\n" ,
02216 "lines will not be drawn.\n" ,
02217 "\n" ,
02218 "-------------------------\n" ,
02219 "Variable: AFNI_XJPEG_IMXY\n" ,
02220 "-------------------------\n" ,
02221 "This variable determines the size of the image saved when via the -xjpeg\n" ,
02222 "option to 3dDeconvolve. It should be in the format AxB, where 'A' is the\n" ,
02223 "number of pixels the image is to be wide (across the matrix rows) and 'B'\n" ,
02224 "is the number of pixels high (down the columns); for example:\n" ,
02225 " setenv AFNI_XJPEG_IMXY 768x1024\n" ,
02226 "which means to set the x-size (horizontal) to 768 pixels and the y-size\n" ,
02227 "(vertical) to 1024 pixels. These values are the default, by the way.\n" ,
02228 "\n" ,
02229 "If the first value 'A' is negative and less than -1, its absolute value\n" ,
02230 "is the number of pixels across PER ROW. If the second value 'B' is\n" ,
02231 "negative, its absolute value is the number of pixels down PER ROW.\n" ,
02232 "(Usually there are many fewer columns than rows.)\n" ,
02233 "\n" ,
02234 "-------------------------\n" ,
02235 "Variable: AFNI_XSAVE_TEXT\n" ,
02236 "-------------------------\n" ,
02237 "If this YES/NO variable is set to YES, then the .xsave file created by\n" ,
02238 "the \"-xsave\" option to 3dDeconvolve will be saved in text format. The\n" ,
02239 "default is a binary format, which preserves the full accuracy of the\n" ,
02240 "matrices stored therein. However, if you want to look at the .xsave\n" ,
02241 "file yourself, the binary format is hard to grok. Note that the two\n" ,
02242 "forms are not quite equivalent, since the binary format stores the\n" ,
02243 "exact matrices used internally in the program, whereas the ASCII format\n" ,
02244 "stores only a decimal approximation of these matrices.\n" ,
02245 "\n" ,
02246 "---------------------------\n" ,
02247 "Variable: AFNI_GLTSYM_PRINT\n" ,
02248 "---------------------------\n" ,
02249 "If this YES/NO variable is set to YES, then the GLT matrices generated\n" ,
02250 "in 3dDeconvolve by the \"-gltsym\" option will be printed to the screen\n" ,
02251 "when the program starts up.\n" ,
02252 NULL } ;
02253 #define NUM_readme_env 2250
