1 /** automatically generated by AFNI program quotize **/
2 static char *readme_env[] = {
3 "###########################################\n" ,
4 "### Intro: Unix env vars used by AFNI ###\n" ,
5 "###########################################\n" ,
6 "\n" ,
7 "The AFNI program allows you to use several Unix environment variables\n" ,
8 "to influence its behavior. The mechanics of setting an environment\n" ,
9 "variable depend on which shell you are using. To set an environment\n" ,
10 "variable named \"FRED\" to the string \"Elvis\":\n" ,
11 "\n" ,
12 " csh or tcsh: setenv FRED Elvis\n" ,
13 " bash or ksh: FRED=Elvis ; export FRED\n" ,
14 "\n" ,
15 "Normally, these commands would go in your .cshrc or .profile files,\n" ,
16 "so that they would be invoked when you login. If in doubt, consult\n" ,
17 "your local Unix guru. If you don't have one, well....\n" ,
18 "\n" ,
19 "You don't NEED to set any of these variables -- AFNI will still work\n" ,
20 "correctly. But they are an easy way to set up certain defaults to\n" ,
21 "make AFNI a little easier on your neocortex and hippocampus.\n" ,
22 "\n" ,
23 "N.B.: Changes to environment variables AFTER you start a program will\n" ,
24 " not be seen by that program, since each running program gets\n" ,
25 " a private copy of the entire set of environment variables when\n" ,
26 " it starts. This is a standard Unix feature, and is not specific\n" ,
27 " to AFNI. Some variables can be set internally in AFNI using\n" ,
28 " the \"Edit Environment\" control from the \"Datamode->Misc\" menu\n" ,
29 " or from the image window Button-3 popup menu. Such variables\n" ,
30 " are marked with \"(editable)\" in the descriptions below.\n" ,
31 "\n" ,
32 "N.B.: Some variables below are described as being of \"YES/NO\" type.\n" ,
33 " This means that they should either be set to the value \"YES\"\n" ,
34 " or to the value \"NO\".\n" ,
35 "\n" ,
36 "N.B.: You can now set environment variables on the 'afni' command\n" ,
37 " line; for example:\n" ,
38 " afni -DAFNI_SESSTRAIL=3 -DAFNI_FUNC_ALPHA=YES\n" ,
39 " This may be useful for a 'one time' situation, or as an alias.\n" ,
40 " You can also use this '-Dname=val' option in 1dplot and 3dDeconvolve.\n" ,
41 " [RWCox: 22 Mar 2005]\n" ,
42 " And now you can use this feature on most program command lines.\n" ,
43 " [RWCox: 13 Dec 2007]\n" ,
44 "\n" ,
45 "N.B.: At the end of this file is a list of several environment variables\n" ,
46 " that affect the program 3dDeconvolve, rather than the interactive\n" ,
47 " AFNI program itself.\n" ,
48 "\n" ,
49 "N.B.: If you set an AFNI environment variable on the command line, or\n" ,
50 " in a shell startup file (e.g., ~/.cshrc), and also have that\n" ,
51 " variable in your ~/.afnirc file, you will get a warning telling\n" ,
52 " you that the value in the ~/.afnirc file is being ignored.\n" ,
53 " To turn off these warnings, set environment variable\n" ,
54 " AFNI_ENVIRON_WARNINGS to NO.\n" ,
55 "\n" ,
56 "N.B.: You can allow the .afnirc file to re-set existing environment\n" ,
57 " variables by setting environment variable AFNI_ENVIRON_RESET to YES.\n" ,
58 "\n" ,
59 "#################################################\n" ,
60 "### Setting env variables in file ~/.afnirc ###\n" ,
61 "#################################################\n" ,
62 "\n" ,
63 "As of June, 1999, you can now set environment variables for an interactive\n" ,
64 "AFNI run in the setup (~/.afnirc) file. This is provided as a convenience.\n" ,
65 "An example:\n" ,
66 "\n" ,
67 " ***ENVIRONMENT\n" ,
68 " AFNI_HINTS = YES\n" ,
69 " AFNI_SESSTRAIL = 3\n" ,
70 "\n" ,
71 "Note that the spaces around the \"=\" sign are required. See README.setup\n" ,
72 "for more information about the possible contents of .afnirc besides the\n" ,
73 "environment variables.\n" ,
74 "\n" ,
75 "A few other programs in the AFNI package also read the ***ENVIRONMENT\n" ,
76 "section of the .afnirc file. This is needed so that environment settings\n" ,
77 "that affect those programs (e.g., AFNI_COMPRESSOR for auto-compression of\n" ,
78 "output datasets) can be properly initialized in .afnirc.\n" ,
79 "\n" ,
80 "At the same time, the routine in AFNI that initializes certain internal\n" ,
81 "constants from X11 resources (usually in your .Xdefaults or .Xresources\n" ,
82 "file, and described in file AFNI.Xdefaults) has been modified to also\n" ,
83 "allow the same constants to be set from Unix environment variables.\n" ,
84 "For example, the gap (in pixels) between sub-graphs is set by the\n" ,
85 "X11 resource \"AFNI*graph_ggap\", and can now be set by the environment\n" ,
86 "variables \"AFNI_graph_ggap\" or \"AFNI_GRAPH_GGAP\", as in:\n" ,
87 "\n" ,
88 " AFNI_graph_ggap = 6 // this is a comment\n" ,
89 "\n" ,
90 "If an X11 resource is actually set, it will take priority over the\n" ,
91 "environment variable. Some of the variables that can be set in this\n" ,
92 "way are:\n" ,
93 "\n" ,
94 " AFNI_ncolors = number of gray levels to use\n" ,
95 " AFNI_gamma = gamma correction for image intensities\n" ,
96 " AFNI_graph_boxes_thick = 0=thin lines, 1=thick lines, for graph boxes\n" ,
97 " AFNI_graph_grid_thick = ditto for the graph vertical grid lines\n" ,
98 " AFNI_graph_data_thick = ditto for the data graphs\n" ,
99 " AFNI_graph_ideal_thick = ditto for the ideal graphs\n" ,
100 " AFNI_graph_ort_thick = ditto for the ort graphs\n" ,
101 " AFNI_graph_dplot_thick = ditto for the dplot graphs\n" ,
102 " AFNI_graph_ggap = initial spacing between graph boxes\n" ,
103 " AFNI_graph_matrix = initial number of sub-graphs\n" ,
104 " AFNI_fim_polort = polynomial detrending order for FIM\n" ,
105 " AFNI_fim_ignore = how many pts to ignore at start when doing FIM\n" ,
106 " AFNI_montage_periodic = True allows periodic montage wraparound\n" ,
107 " AFNI_purge = True allows automatic dataset memory purge\n" ,
108 " AFNI_resam_vox = dimension of voxel (mm) for resampled datasets\n" ,
109 " AFNI_resam_anat = One of NN, Li, Cu, Bk for Anat resampling mode\n" ,
110 " AFNI_resam_func = ditto for Func resampling mode\n" ,
111 " AFNI_resam_thr = ditto for Threshold resampling mode\n" ,
112 " AFNI_pbar_posfunc = True will start color pbar as all positive\n" ,
113 " AFNI_pbar_sgn_pane_count = # of panes to start signed color pbar with\n" ,
114 " AFNI_pbar_pos_pane_count = # of panes to start positive color pbar with\n" ,
115 "\n" ,
116 "Some other such variables are described in file AFNI.Xdefaults. Note that\n" ,
117 "values that actually affect the way the X11/Motif interface appears, such as\n" ,
118 "AFNI*troughColor, must be set via the X11 mechanism and cannot be set using\n" ,
119 "Unix environment variables. This is because they are interpreted by the\n" ,
120 "Motif graphics library when it starts and not by any actual AFNI code.\n" ,
121 "\n" ,
122 "The following example is from my own .afnirc file on the Linux system on\n" ,
123 "which I do most of the AFNI development. The first ones (in lower case)\n" ,
124 "are described in AFNI.Xdefaults. The later ones (all upper case) are\n" ,
125 "documented in this file. (You can tell from this file that I like to\n" ,
126 "have things line up. You would never be able to tell this from the\n" ,
127 "piles of paper in my office, though.) And the file is:\n" ,
128 "\n" ,
129 " ***ENVIRONMENT\n" ,
130 " AFNI_ncolors = 60 // number of gray levels\n" ,
131 " AFNI_gamma = 1.5 // adjust for proper display\n" ,
132 " AFNI_purge = True // purge datasets from memory when not used\n" ,
133 " AFNI_chooser_doubleclick = Apply // like Apply button; could also be Set\n" ,
134 " AFNI_chooser_listmax = 25 // max nonscrolling items in chooser lists\n" ,
135 " AFNI_graph_width = 512 // initial width of graph window (pixels)\n" ,
136 " AFNI_graph_height = 384 // initial height of graph window\n" ,
137 " AFNI_graph_data_thick = 1 // graph time series with thick lines\n" ,
138 " AFNI_fim_ignore = 2 // default value for FIM ignore\n" ,
139 " AFNI_graph_ggap = 7 // gap between sub-graphs (pixels)\n" ,
140 " AFNI_pbar_hide = True // hide color pbar when it changes size\n" ,
141 " AFNI_hotcolor = Violet // color to use on Done and Set buttons\n" ,
142 " AFNI_SESSTRAIL = 2 // see below for these ...\n" ,
143 " AFNI_RENDER_ANGLE_DELTA = 4.0 // |\n" ,
144 " AFNI_RENDER_CUTOUT_DELTA = 4.0 // |\n" ,
145 " AFNI_FIM_BKTHR = 25.0 // |\n" ,
146 " AFNI_SPLASHTIME = 3.0 // v\n" ,
147 "\n" ,
148 "###################################\n" ,
149 "### Env vars: the looong list ###\n" ,
150 "###################################\n" ,
151 "\n" ,
152 "-----------------------------\n" ,
153 "Variable: AFNI_MESSAGE_PREFIX\n" ,
154 "-----------------------------\n" ,
155 "Most AFNI programs output various messages prefixed by '++', '**', and\n" ,
156 "divers variations. If you are running several programs at once, you can\n" ,
157 "pre-pend a string to these prefixes to distinguish them in the output\n" ,
158 "terminal stream. For example, a csh script might look like so:\n" ,
159 " foreach fred ( 1 2 3 4 )\n" ,
160 " setenv AFNI_MESSAGE_PREFIX case$fred\n" ,
161 " run_some_program -option $fred ... |& tee out${fred}.txt &\n" ,
162 " end\n" ,
163 " wait\n" ,
164 "\n" ,
165 "-------------------------------\n" ,
166 "Variable: AFNI_MESSAGE_COLORIZE [22 Feb 2016]\n" ,
167 "-------------------------------\n" ,
168 "When AFNI programs print WARNING or ERROR messages, they normally\n" ,
169 "print the 'WARNING' or 'ERROR' label using inverted colors, to aid in\n" ,
170 "picking out these messages from other text on the screen. To turn\n" ,
171 "this feature off, set this environment variable to 'NO'.\n" ,
172 "\n" ,
173 "-----------------------\n" ,
174 "Variable: AFNI_FONTSIZE [06 Nov 2018]\n" ,
175 "-----------------------\n" ,
176 "This variable can be used to set the AFNI controller font sizes.\n" ,
177 "It is a convenient way to avoid using the '-XXXfontsize' option.\n" ,
178 "The values this variable can take are:\n" ,
179 " MINUS ==> smaller than normal fonts\n" ,
180 " PLUS ==> larger than normal fonts\n" ,
181 " BIG ==> much larger than normal fonts\n" ,
182 "\n" ,
183 "------------------------------------\n" ,
184 "Variable: AFNI_DONT_SORT_ENVIRONMENT\n" ,
185 "------------------------------------\n" ,
186 "If this YES/NO variable is YES, then the Edit Environment controls\n" ,
187 "will NOT be sorted alphabetically. The default action is to sort them\n" ,
188 "alphabetically. If they are unsorted, the editable environment\n" ,
189 "variables will appear in the control panel in the order in which they\n" ,
190 "were added to the code (that is, in an order that makes no real\n" ,
191 "sense).\n" ,
192 "\n" ,
193 "---------------------\n" ,
194 "Variable: AFNI_ORIENT (editable)\n" ,
195 "---------------------\n" ,
196 "This is a string used to control the display of coordinates in the AFNI\n" ,
197 "main control window. The string must be 3 letters, one each from the\n" ,
198 "pairs {R,L} {A,P} {I,S}. The first letter in the string gives the\n" ,
199 "orientation of the x-axis, the second the orientation of the y-axis,\n" ,
200 "the third the z-axis:\n" ,
201 "\n" ,
202 " R = right-to-left L = left-to-right\n" ,
203 " A = anterior-to-posterior P = posterior-to-anterior\n" ,
204 " I = inferior-to-superior S = superior-to-inferior\n" ,
205 "\n" ,
206 "If AFNI_ORIENT is undefined, the default is RAI. This is the order\n" ,
207 "used by DICOM, and means\n" ,
208 "\n" ,
209 " the -x axis is Right, the +x axis is Left,\n" ,
210 " the -y axis is Anterior, the +y axis is Posterior,\n" ,
211 " the -z axis is Inferior, the +z axis is Superior.\n" ,
212 "\n" ,
213 "As a special case, using the code 'flipped' is equivalent to 'LPI',\n" ,
214 "which is the orientation used in many neuroscience journals.\n" ,
215 "\n" ,
216 "This variable is also recognized by program 3dclust, which will report\n" ,
217 "the cluster coordinates in the (x,y,z) order given by AFNI_ORIENT.\n" ,
218 "Both AFNI and 3dclust also recognize the command line switch\n" ,
219 "\"-orient string\", where string is a 3 letter code that can be used\n" ,
220 "to override the value of AFNI_ORIENT.\n" ,
221 "\n" ,
222 "The plugin \"Coord Order\" (plug_coord.c) allows you to interactively\n" ,
223 "change the orientation of the variable display within AFNI.\n" ,
224 "\n" ,
225 "-------------------------\n" ,
226 "Variable: AFNI_PLUGINPATH\n" ,
227 "-------------------------\n" ,
228 "This variable should be the directory in which AFNI should search for\n" ,
229 "plugins, executable files, atlases, templates and atlas definition\n" ,
230 "files. See the atlas environment variable section below for more\n" ,
231 "details. If there is more than one appropriate directory, they can be\n" ,
232 "separated by colons, as in\n" ,
233 "\n" ,
234 " setenv AFNI_PLUGINPATH /directory/one:/directory/two\n" ,
235 "\n" ,
236 "If this variable is not set, then AFNI will use the PATH variable\n" ,
237 "instead. This will waste time, since most directories in the PATH\n" ,
238 "will not have plugins. On some systems, using the PATH has been\n" ,
239 "known to cause problems when AFNI starts. I believe this is due to\n" ,
240 "bugs in the system library routines (e.g., dlopen) used to manage\n" ,
241 "dynamically loaded shared objects. Take care to remove any slow or\n" ,
242 "non-existent directories from the PATH because these problems will cause\n" ,
243 "searches to fail or become excessively slow.\n" ,
244 "\n" ,
245 "------------------------\n" ,
246 "Variable: AFNI_NOPLUGINS\n" ,
247 "------------------------\n" ,
248 "If this YES/NO variable is set to YES, then AFNI will not try to\n" ,
249 "read plugins when it starts up. The command line switch \"-noplugins\"\n" ,
250 "will have the same effect.\n" ,
251 "\n" ,
252 "--------------------------------\n" ,
253 "Variable: AFNI_ALLOW_ALL_PLUGINS\n" ,
254 "--------------------------------\n" ,
255 "Setting this variable to YES will allow all defined plugins to\n" ,
256 "be loaded. Otherwise, little-used plugins must be allowed one\n" ,
257 "at a time, using the next set of variable names.\n" ,
258 "\n" ,
259 "-------------------------------------\n" ,
260 "Variables: AFNI_ALLOW_somename_PLUGIN\n" ,
261 "-------------------------------------\n" ,
262 "Some plugins distributed with AFNI are not commonly used, and are\n" ,
263 "disabled by default. If you wish to turn one of these plugins\n" ,
264 "back on, set the corresponding environment variable to YES.\n" ,
265 "The list of these plugins is:\n" ,
266 " --- somename --- --- name in menu ---\n" ,
267 " 2DREGISTRATION 2D Registration\n" ,
268 " 3DCLUSTER 3D Cluster\n" ,
269 " 3DCORRELATION 3D Correlation\n" ,
270 " 3DDUMP98 3D Dump98\n" ,
271 " 3DEDIT 3D Edit\n" ,
272 " 3DEXTRACT 3D+t Extract\n" ,
273 " 3DREGISTRATION 3D Registration\n" ,
274 " 3DSTATISTIC 3D+t Statistic\n" ,
275 " 4DDUMP 4D Dump\n" ,
276 " ASL ASL a3/d3\n" ,
277 " BRIKCOMPRESSOR BRIK Compressor\n" ,
278 " COORDORDER Coord Order\n" ,
279 " DATASETCOPY Dataset Copy\n" ,
280 " DATASETDUP Dataset Dup\n" ,
281 " DATASETRENAME Dataset Rename\n" ,
282 " DECONVOLVE Deconvolution\n" ,
283 " DSETZEROPAD Dset Zeropad\n" ,
284 " FOURIER Fourier\n" ,
285 " GYRUSFINDER Gyrus Finder\n" ,
286 " HEMISUBTRACT Hemi-subtract\n" ,
287 " HILBERTDELAY98 Hilbert Delay98\n" ,
288 " HISTOGRAMBFIT Histogram: BFit\n" ,
289 " L1FIT L1_Fit & Dtr\n" ,
290 " L2FIT LSqFit & Dtr\n" ,
291 " MASKCALC maskcalc\n" ,
292 " PERMUTATIONTEST Permutation Test\n" ,
293 " POWERSPECTRUM Power Spectrum\n" ,
294 " REORDER Reorder\n" ,
295 " RETROICOR RETROICOR\n" ,
296 " ROIAVERAGE ROI Average\n" ,
297 " ROIPLOT ROI Plot\n" ,
298 " SINGLETRIALAVG SingleTrial Avg\n" ,
299 " THRESHOLD Threshold\n" ,
300 " TSGENERATE TS Generate\n" ,
301 " WAVELETS Wavelets\n" ,
302 "\n" ,
303 "--------------------------\n" ,
304 "Variable: AFNI_YESPLUGOUTS\n" ,
305 "--------------------------\n" ,
306 "If this YES/NO variable is set to YES, then AFNI will try to listen\n" ,
307 "for plugouts when it starts. The command line switch \"-yesplugouts\"\n" ,
308 "will have the same effect. (Plugouts are an experimental feature\n" ,
309 "that allow external programs to exchange data with AFNI.) It is now\n" ,
310 "also possible to start plugout listening from the Datamode->Misc menu.\n" ,
311 "\n" ,
312 "---------------------\n" ,
313 "Variable: AFNI_TSPATH\n" ,
314 "---------------------\n" ,
315 "This variable should be set to any directory which you want to have\n" ,
316 "AFNI scan for timeseries files (*.1D -- see the AFNI manual). If\n" ,
317 "more than one directory is desired, then colons can be used to\n" ,
318 "separate them, as in AFNI_PLUGINPATH. Note that timeseries files\n" ,
319 "are read from all session directories, so directories provided by\n" ,
320 "AFNI_TSPATH are designed to contain extra timeseries files that\n" ,
321 "you want loaded no matter what AFNI sessions and datasets are being\n" ,
322 "viewed.\n" ,
323 "\n" ,
324 "---------------------------\n" ,
325 "Variable: AFNI_TCSV_VIEWNUM\n" ,
326 "---------------------------\n" ,
327 "This numeric value sets the number of preview lines for the AFNI\n" ,
328 "*.tsv/*.csv (TCSV) file chooser. If you don't set this to a\n" ,
329 "positive value, then the default number of preview lines is 4.\n" ,
330 "\n" ,
331 "------------------------\n" ,
332 "Variable: AFNI_MODELPATH\n" ,
333 "------------------------\n" ,
334 "This variable should be set to the directory from which you want AFNI\n" ,
335 "timeseries models to be loaded. These models are similar to plugins,\n" ,
336 "and are used by programs 3dNLfim, 3dTSgen, and the plugin plug_nlfit\n" ,
337 "(menu label \"NLfit & NLerr\") -- see documentation file 3dNLfim.ps.\n" ,
338 "If AFNI_MODELPATH is not given, then AFNI_PLUGINPATH will be used\n" ,
339 "instead.\n" ,
340 "\n" ,
341 "-----------------------------------------\n" ,
342 "Variable: AFNI_IMSIZE_* (or MCW_IMSIZE_*)\n" ,
343 "-----------------------------------------\n" ,
344 "These variables (named AFNI_IMSIZE_1 to AFNI_IMSIZE_99) allow you\n" ,
345 "to control how the AFNI programs read binary image files. The use of\n" ,
346 "these is somewhat complicated, and is explained in detail at the end\n" ,
347 "of the auxiliary programs manual (afni_aux.ps), in the section on \"3D:\"\n" ,
348 "file specifications, and is also explained in the AFNI FAQ list.\n" ,
349 "\n" ,
350 "------------------------\n" ,
351 "Variable: AFNI_SESSTRAIL (editable)\n" ,
352 "------------------------\n" ,
353 "This variable controls the number of directory levels shown when\n" ,
354 "choosing between session directories with the \"Switch Session\"\n" ,
355 "button. This variable should be set to a nonnegative integer.\n" ,
356 "If a session directory name were\n" ,
357 " this/is/a/directory/name/\n" ,
358 "then the \"Switch Session\" chooser would display the following:\n" ,
359 "\n" ,
360 " AFNI_SESSTRAIL Display\n" ,
361 " -------------- -------\n" ,
362 " 0 name/\n" ,
363 " 1 directory/name/\n" ,
364 " 2 a/directory/name/\n" ,
365 " 3 is/a/directory/name/\n" ,
366 " 4 this/is/a/directory/name/\n" ,
367 "\n" ,
368 "That is, AFNI_SESSTRAIL determines how many trailing levels of\n" ,
369 "the directory name are used for the display. If AFNI_SESSTRAIL\n" ,
370 "is not set, then it is equivalent to setting it to 0 (which\n" ,
371 "was the old method).\n" ,
372 "\n" ,
373 "--------------------\n" ,
374 "Variable: AFNI_HINTS\n" ,
375 "--------------------\n" ,
376 "This is a string controlling whether or not the popup \"hints\" are\n" ,
377 "displayed when AFNI starts. If the string is \"NO\", then the hints\n" ,
378 "are disabled when AFNI starts, otherwise they are enabled. In\n" ,
379 "either case, they can be turned off and on interactively from the\n" ,
380 "Define Datamode->Misc menu.\n" ,
381 "\n" ,
382 "Hints can be permanently disabled by setting the C macro\n" ,
383 "DONT_USE_HINTS in machdep.h and recompiling AFNI. They can also\n" ,
384 "be disabled at runtime by setting AFNI_HINTS to \"KILL\".\n" ,
385 "\n" ,
386 "-------------------------\n" ,
387 "Variable: AFNI_COMPRESSOR (cf. AFNI_AUTOGZIP) (editable)\n" ,
388 "-------------------------\n" ,
389 "This variable is used to control automatic compression of .BRIK files\n" ,
390 "on output. The legal values are \"COMPRESS\", \"GZIP\", \"BZIP2\", \"PIGZ\",\n" ,
391 "which respectively invoke programs \"compress\", \"gzip\",\"bzip2\" and\n" ,
392 "\"pigz\" (these must be in your path for compression to work). If\n" ,
393 "AFNI_COMPRESSOR is equal to one of these, then all AFNI programs will\n" ,
394 "automatically pass .BRIK data through the appropriate compression\n" ,
395 "program as it is written to disk. Note that this will slow down\n" ,
396 "dataset write operations. Note also that compressed datasets cannot\n" ,
397 "be mapped directly from disk into memory ('mmap'), but must occupy\n" ,
398 "actual memory (RAM) and swap space. For more details, see file\n" ,
399 "README.compression.\n" ,
400 "\n" ,
401 "Note that compressed (.BRIK.Z, .BRIK.gz, and .BRIK.bz2) datasets will\n" ,
402 "automatically be uncompressed on input, no matter what the setting of\n" ,
403 "this variable. AFNI_COMPRESSOR only controls how the datasets are\n" ,
404 "written.\n" ,
405 "\n" ,
406 "----------------------------\n" ,
407 "Variable: AFNI_DONT_USE_PIGZ\n" ,
408 "----------------------------\n" ,
409 "On some systems, the multi-threaded version of gzip -- program pigz --\n" ,
410 "can fail randomly. To prevent the use of pigz even if it is found,\n" ,
411 "set this variable to YES. Note that if you explicitly set\n" ,
412 "AFNI_COMPRESSOR to PIGZ, then AFNI_DONT_USE_PIGZ will be ignored. The\n" ,
413 "purpose of AFNI_DONT_USE_PIGZ is to prevent the automatic use of the\n" ,
414 "pigz program in cases where you don't provide AFNI_COMPRESSOR\n" ,
415 "explicitly.\n" ,
416 "\n" ,
417 "------------------------\n" ,
418 "Variable: AFNI_BYTEORDER\n" ,
419 "------------------------\n" ,
420 "This variable is used to control the byte order for output files.\n" ,
421 "If you use it, the two legal values are \"LSB_FIRST\" and \"MSB_FIRST\".\n" ,
422 "If you don't use it, the default order on your CPU will be used.\n" ,
423 "The main purpose of this would be if you were using a mixture of\n" ,
424 "CPU types reading shared disks (i.e., using NFS). If the majority\n" ,
425 "of the systems were MSB_FIRST (e.g., SGI, HP, Sun), but there were\n" ,
426 "a few LSB_FIRST systems (e.g., Intel, DEC Alpha), then you might\n" ,
427 "want to do 'setenv AFNI_BYTEORDER MSB_FIRST' on all of the MSB_FIRST\n" ,
428 "systems to make sure that the datasets that they write out are\n" ,
429 "readable by the other computers.\n" ,
430 "\n" ,
431 "Note that AFNI programs can now check the .HEAD file for the byte\n" ,
432 "order of a dataset, and will swap the bytes on input, if needed.\n" ,
433 "If you wish to mark all of the datasets on a given system as\n" ,
434 "being in a particular order, the following command should work:\n" ,
435 "\n" ,
436 " find /top/dir -name \\*.HEAD -exec 3drefit -byteorder NATIVE_ORDER {} \\;\n" ,
437 "\n" ,
438 "Here, '/top/dir' is the name of the top level directory under\n" ,
439 "which you wish to search for AFNI datasets. The string NATIVE_ORDER\n" ,
440 "means to set all datasets to the CPU default order, which is probably\n" ,
441 "what you are using now. (You can use the program 'byteorder' to\n" ,
442 "find out the native byte ordering of your CPU.)\n" ,
443 "\n" ,
444 "------------------------------\n" ,
445 "Variable: AFNI_BYTEORDER_INPUT\n" ,
446 "------------------------------\n" ,
447 "This variable is used to control the byte order for input files.\n" ,
448 "If you use it, the two legal values are \"LSB_FIRST\" and \"MSB_FIRST\".\n" ,
449 "The value of this variable is only used for old datasets that do\n" ,
450 "not have the byte order encoded in their headers. If this variable\n" ,
451 "is not present, then the CPU native byte order is used. If this\n" ,
452 "variable is present, and its value differs from the native byte\n" ,
453 "order, then 2 byte dataset BRIKs (short) are 2-swapped (as in\n" ,
454 "\"ab\" -> \"ba\") when they are read from disk, and 4 byte datasets\n" ,
455 "(float, complex) are 4-swapped (\"abcd\" -> \"dcba\").\n" ,
456 "\n" ,
457 "[per the request of John Koger]\n" ,
458 "\n" ,
459 "---------------------\n" ,
460 "Variable: AFNI_NOMMAP\n" ,
461 "---------------------\n" ,
462 "This YES/NO variable can be used to turn off the mmap feature by which\n" ,
463 "AFNI can load datasets into memory using the map-file-to-memory\n" ,
464 "functionality of Unix. (Dataset .BRIK files will only be mmap-ed if\n" ,
465 "they are not compressed and are in the native byte order of the CPU.)\n" ,
466 "On some systems, mmap doesn't seem to work very well (e.g., Linux kernel\n" ,
467 "version 1.2.13). You can disable mmap by 'setenv AFNI_NOMMAP YES'.\n" ,
468 "\n" ,
469 "The penalty for disabling mmap is that all datasets must be loaded\n" ,
470 "into actual RAM. AFNI does not have the ability to load a dataset\n" ,
471 "only partially, so if a 20 Megabyte .BRIK file is accessed, all of it\n" ,
472 "will be loaded into RAM. With mmap, the Unix operating system will\n" ,
473 "decide how much of the file to load. In this way, it is possible to\n" ,
474 "deal with more files than you have swap space on your computer (since\n" ,
475 ".BRIK files are mmap-ed in readonly mode, so they don't take up swap\n" ,
476 "space, which is for saving modified memory pages).\n" ,
477 "\n" ,
478 "The moral of the story: buy more memory, it's cheap. At the time\n" ,
479 "I write this line [Aug 1998], I have a PC with 384 MB of RAM, and\n" ,
480 "it is great to use with AFNI.\n" ,
481 "\n" ,
482 "[Feb 2004] I now have a Mac G5 with 8 GB of RAM, and it is even\n" ,
483 "greater! [Oct 2010] Now I have 32 GB of RAM (more than Ziad - ha!),\n" ,
484 "and it's nice!\n" ,
485 "\n" ,
486 "----------------------\n" ,
487 "Variable: AFNI_PSPRINT (editable)\n" ,
488 "----------------------\n" ,
489 "This variable is used to define a command that will print the\n" ,
490 "standard input (stdin) to a PostScript printer. If it is defined,\n" ,
491 "the \"->printer\" button on the timeseries \"Plot\" windows will work.\n" ,
492 "For some Unix systems, the following should work:\n" ,
493 " setenv AFNI_PSPRINT \"lp -\"\n" ,
494 "For others, this may work\n" ,
495 " setenv AFNI_PSPRINT \"lpr -\"\n" ,
496 "It all depends on the printer software setup you have. To send the\n" ,
497 "output into GhostView\n" ,
498 " setenv AFNI_PSPRINT \"ghostview -landscape -\"\n" ,
499 "\n" ,
500 "In the (very far distant) future, other windows (e.g., image and graph\n" ,
501 "displays) may get the ability to print to a PostScript file or printer.\n" ,
502 "\n" ,
503 "---------------------------\n" ,
504 "Variable: AFNI_LEFT_IS_LEFT (editable)\n" ,
505 "---------------------------\n" ,
506 "Setting this YES/NO variable to YES tells AFNI to display images with\n" ,
507 "the left side of the subject on the left side of the window. The\n" ,
508 "default mode is to display the right side of the subject on the left\n" ,
509 "side of the window - the radiology convention. This setting affects\n" ,
510 "the coronal and axial image and graph viewers.\n" ,
511 "\n" ,
512 "--------------------------------\n" ,
513 "Variable: AFNI_LEFT_IS_POSTERIOR (editable)\n" ,
514 "--------------------------------\n" ,
515 "Setting this YES/NO variable to YES tells AFNI to display images with\n" ,
516 "the posterior side of the subject on the left side of the window. The\n" ,
517 "default mode is to display the anterior side of the subject on the\n" ,
518 "left side of the window. This setting affects the sagittal image and\n" ,
519 "graph viewers.\n" ,
520 "\n" ,
521 "--------------------------\n" ,
522 "Variable: AFNI_ALWAYS_LOCK\n" ,
523 "--------------------------\n" ,
524 "Setting this YES/NO variable to YES tells AFNI to start up with all\n" ,
525 "the controller windows locked together. If you mostly use multiple\n" ,
526 "controllers to view datasets in unison, then this will be useful.\n" ,
527 "Notice that the Time Lock feature is not automatically enabled\n" ,
528 "by this -- you must still actuate it manually from the Lock menu\n" ,
529 "on the Define Datamode panel.\n" ,
530 "\n" ,
531 "--------------------------\n" ,
532 "Variable: AFNI_TIME_LOCK\n" ,
533 "--------------------------\n" ,
534 "Setting this YES/NO variable to YES tells AFNI to start up with\n" ,
535 "Time lock turned on. The Time Lock feature can be set manually\n" ,
536 "from the Lock menu on the Define Datamode panel.\n" ,
537 "\n" ,
538 "--------------------------\n" ,
539 "Variable: AFNI_ZOOM_LOCK\n" ,
540 "--------------------------\n" ,
541 "Setting this YES/NO variable to YES tells AFNI to start up with\n" ,
542 "Zoom lock turned on. The Zoom Lock feature can be set manually\n" ,
543 "from the Lock menu on the Define Datamode panel.\n" ,
544 "\n" ,
545 "------------------------\n" ,
546 "Variables: AFNI_RENDER_* (editable)\n" ,
547 "------------------------\n" ,
548 "These variables set some defaults in the \"Render Dataset\" (volume\n" ,
549 "rendering) plugin. The first two variables are\n" ,
550 "\n" ,
551 " AFNI_RENDER_ANGLE_DELTA = stepsize for viewing angles, in degrees\n" ,
552 " AFNI_RENDER_CUTOUT_DELTA = stepsize for cutout dimensions, in mm\n" ,
553 "\n" ,
554 "These stepsizes control how much the control parameters change when\n" ,
555 "one of their up- or down-arrows is pressed. Both of these stepsize\n" ,
556 "values default to 5.0.\n" ,
557 "\n" ,
558 "The third variable is\n" ,
559 "\n" ,
560 " AFNI_RENDER_PRECALC_MODE = \"Low\", \"Medium\", or \"High\"\n" ,
561 "\n" ,
562 "This is used to set the initial precalculation mode for the renderer\n" ,
563 "(this mode can be altered interactively, unlike the stepsizes).\n" ,
564 "\n" ,
565 "The fourth variable is\n" ,
566 "\n" ,
567 " AFNI_RENDER_SHOWTHRU_FAC = some number between 0.0 and 1.0\n" ,
568 "\n" ,
569 "This is used to control the way in which the \"ShowThru\" Color Opacity\n" ,
570 "option renders images. See the rendering plugin Help window for more\n" ,
571 "information.\n" ,
572 "\n" ,
573 "-------------------------\n" ,
574 "Variable: AFNI_NOREALPATH\n" ,
575 "-------------------------\n" ,
576 "Normally, when AFNI reads a list of session directories, it converts\n" ,
577 "their names to the \"real path\" form, which follows symbolic links, and\n" ,
578 "removes '/./' and '/../' components. These converted names are used\n" ,
579 "for display purposes in the \"Switch Session\" chooser and in other\n" ,
580 "places. If you wish to have the names NOT converted to the \"real path\"\n" ,
581 "format, set this YES/NO environment variable to YES, as in\n" ,
582 "\n" ,
583 " setenv AFNI_NOREALPATH YES\n" ,
584 "\n" ,
585 "(For more information on the \"real path\" conversion, see the Unix\n" ,
586 "man page for the realpath() function.) Note that if you use this\n" ,
587 "feature, then the effect of AFNI_SESSTRAIL will be limited to what\n" ,
588 "you type on the command line, since it is the realpath() function\n" ,
589 "that provides the higher level hierarchies of the session names.\n" ,
590 "\n" ,
591 "----------------------------\n" ,
592 "Variable: AFNI_NO_MCW_MALLOC\n" ,
593 "----------------------------\n" ,
594 "AFNI uses a set of \"wrapper\" macros and functions to let itself keep\n" ,
595 "track of the memory allocated and freed by the C malloc() library.\n" ,
596 "This is useful for debugging purposes (see the last items on the 'Misc'\n" ,
597 "menu in the AFNI 'Define Datamode' control panel), but carries a small\n" ,
598 "overhead (both in memory and speed). Setting this YES/NO environment\n" ,
599 "variable to YES provides one way to disable this facility, as in\n" ,
600 "\n" ,
601 " setenv AFNI_NO_MCW_MALLOC YES\n" ,
602 "\n" ,
603 "Another way to permanently disable this capability (so that it isn't\n" ,
604 "even compiled) is outlined in the file machdep.h. Also, the interactive\n" ,
605 "AFNI program takes the command line switch \"-nomall\", which will turn\n" ,
606 "off these functions for the given run.\n" ,
607 "\n" ,
608 "N.B.: Setting this variable in the .afnirc file will have no effect,\n" ,
609 " since the decision whether to use the routines in mcw_malloc.c\n" ,
610 " is made at the very start of the program, before .afnirc is\n" ,
611 " scanned. Therefore, to use this variable, you must set it\n" ,
612 " externally, perhaps in your .cshrc or .profile initialization\n" ,
613 " file.\n" ,
614 "\n" ,
615 "------------------------\n" ,
616 "Variable: AFNI_FIM_BKTHR\n" ,
617 "------------------------\n" ,
618 "This sets the threshold for the elimination of the background voxels\n" ,
619 "during the interactive FIM calculations. The average intensity of\n" ,
620 "all voxels in the first 3D volume used in the correlation is calculated.\n" ,
621 "Voxels with intensity below 0.01 * AFNI_FIM_BKTHR * (this average)\n" ,
622 "will not have the correlation computed. The default value is 10.0, but\n" ,
623 "values as large as 50.0 may be useful. This parameter may be changed\n" ,
624 "interactively from the FIM->Edit Ideal submenu in a graph viewer.\n" ,
625 "\n" ,
626 "------------------------\n" ,
627 "Variable: AFNI_FLOATSCAN (editable)\n" ,
628 "------------------------\n" ,
629 "If this YES/NO variable is set to YES, then floating point bricks\n" ,
630 "are checked for illegal values (NaN and Infinity) when they are\n" ,
631 "read into an AFNI program -- illegal values will be replaced by\n" ,
632 "zeros. If a dataset brick contains such illegal values that go\n" ,
633 "undetected, AFNI programs will probably fail miserably, and have\n" ,
634 "been known to go into nearly-infinite loops.\n" ,
635 "\n" ,
636 "Setting this variable implies setting AFNI_NOMMAP to YES, since\n" ,
637 "only in-memory bricks can be altered (mmap-ed bricks are readonly).\n" ,
638 "\n" ,
639 "The command line program 'float_scan' can be used to check and\n" ,
640 "patch floating point files.\n" ,
641 "\n" ,
642 "[14 Sep 1999] The program to3d will scan input float and complex\n" ,
643 "files for illegal values, and patch illegal input numbers with\n" ,
644 "zeros in the output dataset. If this behavior is not desired for\n" ,
645 "some bizarre reason, the '-nofloatscan' command line option to\n" ,
646 "to3d must be used.\n" ,
647 "\n" ,
648 "-----------------------\n" ,
649 "Variable: AFNI_NOSPLASH\n" ,
650 "-----------------------\n" ,
651 "If this YES/NO variable is set to YES, then the AFNI splash screen\n" ,
652 "will not be displayed when the program starts. I'm not sure WHY\n" ,
653 "you would want to disable this thing of beauty (which is a joy\n" ,
654 "forever), but if your soul is thusly degraded, so be it.\n" ,
655 "\n" ,
656 "------------------------\n" ,
657 "Variable: AFNI_SPLASH_XY\n" ,
658 "------------------------\n" ,
659 "If set, this variable should be in the form \"100:37\" (two integers\n" ,
660 "separated by a colon). These values specify the (x,y) screen location\n" ,
661 "where the splash window's upper left corner will be placed. If not\n" ,
662 "set, x will be set to center the splash window on the display and\n" ,
663 "y will be 100.\n" ,
664 "\n" ,
665 "-------------------------\n" ,
666 "Variable: AFNI_SPLASHTIME\n" ,
667 "-------------------------\n" ,
668 "The value of this variable determines how long the AFNI splash screen\n" ,
669 "will stay popped up, in seconds (default value = 5.0). The splash\n" ,
670 "screen will always stay up until the first AFNI controller window is\n" ,
671 "ready for use. If the time from program start to this ready condition\n" ,
672 "is less than AFNI_SPLASHTIME, the splash screen will stay up until\n" ,
673 "AFNI_SPLASHTIME has elapsed; otherwise, the splash screen will be\n" ,
674 "removed as soon as AFNI is ready to go. By setting AFNI_SPLASHTIME\n" ,
675 "to 0.0, you can have the splash screen removed as soon as possible\n" ,
676 "(and the fade-out feature will be disabled).\n" ,
677 "\n" ,
678 "-----------------------------\n" ,
679 "Variable: AFNI_SPLASH_ANIMATE\n" ,
680 "-----------------------------\n" ,
681 "If this variable is NO, then the splash screen animation will be disabled.\n" ,
682 "Otherwise, it will run.\n" ,
683 "\n" ,
684 "--------------------------\n" ,
685 "Variable: AFNI_SPLASH_MELT\n" ,
686 "--------------------------\n" ,
687 "If this variable is YES, then the splash screen will close via 'melting'.\n" ,
688 "\n" ,
689 "--------------------------------\n" ,
690 "Variable: AFNI_FIM_PERCENT_LIMIT (editable)\n" ,
691 "--------------------------------\n" ,
692 "This sets an upper limit on the % Change that the FIM+ computation\n" ,
693 "will compute. For example\n" ,
694 "\n" ,
695 " setenv AFNI_FIM_PERCENT_LIMIT 50\n" ,
696 "\n" ,
697 "means that computed values over 50% will be set to 50%, and values\n" ,
698 "below -50% will be set to -50%. This can be useful to avoid scaling\n" ,
699 "problems that arise when some spurious voxels with tiny baselines have\n" ,
700 "huge percent changes. This limit applies to all 3 possible percentages\n" ,
701 "that FIM and FIM+ can compute: % from baseline, % from average, and\n" ,
702 "% from top.\n" ,
703 "\n" ,
704 "---------------------------\n" ,
705 "Variable: AFNI_NOTES_DLINES\n" ,
706 "---------------------------\n" ,
707 "This sets the upper limit on the number of lines displayed in the\n" ,
708 "Notes plugin, for each note. If not present, the limit is 9 lines\n" ,
709 "shown per note at once. To see a note longer than this limit, you'll\n" ,
710 "have to use the vertical scrollbar.\n" ,
711 "\n" ,
712 "-----------------------\n" ,
713 "Variable: AFNI_FIM_MASK\n" ,
714 "-----------------------\n" ,
715 "This chooses the default subset of values computed with the FIM+\n" ,
716 "button in a graph window. The mask should be the sum of the desired\n" ,
717 "values from this list:\n" ,
718 "\n" ,
719 " 1 = Fit Coef\n" ,
720 " 2 = Best Index\n" ,
721 " 4 = % Change\n" ,
722 " 8 = Baseline\n" ,
723 " 16 = Correlation\n" ,
724 " 32 = % From Ave\n" ,
725 " 64 = Average\n" ,
726 " 128 = % From Top\n" ,
727 " 256 = Topline\n" ,
728 " 512 = Sigma Resid\n" ,
729 "\n" ,
730 "If you don't set this variable, the default mask is 23 = 1+2+4+16.\n" ,
731 "\n" ,
732 "-----------------------------------\n" ,
733 "Variable: AFNI_NO_BYTEORDER_WARNING\n" ,
734 "-----------------------------------\n" ,
735 "If this YES/NO variable is set to YES, then AFNI program will not\n" ,
736 "warn you when reading in a dataset that does not contain a byte\n" ,
737 "order flag. The default is to issue such a warning. Only older\n" ,
738 "versions of AFNI create datasets that don't have the byte order\n" ,
739 "flag. (See also the variable AFNI_BYTEORDER, described far above.)\n" ,
740 "The purpose of this warning is to alert you to possible problems\n" ,
741 "when you move datasets between computers with different CPU types.\n" ,
742 "\n" ,
743 "--------------------------\n" ,
744 "Variable: AFNI_PCOR_DENEPS\n" ,
745 "--------------------------\n" ,
746 "The correlation coefficient calculated in FIM is calculated as the\n" ,
747 "ratio of two quantities. If the denominator is negative or zero,\n" ,
748 "then this value is meaningless and may even cause the program to\n" ,
749 "crash. Mathematically, the denominator cannot be zero or negative,\n" ,
750 "but this could arise due to finite precision arithmetic on the computer\n" ,
751 "(i.e., roundoff error accumulation). To avoid this problem, the routine\n" ,
752 "that computes the correlation coefficient compares the denominator to a\n" ,
753 "value (called DENEPS) - if the denominator is less than DENEPS, then\n" ,
754 "the correlation coefficient for that voxel is set to zero.\n" ,
755 "\n" ,
756 "The denominator that is being computed is proportional to the variance\n" ,
757 "of the time series. If the voxel time series data is very small, then\n" ,
758 "the variance will be really small - so much so that the DENEPS test\n" ,
759 "will be failed, even though it shouldn't be. This problem has arisen\n" ,
760 "when people input time series whose typical value is 0.001 or smaller.\n" ,
761 "It never occurred to me that people would input data this small to the\n" ,
762 "AFNI FIM routines. To get around this difficulty, set this environment\n" ,
763 "variable to a value for DENEPS; for example\n" ,
764 " setenv AFNI_PCOR_DENEPS 0.0\n" ,
765 "will turn off the checking entirely. Or you could do\n" ,
766 " setenv AFNI_PCOR_DENEPS 1.e-10\n" ,
767 "\n" ,
768 "-----------------------------\n" ,
769 "Variable: AFNI_ENFORCE_ASPECT (editable)\n" ,
770 "-----------------------------\n" ,
771 "Some X11 window managers do no enforce the aspect ratio (width to height\n" ,
772 "proportion) request that the image display module makes. This means that\n" ,
773 "image windows can become undesirably distorted when manually resized.\n" ,
774 "Setting this YES/NO variable to YES will make AFNI itself enforce the\n" ,
775 "aspect ratio whenever an image window is resized.\n" ,
776 "** NOTICE **\n" ,
777 " As of 10 May 2018, this variable no longer has any effect. The\n" ,
778 " enforcement never worked well, and so you now have to manage this\n" ,
779 " problem manually. To fix the aspect ratio of an image viewer\n" ,
780 " window, Left-click in the image intensity bar (right of the image)\n" ,
781 " or press the 'a' key while the mouse cursor is over the image.\n" ,
782 "\n" ,
783 "----------------------------------------\n" ,
784 "Variables: AFNI_<plug_filename>_butcolor\n" ,
785 "----------------------------------------\n" ,
786 "These variables (one for each AFNI plugin) let you set the menu button\n" ,
787 "colors for the Plugins menu item. For example\n" ,
788 " setenv AFNI_plug_power_butcolor red3\n" ,
789 "will make the \"Power Spectrum\" button appear in a dark red color. The\n" ,
790 "format of the variable is exemplified above: the <plug_filename> is\n" ,
791 "replaced by the filename of the plugin (after removing the suffix).\n" ,
792 "Note that it is possible for the plugin author to hardcode the menu\n" ,
793 "button for his/her plugin, in which case the corresponding environment\n" ,
794 "variable will have no effect.\n" ,
795 "\n" ,
796 "Colors are specified as described in file README.setup. If you are\n" ,
797 "using an X11 PseudoColor visual, then you should be economical with\n" ,
798 "color usage!\n" ,
799 "\n" ,
800 "The purpose of this feature is to let you highlight the plugins that\n" ,
801 "you use most frequently. The size of the of plugin menu is growing,\n" ,
802 "and it is easy to misplace what you most use in the list.\n" ,
803 "\n" ,
804 "-----------------------------\n" ,
805 "Variable: AFNI_MARKERS_NOQUAL (editable)\n" ,
806 "-----------------------------\n" ,
807 "If this YES/NO variable is set to YES, then the interactive AFNI\n" ,
808 "program behaves as if the \"-noqual\" command line option had been\n" ,
809 "included. This feature was added at the request of Dr. Michael\n" ,
810 "S. Beauchamp, who has a very rare neurological disorder called\n" ,
811 "\"noqaulagnosia\".\n" ,
812 "\n" ,
813 "-----------------------------\n" ,
814 "Variable: AFNI_ENABLE_MARKERS\n" ,
815 "-----------------------------\n" ,
816 "As of 28 Apr 2010, the AFNI Talairach 'Define Markers' panel will no\n" ,
817 "longer be visible by default. To use this old feature, you must set\n" ,
818 "this variable to YES before running AFNI.\n" ,
819 "\n" ,
820 "----------------------\n" ,
821 "Variable: AFNI_OPTIONS\n" ,
822 "----------------------\n" ,
823 "In the spirit of the previous variable, this variable can be used to\n" ,
824 "set up command line options that will always be passed to the\n" ,
825 "interactive AFNI program. If more than one option is needed, then\n" ,
826 "they should be separated by spaces, and the whole value of the\n" ,
827 "variable will need to be placed in quotes. For example\n" ,
828 "\n" ,
829 " setenv AFNI_OPTIONS \"-noqual -ncolors 60\"\n" ,
830 "\n" ,
831 "Note that the AFNI command line option \"-nomall\" cannot be specified\n" ,
832 "this way (cf. the discussion under variable AFNI_NO_MCW_MALLOC).\n" ,
833 "\n" ,
834 "------------------------------\n" ,
835 "Variable: AFNI_NO_SIDES_LABELS (editable)\n" ,
836 "------------------------------\n" ,
837 "As of 01 Dec 1999, the interactive AFNI program now displays a label\n" ,
838 "beneath each image window showing which side of the image is on the\n" ,
839 "left edge of the window. This label is based on the anatomical\n" ,
840 "directions encoded in the anatomical dataset .HEAD file, usually when\n" ,
841 "to3d was used to create the file. If you do NOT want these labels\n" ,
842 "displayed (why not?), set this YES/NO environment variable to YES.\n" ,
843 "\n" ,
844 "----------------------------------\n" ,
845 "Variable: AFNI_NO_ADOPTION_WARNING\n" ,
846 "----------------------------------\n" ,
847 "\n" ,
848 "AFNI now can print a warning when it forces a dataset to have an\n" ,
849 "anatomy parent dataset (the \"forced adoption\" function). This happens\n" ,
850 "when there a dataset does not have an anatomy parent encoded into its\n" ,
851 ".HEAD file (either via to3d or 3drefit), and there is more than one\n" ,
852 "anatomical dataset in the directory that has Talairach transformation\n" ,
853 "markers attached. If you wish to enable this warning, set this YES/NO\n" ,
854 "variable to NO. For more information on this subject, please see\n" ,
855 "https://afni.nimh.nih.gov/afni/afni_faq.shtml#AnatParent .\n" ,
856 "\n" ,
857 "-----------------------------------\n" ,
858 "Variable: AFNI_NO_NEGATIVES_WARNING\n" ,
859 "-----------------------------------\n" ,
860 "If this YES/NO variable is set to YES, then to3d will skip the usual\n" ,
861 "warning that it pops up in a message window when it discovers negative\n" ,
862 "values in the input short images. (The warning will still be printed\n" ,
863 "to stdout.)\n" ,
864 "\n" ,
865 "-----------------------------------\n" ,
866 "Variable: AFNI_NO_OBLIQUE_WARNING\n" ,
867 "-----------------------------------\n" ,
868 "If this YES/NO variable is set to YES, then the AFNI GUI will skip the\n" ,
869 "usual warning that it pops up in a message window when an oblique\n" ,
870 "dataset is selected. (The warning will still be printed to stdout.)\n" ,
871 "\n" ,
872 "-----------------------------------\n" ,
873 "Variable: AFNI_ONE_OBLIQUE_WARNING\n" ,
874 "-----------------------------------\n" ,
875 "If this YES/NO variable is set to YES, then the AFNI GUI will pop up a\n" ,
876 "warning just ONCE when an oblique dataset is encountered.\n" ,
877 "\n" ,
878 "\n" ,
879 "----------------------\n" ,
880 "Variable: AFNI_NO_XDBE\n" ,
881 "----------------------\n" ,
882 "If this YES/NO variable is set to YES, then the X11 Double Buffer\n" ,
883 "Extension (XDBE) will not be used, even if the X11 server supports it.\n" ,
884 "This is needed when the X11 server says that it supports it, but actually\n" ,
885 "does not implement it correctly - this is a problem on the Xsgi server\n" ,
886 "running under IRIX 6.5.3 on R4400 machines.\n" ,
887 "\n" ,
888 "----------------------------------------------------\n" ,
889 "Variable: AFNI_VIEW_ANAT_BRICK, AFNI_VIEW_FUNC_BRICK (editable)\n" ,
890 "----------------------------------------------------\n" ,
891 "One of the (very few) confusing parts of AFNI is the \"warp-on-demand\"\n" ,
892 "viewing of transformed datasets (e.g., in the +tlrc coordinate system).\n" ,
893 "This allows you to look at slices taken from transformed volumes without\n" ,
894 "actually computing and storing the entire transformed dataset. This\n" ,
895 "viewing mode is controlled by from the \"Define Datamode\" control panel.\n" ,
896 "When an anatomical dataset has a +tlrc.BRIK file, then you can choose\n" ,
897 "between \"View Anat Data Brick\" and \"Warp Anat on Demand\"; when there\n" ,
898 "is no +tlrc.BRIK file for the dataset, then only \"Warp Anat on Demand\"\n" ,
899 "is possible.\n" ,
900 "\n" ,
901 "If you switch the Talairach view when the current anat dataset does\n" ,
902 "not have a +tlrc.BRIK file, then the \"Warp Anat on Demand\" mode will\n" ,
903 "be turned on. If you then switch to a dataset that does have a\n" ,
904 "+tlrc.BRIK file, \"Warp Anat on Demand\" will still be turned on,\n" ,
905 "although the \"View Anat Data Brick\" option will be enabled.\n" ,
906 "\n" ,
907 "If you set the YES/NO variable AFNI_VIEW_ANAT_BRICK to YES,\n" ,
908 "then \"View Anat Data Brick\" will be turned on whenever possible after\n" ,
909 "switching datasets. Similarly, setting AFNI_VIEW_FUNC_BRICK to YES\n" ,
910 "will engage \"View Func Data Brick\" whenever possible (when the BRIK\n" ,
911 "file exists and its grid spacing matches the anatomical grid spacing).\n" ,
912 "Note that switching any dataset (func or anat) triggers the same\n" ,
913 "routine, and will set either or both \"View Brick\" modes on. When\n" ,
914 "these environment variables are present, the only way to switch to\n" ,
915 "\"Warp\" mode when \"View Brick\" mode is possible is to do it manually\n" ,
916 "(by clicking on the toggle button) when you want this.\n" ,
917 "\n" ,
918 "When you use one of the drawing plugins (\"Draw Dataset\" or \"Gyrus\n" ,
919 "Finder\"), you must operate directly on the dataset BRIK. For this\n" ,
920 "reason, it is important to be in \"View Data Brick\" mode on these\n" ,
921 "occasions. Setting these variables is one way to ensure that this\n" ,
922 "will happen whenever possible.\n" ,
923 "\n" ,
924 "When AFNI is in \"Warp Anat on Demand\" mode, the word \"{warp}\" will\n" ,
925 "appear in the windows' titlebars. This provides a reminder of the\n" ,
926 "viewing mode you are using (warped from a brick, or data directly\n" ,
927 "extracted from a brick), since the \"Define Datamode\" control panel\n" ,
928 "will not always be open.\n" ,
929 "\n" ,
930 "08 Aug 2003: I have modified the way these variables are treated in\n" ,
931 "AFNI so that they now default to the \"YES\" behavior. If you don't\n" ,
932 "want this, you have to explicitly set them to \"NO\" from this day forth.\n" ,
933 "\n" ,
934 "-------------------------------\n" ,
935 "Variable: AFNI_RECENTER_VIEWING (editable)\n" ,
936 "-------------------------------\n" ,
937 "If this variable is set to YES, then AFNI's viewers will reset the\n" ,
938 "crosshair coordinate to the center of the dataset whenever a new\n" ,
939 "dataset or sub-brick is chosen. The only real reason to use this\n" ,
940 "feature is if you are scanning through a collection of datasets with\n" ,
941 "wildly different coordinates, so that the usual method of matching\n" ,
942 "(x,y,z) coordinates at such times gives useless results.\n" ,
943 "\n" ,
944 "----------------\n" ,
945 "Variable: TMPDIR\n" ,
946 "----------------\n" ,
947 "This variable specifies the directory where temporary files are to be\n" ,
948 "written. It is not unique to AFNI, but is used by many Unix programs.\n" ,
949 "You must have permission to write into this directory. If you want to\n" ,
950 "use the current directory, setting TMPDIR to \".\" would work. If TMPDIR\n" ,
951 "is not defined, directory /tmp will be used. On some systems, this\n" ,
952 "directory may not have enough space for the creation of large temporary\n" ,
953 "datasets. On most Unix systems, you can tell the size of various disk\n" ,
954 "partitions using a command like \"df -k\" (on HPUX, \"bdf\" works).\n" ,
955 "\n" ,
956 "----------------------------\n" ,
957 "Variable: AFNI_GRAYSCALE_BOT\n" ,
958 "----------------------------\n" ,
959 "This variable sets the darkest level shown in a grayscale image window.\n" ,
960 "The default value is 55 (a leftover from Andrzej Jesmanowicz). You can\n" ,
961 "set this value to anything from 0 to 254.\n" ,
962 "\n" ,
963 "----------------------------\n" ,
964 "Variable: AFNI_SYSTEM_AFNIRC\n" ,
965 "----------------------------\n" ,
966 "If this variable is set, it is the name of a file to be read like the\n" ,
967 "user's .afnirc file (see README.setup). The purpose is to allow a\n" ,
968 "system-wide setup file to be used. To do this, you would create such\n" ,
969 "a file in a useful place - perhaps where you store the AFNI binaries.\n" ,
970 "Then each user account should have the equivalent of\n" ,
971 "\n" ,
972 " setenv AFNI_SYSTEM_AFNIRC /place/where/setup/is/stored/.afnirc\n" ,
973 "\n" ,
974 "defined in its .cshrc (.bashrc, etc.) file. Note that it doesn't make\n" ,
975 "sense to define this variable in the user's .afnirc file, since that\n" ,
976 "file won't be read until AFTER this file is read. Also note that use\n" ,
977 "of the -skip_afnirc option will cause both the system and user setup\n" ,
978 "files to be skipped.\n" ,
979 "\n" ,
980 "------------------------\n" ,
981 "Variable: AFNI_PBAR_IMXY (editable)\n" ,
982 "------------------------\n" ,
983 "This variable determines the size of the image saved when the\n" ,
984 "\"Save to PPM\" button is selected for a color pbar. It should be\n" ,
985 "in the format\n" ,
986 " setenv AFNI_PBAR_IMXY 20x256\n" ,
987 "which means to set the x-size (horizontal) to 20 pixels and the\n" ,
988 "y-size (vertical) to 256 pixels. These values are the default,\n" ,
989 "by the way.\n" ,
990 "\n" ,
991 "--------------------------\n" ,
992 "Variable: AFNI_LAYOUT_FILE\n" ,
993 "--------------------------\n" ,
994 "If defined, this variable is the name of a file to read at startup\n" ,
995 "to define the \"layout\" of AFNI windows at the program start. If\n" ,
996 "this name starts with a '/' character, then it is an absolute path;\n" ,
997 "otherwise, it is taken to be a path relative to the user's home\n" ,
998 "directory ($HOME). If the AFNI command line switch \"-layout\" is\n" ,
999 "used, it will override this specification.\n" ,
1000 "\n" ,
1001 "The simplest way to produce a layout file is to use the \"Save Layout\"\n" ,
1002 "button on the Datamode->Misc menu. You can then edit this file;\n" ,
1003 "the format should be fairly self-explanatory. The structure of the\n" ,
1004 "file is similar to the .afnirc file (cf. README.setup). In fact,\n" ,
1005 "the layout file can be included into .afnirc (since it is just another\n" ,
1006 "*** section) and then setting AFNI_LAYOUT_FILE = .afnirc in the\n" ,
1007 "***ENVIRONMENT section should work.\n" ,
1008 "\n" ,
1009 "A sample layout file:\n" ,
1010 "\n" ,
1011 "***LAYOUT\n" ,
1012 " A geom=+73+1106 // start controller A\n" ,
1013 " A.sagittalimage geom=320x320+59+159 ifrac=0.8 // and Sagittal image\n" ,
1014 " A.sagittalgraph geom=570x440+490+147 matrix=9 // and Sagittal graph\n" ,
1015 " B // start controller B\n" ,
1016 " B.plugin.ROI_Average // start a plugin\n" ,
1017 "\n" ,
1018 "Each window to be opened has a separate command line in this file.\n" ,
1019 "The \"geom=\" qualifiers specify the size and position of the windows.\n" ,
1020 "For images, \"ifrac=\" can be used to specify the fraction of the window\n" ,
1021 "occupied by the image (if \"ifrac=1.0\", then no control widgets will be\n" ,
1022 "visible). For graphs, \"matrix=\" can be used to control the initial\n" ,
1023 "number of sub-graphs displayed. For plugins, the label on the button\n" ,
1024 "that starts the plugin is used after the \".plugin.\" string (blanks\n" ,
1025 "should be filled with underscores \"_\"). In the example above, the last\n" ,
1026 "two windows to be opened do not have a \"geom=\" qualifier, so their\n" ,
1027 "placement will be chosen by the window manager.\n" ,
1028 "\n" ,
1029 "If you add \"slow\" after the \"***LAYOUT\", then each window operation\n" ,
1030 "will be paused for 1 second to let you watch the layout operations\n" ,
1031 "proceed gradually. Otherwise, they will be executed as fast as\n" ,
1032 "possible (which still may not be all that fast).\n" ,
1033 "\n" ,
1034 "Using layouts with a window manager that requires user placement\n" ,
1035 "of new windows (e.g., twm) is a futile and frustrating exercise.\n" ,
1036 "\n" ,
1037 "If you do NOT have any layout file defined, then AFNI will choose\n" ,
1038 "a layout for you that includes opening image viewers. Some people\n" ,
1039 "find this very annoying. The simplest way to avoid this annoyance\n" ,
1040 "is to set AFNI_LAYOUT_FILE to a name of a file that doesn't exist\n" ,
1041 "(e.g., 'ElvisIsAliveOnPlanetZork'). The reason for this default\n" ,
1042 "layout behavior (added Dec 2010) is that we received complaints\n" ,
1043 "that novice users were finding AFNI too confusing on startup.\n" ,
1044 "(Hard to believe, but true.)\n" ,
1045 "\n" ,
1046 "-------------------------\n" ,
1047 "Variable: AFNI_tsplotgeom\n" ,
1048 "-------------------------\n" ,
1049 "Related to the above, if you set this environment variable (in the\n" ,
1050 "***ENVIRONMENT section, not in the ***LAYOUT section), it is used\n" ,
1051 "to set the geometry of the plotting windows used for time series\n" ,
1052 "plots, histograms, etc. -- all the graphs except the dataset plots.\n" ,
1053 "Its format should be something like \"550x350\"; this example sets\n" ,
1054 "the width to 550 pixels and the height to 350 pixels. If you don't\n" ,
1055 "set this, the default is \"200x200\", which is quite small on a high\n" ,
1056 "resolution display.\n" ,
1057 "\n" ,
1058 "------------------------\n" ,
1059 "Variable: AFNI_FIM_IDEAL\n" ,
1060 "------------------------\n" ,
1061 "This variable specifies the filename of the initial FIM ideal timeseries.\n" ,
1062 "The main use of this would be to be able to initialize the Realtime\n" ,
1063 "plugin without direct user intervention.\n" ,
1064 "\n" ,
1065 "--------------------------\n" ,
1066 "Variable: AFNI_FIM_SAVEREF\n" ,
1067 "--------------------------\n" ,
1068 "When you run the interactive AFNI 'fim' (from the graph viewer FIM menu),\n" ,
1069 "the program saves the reference time series (and ort time series, if any)\n" ,
1070 "in the new functional dataset header, with the attribute name\n" ,
1071 "AFNI_FIM_REF (or AFNI_FIM_ORT). If you do NOT want this information saved,\n" ,
1072 "then set this variable to NO. Two sample ways to use this information is\n" ,
1073 "the command below:\n" ,
1074 " 1dplot \"`3dAttribute -ssep ' ' AFNI_FIM_REF r1_time@1+orig`\"\n" ,
1075 " 1dcat \"`3dAttribute -ssep ' ' AFNI_FIM_REF r1_time@1+orig`\" > ref.1D\n" ,
1076 "The 3 different styles of Unix quotes must be used exactly as shown here!\n" ,
1077 "\n" ,
1078 "----------------------------------\n" ,
1079 "Variable: AFNI_PLUGINS_ALPHABETIZE\n" ,
1080 "----------------------------------\n" ,
1081 "If this YES/NO variable is set to NO, then the plugin buttons will\n" ,
1082 "not be alphabetized on the menu, and they will appear in the\n" ,
1083 "order which AFNI chooses. Otherwise, the plugin menu buttons will\n" ,
1084 "be alphabetized by default. Alphabetizing is done without regard to\n" ,
1085 "case (using the C library routine strcasecmp).\n" ,
1086 "\n" ,
1087 "----------------------------\n" ,
1088 "Variable: AFNI_VOLREG_EDGING\n" ,
1089 "----------------------------\n" ,
1090 "This variable affects the operation of 3dvolreg, the volume registration\n" ,
1091 "plugin, and the 3D registration code in the realtime acquisition plugin.\n" ,
1092 "It determines the size of the region around the edges of the base volume\n" ,
1093 "where the default weight will be set to zero. Call the value of this\n" ,
1094 "variable 'ee'. If 'ee' is a plain number (e.g., 5), then it is a voxel\n" ,
1095 "count, giving the thickness along each face of the 3D brick. If 'ee' is\n" ,
1096 "of the form '5%', then it is a fraction of of each brick size. For\n" ,
1097 "example, '5%' of a 256x256x124 volume means that 13 voxels on each side\n" ,
1098 "of the xy-axes will get zero weight, and 6 along the z-axis. '5%' is\n" ,
1099 "the default value used by the 3D registration routines (in mri_3dalign.c)\n" ,
1100 "if no other value is specified.\n" ,
1101 "\n" ,
1102 "--------------------\n" ,
1103 "Variable: AFNI_TRACE\n" ,
1104 "--------------------\n" ,
1105 "This variable controls the initial setting of the tracing (debugging)\n" ,
1106 "code when AFNI programs startup. If it is set to 'y', then tracing\n" ,
1107 "is turned on and set to the LOW mode (like -trace in AFNI). If it is\n" ,
1108 "set to 'Y', then tracing is turned on and set to the HIGH mode (like\n" ,
1109 "-TRACE in AFNI). Anything else, and tracing is turned off.\n" ,
1110 "\n" ,
1111 "N.B.: You can't set this variable in .afnirc and expect it to have\n" ,
1112 " any effect (and why would you want to?), since it is read from\n" ,
1113 " the environment BEFORE the .afnirc file is read in.\n" ,
1114 "\n" ,
1115 "N.B.: At this moment (26 Jan 2001), only the AFNI program itself is\n" ,
1116 " configured for tracing. As time goes on, the entire AFNI\n" ,
1117 " programming library and suite of programs will be revamped for\n" ,
1118 " this purpose. The goal is to make it easier to find bugs, and\n" ,
1119 " localize crashes.\n" ,
1120 "\n" ,
1121 "-------------------------\n" ,
1122 "Variable: AFNI_TRACE_FILE\n" ,
1123 "-------------------------\n" ,
1124 "If this variable is set, then the output from the AFNI function tracing\n" ,
1125 "macros will be written to a file with that name, rather than to stdout.\n" ,
1126 "This variable cannot be set in .afnirc; the intention is to provide a\n" ,
1127 "way to get 'clean' tracing output (not mixed up with other program junk)\n" ,
1128 "that can be fed to Ziad Saad's AnalyzeTrace function.\n" ,
1129 "\n" ,
1130 "------------------------\n" ,
1131 "Variable: AFNI_ROTA_ZPAD\n" ,
1132 "------------------------\n" ,
1133 "This variable controls the amount of zero-padding used during 3D rotations\n" ,
1134 "in 3drotate, 3dvolreg, etc. It provides a default value for the \"-zpad\"\n" ,
1135 "options of these programs. If zero-padding is used, then this many voxels\n" ,
1136 "are padded out on each edge (all 6 faces) of a 3D brick before rotation.\n" ,
1137 "After the rotation, these perimeter values (whatever they might be) will\n" ,
1138 "be stripped off. If \"-zpad\" is used on the command line, it overrides\n" ,
1139 "this value. Zero padding during rotation is useful to avoid edge effects,\n" ,
1140 "the worst of which is the loss of data off the edge of the volume during\n" ,
1141 "the 4 shearing stages.\n" ,
1142 "\n" ,
1143 "------------------------\n" ,
1144 "Variable: AFNI_TO3D_ZPAD\n" ,
1145 "------------------------\n" ,
1146 "This variable sets the number of slices added on each z-face in datasets\n" ,
1147 "created by program to3d. It provides a default value for the \"-zpad\" option\n" ,
1148 "of that program. It can be set to an integer, meaning a slice count, or\n" ,
1149 "a number of millimeters, meaning a minimum distance to pad:\n" ,
1150 " setenv AFNI_TO3D_ZPAD 2\n" ,
1151 " setenv AFNI_TO3D_ZPAD 16mm\n" ,
1152 "If \"-zpad\" is used on the to3d command line, it overrides this value.\n" ,
1153 "If neither is present, no zero padding is used. Note well that this\n" ,
1154 "padding is only in the z-direction, unlike that of AFNI_ROTA_ZPAD.\n" ,
1155 "\n" ,
1156 "-----------------------------------------------------------------\n" ,
1157 "Variables: AFNI_OPEN_AXIAL, AFNI_OPEN_SAGITTAL, AFNI_OPEN_CORONAL\n" ,
1158 "-----------------------------------------------------------------\n" ,
1159 "When the AFNI GUI starts, by default it opens all 3 image viewer\n" ,
1160 "windows. If you do NOT want a particular one of these, set the\n" ,
1161 "corresponding variable named above to NO. For finer control over\n" ,
1162 "AFNI startup, see the AFNI_STARTUP_SCRIPT variable and README.driver.\n" ,
1163 "\n" ,
1164 "----------------------------\n" ,
1165 "Variable: AFNI_IMAGE_MINFRAC (editable)\n" ,
1166 "----------------------------\n" ,
1167 "This variable sets the minimum size of an image window when it is first\n" ,
1168 "opened, in terms of a fraction of the overall screen area. By default,\n" ,
1169 "this value is set to 0.02; you can override this by (for example)\n" ,
1170 " setenv AFNI_IMAGE_MINFRAC 0.05\n" ,
1171 "If you set this value to 0.0, then there will be no minimum. This is\n" ,
1172 "the old behavior, where the initial window size is always 1 screen pixel\n" ,
1173 "per data pixel, and can lead to image windows that are hard to resize or\n" ,
1174 "otherwise use (when the dataset is small). The largest value I recommend\n" ,
1175 "for AFNI_IMAGE_MINFRAC is 0.1; however, you can set it to as large as 0.9\n" ,
1176 "if you are completely crazy, but I'm not responsible for the results --\n" ,
1177 "don't even think of complaining or commenting to me about problems that\n" ,
1178 "arise if you try this!\n" ,
1179 "\n" ,
1180 "----------------------------\n" ,
1181 "Variable: AFNI_IMAGE_MAXFRAC\n" ,
1182 "----------------------------\n" ,
1183 "This variable sets the maximum size of an image window, as a fraction\n" ,
1184 "of the width and height of the screen. The default value is 0.9.\n" ,
1185 "This lets you prevent image windows from auto-resizing to be too big\n" ,
1186 "when you change datasets. Note that if you have turned on\n" ,
1187 "AFNI_ENFORCE_ASPECT, then this feature will prevent you from resizing\n" ,
1188 "a window to be larger than the AFNI_IMAGE_MAXFRAC fraction of the\n" ,
1189 "screen dimensions.\n" ,
1190 "\n" ,
1191 "-----------------------\n" ,
1192 "Variable: AFNI_AUTOGZIP (cf. AFNI_COMPRESSOR) (editable)\n" ,
1193 "-----------------------\n" ,
1194 "If this YES/NO variable is set to YES, then when AFNI programs write a\n" ,
1195 "dataset .BRIK file to disk, they will test to see if the data is easily\n" ,
1196 "compressible (at least 80%). If so, then the GZIP compression will be\n" ,
1197 "used. (For this to work, the gzip program must be in your path.) This\n" ,
1198 "can be useful if you are dealing with mask datasets, which are usually\n" ,
1199 "highly compressible, but don't want the overhead of trying to compress\n" ,
1200 "and decompress arbitrary MRI datasets.\n" ,
1201 "\n" ,
1202 "A command line method to carry out compression of datasets that will\n" ,
1203 "compress well is to use a csh script like the following:\n" ,
1204 "\n" ,
1205 " #!/bin/csh\n" ,
1206 " foreach fred ( `find . -name \\*.BRIK -print` )\n" ,
1207 " ent16 -%50 < $fred\n" ,
1208 " if( $status == 1 ) gzip -1v $fred\n" ,
1209 " end\n" ,
1210 "\n" ,
1211 "This will only gzip .BRIK files that the program ent16 estimates will\n" ,
1212 "compress by at least 50%. Note that ent16's estimate of compression\n" ,
1213 "may be high or low relative to what gzip actually does.\n" ,
1214 "\n" ,
1215 "------------------------------\n" ,
1216 "Variable: AFNI_DONT_MOVE_MENUS (editable)\n" ,
1217 "------------------------------\n" ,
1218 "If this YES/NO variable is set to YES, then the functions that try\n" ,
1219 "to move popup menus to \"good\" locations on screens will be skipped.\n" ,
1220 "This seems to be necessary on some Solaris systems, where the menus\n" ,
1221 "can end up being moved to bizarre locations.\n" ,
1222 "\n" ,
1223 "-----------------------------\n" ,
1224 "Variable: AFNI_IMAGE_DATASETS\n" ,
1225 "-----------------------------\n" ,
1226 "If this YES/NO variable is not set to NO, then 2D image files\n" ,
1227 "(*.png and *.jpg) will be read as datasets when the interactive\n" ,
1228 "AFNI program starts. That is, you have to set this variable explicitly\n" ,
1229 "to NO if you do not want image files read into the AFNI GUI at\n" ,
1230 "startup. Image files can be opened using the Axial image viewer.\n" ,
1231 "\n" ,
1232 "----------------------------\n" ,
1233 "Variable: AFNI_MINC_DATASETS\n" ,
1234 "----------------------------\n" ,
1235 "If this YES/NO variable is not set to NO, then MINC-format files\n" ,
1236 "with name suffix .mnc will be read into the interactive AFNI\n" ,
1237 "program at startup, along with standard .HEAD/.BRIK datasets.\n" ,
1238 "That is, you have to set this variable explicitly to NO if you\n" ,
1239 "don't want MINC-format files to be automatically recognized by\n" ,
1240 "the interactive AFNI program. This variable does not affect\n" ,
1241 "the ability of command line programs (3dSomething) to read\n" ,
1242 ".mnc input files.\n" ,
1243 "\n" ,
1244 "----------------------------\n" ,
1245 "Variable: AFNI_MINC_FLOATIZE\n" ,
1246 "----------------------------\n" ,
1247 "If this YES/NO variable is set to YES, then when MINC-format files\n" ,
1248 "are read in as datasets, their values will be scaled to floats.\n" ,
1249 "Otherwise, their values will be scaled to the same data type as\n" ,
1250 "stored in the file. In some cases, the latter behavior is not\n" ,
1251 "good; for example, if a byte-valued file (intrinsic range 0..255)\n" ,
1252 "is scaled to the range 0..0.5 in the MINC header, then after\n" ,
1253 "conversion back to bytes, the resulting AFNI dataset values will\n" ,
1254 "all be zero. Setting AFNI_MINC_FLOATIZE to YES will cause the\n" ,
1255 "scaled values to be stored as floats.\n" ,
1256 "\n" ,
1257 "------------------------------\n" ,
1258 "Variable: AFNI_MINC_SLICESCALE\n" ,
1259 "------------------------------\n" ,
1260 "If this YES/NO variable is set to NO, then AFNI will not use the\n" ,
1261 "image-min and image-max scaling when reading data from MINC files.\n" ,
1262 "Normally, you want this scaling, since MINC files are scaled separately\n" ,
1263 "in each slice. However, if the image-min and image-max values in the\n" ,
1264 "MINC file are damaged, then you can turn off the scaling this way.\n" ,
1265 "\n" ,
1266 "----------------------------\n" ,
1267 "Variable: AFNI_ANALYZE_SCALE\n" ,
1268 "----------------------------\n" ,
1269 "If this YES/NO variable is set to NO, then the \"funused1\" entry\n" ,
1270 "in the Mayo Analyze .hdr file will not be used as a scale factor\n" ,
1271 "for the images contained in the corresponding .img file. Otherwise,\n" ,
1272 "if funused1 is positive and not equal to 1.0, all the image data\n" ,
1273 "in the .img file will be scaled by this value.\n" ,
1274 "\n" ,
1275 "-------------------------------\n" ,
1276 "Variable: AFNI_ANALYZE_FLOATIZE\n" ,
1277 "-------------------------------\n" ,
1278 "If this YES/NO variable is set to YES, then Mayo Analyze files\n" ,
1279 "will be scaled to floats on input. Otherwise, they will be read\n" ,
1280 "in the format in which they are stored in the .img file. Conversion\n" ,
1281 "to floats can be useful if the scaling factor is such that the image\n" ,
1282 "native format can't hold the scaled values; for example, if short\n" ,
1283 "values in the image range from -1000..1000 and the scale factor\n" ,
1284 "is 0.0001, then the scaled values range from -0.1..0.1, which would\n" ,
1285 "be truncated to 0 in the scaled image if it is not \"floatized\".\n" ,
1286 "(Conversion to floats will only be done to byte, short, and int\n" ,
1287 "image types.)\n" ,
1288 "\n" ,
1289 "---------------------------------\n" ,
1290 "Variable: AFNI_ANALYZE_ORIGINATOR\n" ,
1291 "---------------------------------\n" ,
1292 "If this YES/NO variable is set to YES, then AFNI will attempt\n" ,
1293 "to read and use the ORIGINATOR field in a Mayo Analyze file\n" ,
1294 "to set the origin of the pixel space in AFNI. This origin\n" ,
1295 "can be used directly by several programs--the main AFNI viewer,\n" ,
1296 "and all of the 3dxxxx programs, including especially 3dcopy,\n" ,
1297 "which is the preferred way to convert an Analyze format file\n" ,
1298 "to an AFNI native file.\n" ,
1299 "This variable will also force 3dAFNItoANALYZE to write the\n" ,
1300 "ORIGINATOR field into the output Analyze file based on the\n" ,
1301 "input AFNI file's origin information.\n" ,
1302 "The ORIGINATOR field should be compatible with SPM in most\n" ,
1303 "cases, but please verify this.\n" ,
1304 "\n" ,
1305 "--------------------------\n" ,
1306 "Variable: AFNI_START_SMALL\n" ,
1307 "--------------------------\n" ,
1308 "If this YES/NO variable is set to YES, then when AFNI starts, it will\n" ,
1309 "look for the smallest dataset in the first session, and choose this\n" ,
1310 "as its starting point. This can be useful if you also use the layout\n" ,
1311 "feature to pop open an image window on startup; in that case, if the\n" ,
1312 "default starting dataset (the first alphabetical) is huge, you won't\n" ,
1313 "see anything while the program reads all of into memory before displaying\n" ,
1314 "the first image.\n" ,
1315 "\n" ,
1316 "The old behavior of this variable was to set the smallest dataset\n" ,
1317 "marked as 'Anatomical' to be the underlay, and the smallest dataset\n" ,
1318 "marked as 'Functional' to be the overlay. The new behavior just\n" ,
1319 "sets both the underlay and overlay to be the smallest dataset.\n" ,
1320 "If you want the old behavior, set this variable to the string 'OLD'.\n" ,
1321 "\n" ,
1322 "---------------------------\n" ,
1323 "Variable: AFNI_MENU_COLSIZE\n" ,
1324 "---------------------------\n" ,
1325 "This numerical variable sets the maximum number of entries in a popup\n" ,
1326 "menu column (e.g., like the sub-brick menus for bucket datasets). The\n" ,
1327 "default value is 20, but you may want to make this larger (say 40). When\n" ,
1328 "you have a menu with a huge number of entries, the menu can become so\n" ,
1329 "wide that it doesn't fit on the screen. Letting the columns be longer\n" ,
1330 "will make the menus be narrower across the screen.\n" ,
1331 "\n" ,
1332 "Another way to get a handle on such huge menus is to Button-3 (right)\n" ,
1333 "click on the label to the left of the menu. This will popup a one-\n" ,
1334 "column scrollable list chooser that is equivalent to the menu. In\n" ,
1335 "this way, it is still possible to use menus that have hundreds of\n" ,
1336 "entries. The maximum number of entries shown at one time in a\n" ,
1337 "scrollable list chooser is given by variable AFNI_chooser_listmax if\n" ,
1338 "it exists, otherwise by AFNI_MENU_COLSIZE.\n" ,
1339 "\n" ,
1340 "-----------------------------\n" ,
1341 "Variable: AFNI_GLOBAL_SESSION\n" ,
1342 "-----------------------------\n" ,
1343 "This variable, if it exists, is the name of a directory that contains\n" ,
1344 "\"global\" datasets - ones that you want to be visible in each \"Switch\n" ,
1345 "Underlay\" or \"Switch Overlay\" menu. Pointers to the datasets read\n" ,
1346 "from this directory will be appended to the dataset list for each\n" ,
1347 "directory read from the command line. In the \"Switch\" choosers, these\n" ,
1348 "datasets are marked with the character 'G' at the right, and they\n" ,
1349 "appear last in the list.\n" ,
1350 "\n" ,
1351 "It really only makes sense to put +tlrc (i.e., in a template\n" ,
1352 "space) datasets in the global session directory, since only they\n" ,
1353 "can be presumed to be aligned with other datasets. Also, it is probably\n" ,
1354 "best if you make sure each global anatomical dataset has itself\n" ,
1355 "as the anatomy parent; this can be enforced by issuing the command\n" ,
1356 " 3drefit -apar SELF *.HEAD *.nii *.nii.gz\n" ,
1357 "in the global session directory.\n" ,
1358 "\n" ,
1359 "In my [RWC's] global session directory, there is one file:\n" ,
1360 " MNI152_2009_template_SSW.nii.gz\n" ,
1361 "which I copied there from the AFNI binaries download. In this way,\n" ,
1362 "I always have available the human template which I use most often.\n" ,
1363 "\n" ,
1364 "When you Switch Sessions and are viewing a global dataset, it is\n" ,
1365 "likely that you will NOT be viewing the same dataset after the Switch\n" ,
1366 "Session. You will have to then Switch Underlay and/or Switch Overlay\n" ,
1367 "to get back to the same global dataset(s).\n" ,
1368 "\n" ,
1369 "If you start AFNI and there are no datasets in the sessions given on\n" ,
1370 "the command line, then the directory specified by this variable\n" ,
1371 "becomes the default session. If there are no datasets there, either,\n" ,
1372 "then AFNI makes up a dummy dataset (AFNI cannot operate without at\n" ,
1373 "least one dataset present).\n" ,
1374 "\n" ,
1375 "------------------------------\n" ,
1376 "Variable: AFNI_DISP_SCROLLBARS (editable)\n" ,
1377 "------------------------------\n" ,
1378 "If this YES/NO variable is set to YES, then the 'Disp' control window\n" ,
1379 "(on the image viewers) will have scrollbars attached. This window has\n" ,
1380 "grown larger over the years, and for some people with pitifully small\n" ,
1381 "displays (e.g., laptops), it is now taller than their screens. If\n" ,
1382 "activated, this option will prevent the Disp window from being so tall\n" ,
1383 "and will attach scrollbars so you can access all of its contents.\n" ,
1384 "\n" ,
1385 "Note: If you change this value interactively, via Edit Environment,\n" ,
1386 "the change will only affect Disp windows opened after you 'Set' the\n" ,
1387 "variable. That is, already opened Disp windows won't suddenly get\n" ,
1388 "scrollbars if you change this to YES.\n" ,
1389 "\n" ,
1390 "------------------------------\n" ,
1391 "Variable: AFNI_GRAPH_TEXTLIMIT (editable)\n" ,
1392 "------------------------------\n" ,
1393 "This numerical variable sets the upper limit on the number of rows\n" ,
1394 "shown in the Button-3 popup in a sub-graph. If the number of rows in\n" ,
1395 "the popup would be more than this value, a text window with scrollbars\n" ,
1396 "is used instead of a \"spring-loaded\" menu pane. If you set this value\n" ,
1397 "to 1, then the text window will always be used. Note that a text\n" ,
1398 "window does not automatically popdown, but must be explicitly\n" ,
1399 "dismissed by the user pressing the \"Quit\" button.\n" ,
1400 "\n" ,
1401 "-----------------------------\n" ,
1402 "Variable: AFNI_GRAPH_BASELINE\n" ,
1403 "-----------------------------\n" ,
1404 "This variable should be set to one of the strings \"Individual\", \"Common\",\n" ,
1405 "or \"Global\", corresponding to the choices on the Opt->Baseline menu in\n" ,
1406 "a graph window. (Actually, only the first letter of the string will be\n" ,
1407 "used.) This variable will determine the initial setting of the Baseline\n" ,
1408 "menu when a graph window opens.\n" ,
1409 "\n" ,
1410 "-------------------------------\n" ,
1411 "Variable: AFNI_GRAPH_GLOBALBASE\n" ,
1412 "-------------------------------\n" ,
1413 "Normally, the global baseline for a graph window is set to the\n" ,
1414 "smallest value found in the entire 3D+time dataset. This variable\n" ,
1415 "lets you specify a numerical value to be used for this purpose\n" ,
1416 "instead. Probably the most common setting (for those who want to use\n" ,
1417 "this feature at all, which means Mike Beauchamp) would be\n" ,
1418 " setenv AFNI_GRAPH_GLOBALBASE 0\n" ,
1419 "Of course, you can always change the global baseline from the\n" ,
1420 "Opt->Baseline menu.\n" ,
1421 "\n" ,
1422 "-------------------------\n" ,
1423 "Variable: AFNI_GRAPH_CX2R (editable)\n" ,
1424 "-------------------------\n" ,
1425 "This variable determines how the AFNI time series graphing window\n" ,
1426 "displays complex-valued datasets. The possible values are ABS, PHASE,\n" ,
1427 "REAL, and IMAG. (Actually, only the first letter matters to the\n" ,
1428 "program.) The default method is ABS. (If you edit this method\n" ,
1429 "interactively, the graph won't automatically be redrawn -- you'll have\n" ,
1430 "to force a graph window redraw to see the effects.)\n" ,
1431 "\n" ,
1432 "---------------------------\n" ,
1433 "Variable: AFNI_GRAPH_BOXLAB --- THIS VARIABLE HAS BEEN REMOVED [11 Jan 2021]\n" ,
1434 "---------------------------\n" ,
1435 "Formerly, this variable determined how the AFNI grapher displays sub-brick\n" ,
1436 "labels on top of the Box graphs (from the 'Colors, Etc.' menu, or via\n" ,
1437 "the 'B' keypress).\n" ,
1438 "Now, the choice of if and where the labels appear is made directly in\n" ,
1439 "the graph viewer menus.\n" ,
1440 "\n" ,
1441 "-------------------------\n" ,
1442 "Variable: AFNI_GRAPH_FONT\n" ,
1443 "-------------------------\n" ,
1444 "This variable is the name of a font to use for text overlays in the\n" ,
1445 "AFNI time series graph viewers. If this variable is not set, the\n" ,
1446 "program has a list of fonts to try to load. If none of those can\n" ,
1447 "be loaded (something I've never seen happen), text may not display.\n" ,
1448 "For best results, this should be a fixed width font. To see a full\n" ,
1449 "list of all X11 fonts available, use the system command 'xlsfonts'\n" ,
1450 "(you probably want to pipe this output through 'more'). The first\n" ,
1451 "default font is currently [Apr 2011] set to\n" ,
1452 " -adobe-courier-bold-r-normal--12-120-75-75-m-70-iso8859-1\n" ,
1453 "For a font that is larger than the default, try 9x15bold or even\n" ,
1454 "10x20, as in the command\n" ,
1455 " afni -DAFNI_GRAPH_FONT=9x15bold\n" ,
1456 "The entire list of fonts that will be tried can be found in the\n" ,
1457 "source code file display.h, in the string array tfont_hopefuls[].\n" ,
1458 "\n" ,
1459 "-------------------------\n" ,
1460 "Variable: AFNI_GRAPH_FADE\n" ,
1461 "-------------------------\n" ,
1462 "If this variable is set to YES, then the 'threshold fade' feature\n" ,
1463 "of the AFNI graph window is turned on for all graph viewers when\n" ,
1464 "they open. Otherwise, you have to turn this feature on via the\n" ,
1465 "'F' key or the toggle control in the Opt menu.\n" ,
1466 "\n" ,
1467 "---------------------------------\n" ,
1468 "Variable: AFNI_GRAPH_ALLOW_SHIFTN\n" ,
1469 "---------------------------------\n" ,
1470 "If set to YES, this variable allows the use of the following keystroke\n" ,
1471 "sequence in the AFNI graph viewer:\n" ,
1472 " shift-N\n" ,
1473 " digit [digit ...]\n" ,
1474 " <Enter>\n" ,
1475 "The result is to immediately shift the graph matrix count (number of\n" ,
1476 "sub-graphs) to the decimal integer expressed by the digits. For example:\n" ,
1477 " N7<Enter>\n" ,
1478 "will set the graph window to show a 7x7 matrix of sub-graphs. By default,\n" ,
1479 "this is disabled, since it confuses some beginners -- until you press\n" ,
1480 "the <Enter> key, the graph window will be unresponsive to other keys.\n" ,
1481 "\n" ,
1482 "------------------------------\n" ,
1483 "Variable: AFNI_AdptMeanWidth1D\n" ,
1484 "------------------------------\n" ,
1485 "This variable lets you add a new Adaptive Mean filter to the 'Tran 1D'\n" ,
1486 "transformations menu in the AFNI graph viewer. The built in adaptive\n" ,
1487 "mean filter widths are 9 time points (plus/minus 4 about each value)\n" ,
1488 "and 19 time points (plus/minus 9). If you define this variable to\n" ,
1489 "be an odd integer larger than 9, not equal to 19, and less than 100,\n" ,
1490 "then a new function labeled 'AdptMeanXX' will appear in the 'Tran 1D'\n" ,
1491 "menu, where 'XX' is the width you choose here. This transformation\n" ,
1492 "is mainly for 'fun' -- to smooth out a time series to see structure\n" ,
1493 "obscured by noise. You can combine this function with the |FFT|\n" ,
1494 "function using the 'Edit 1Dchain' item in the Datamode->Misc menu.\n" ,
1495 "\n" ,
1496 "--------------------------\n" ,
1497 "Variable: AFNI_VALUE_LABEL (editable)\n" ,
1498 "--------------------------\n" ,
1499 "If this YES/NO variable is set to YES, then the data value label on\n" ,
1500 "the Define Overlay control panel will be turned on when only 1 or 2\n" ,
1501 "image viewer windows are open. This will consume more CPU time and\n" ,
1502 "redrawing time than the default, which is that this label is only\n" ,
1503 "turned on when all 3 image viewer windows are open. If you are\n" ,
1504 "operating X11 remotely over a slow connection, this option should not\n" ,
1505 "be turned on.\n" ,
1506 "\n" ,
1507 "--------------------------------\n" ,
1508 "Variable: AFNI_SUMA_BOXCOLOR_xxx\n" ,
1509 "--------------------------------\n" ,
1510 "This string defines the color used for overlaying surface nodes\n" ,
1511 "transmitted from SUMA to AFNI. This applies to surface number 'xxx',\n" ,
1512 "for xxx=001, 002, etc. If this is set to \"none\", then these boxes (at\n" ,
1513 "each node near a slice) won't be plotted.\n" ,
1514 "**NOTE** This variable, and the immediately following AFNI_SUMA_something\n" ,
1515 " variables, can be set interactively from the 'Control Surface'\n" ,
1516 " chooser window in the AFNI GUI.\n" ,
1517 "**NOTE** The colors allowed for surface display in AFNI are chosen via\n" ,
1518 " AFNI's color chooser menu. So no matter what color you specify\n" ,
1519 " in one of these AFNI_SUMA_something variables, it will be mapped\n" ,
1520 " to be the closest color on the color chooser menu.\n" ,
1521 "\n" ,
1522 "---------------------------------\n" ,
1523 "Variable: AFNI_SUMA_LINECOLOR_xxx\n" ,
1524 "---------------------------------\n" ,
1525 "This string defines the color used for overlaying surfaces transmitted\n" ,
1526 "from SUMA to AFNI. This applies to surface number 'xxx', for xxx=001,\n" ,
1527 "002, etc. If this is set to \"none\", then these lines (intersections\n" ,
1528 "of surfaces with slices) won't be plotted.\n" ,
1529 "\n" ,
1530 "In the special case that xxx=DEF, then the supplied color becomes\n" ,
1531 "'default' for all lines. Individual line colors can still be set by\n" ,
1532 "additional variables with xxx=001, 002, etc. being set.\n" ,
1533 "\n" ,
1534 "---------------------------------------\n" ,
1535 "Variable: AFNI_SUMA_LINECOLOR_FORCE_xxx\n" ,
1536 "---------------------------------------\n" ,
1537 "\n" ,
1538 "This variable is similar to AFNI_SUMA_LINECOLOR_xxx (again, for\n" ,
1539 "xxx=001 etc.), except for one detail. When SUMA sends a surface to\n" ,
1540 "AFNI for display, it can also send a color. If that happens, then\n" ,
1541 "AFNI_SUMA_LINECOLOR_xxx will have no effect. But\n" ,
1542 "AFNI_SUMA_LINECOLOR_FORCE_xxx will over-ride the choice SUMA makes and\n" ,
1543 "forces the color for surface number 'xxx' to be this color.\n" ,
1544 "\n" ,
1545 "The special usage of xxx=DEF (see AFNI_SUMA_LINECOLOR_xxx) also\n" ,
1546 "applies here.\n" ,
1547 "\n" ,
1548 "---------------------------\n" ,
1549 "Variable: AFNI_SUMA_BOXSIZE\n" ,
1550 "---------------------------\n" ,
1551 "This variable defines the size of the boxes drawn at each surface node\n" ,
1552 "transmitted from SUMA. The default is 0.25, which means that each box\n" ,
1553 "is plus and minus 1/4 of a voxel size about the node location. If you\n" ,
1554 "want a larger box, you could try\n" ,
1555 " setenv AFNI_SUMA_BOXSIZE 0.5\n" ,
1556 "\n" ,
1557 "----------------------------\n" ,
1558 "Variable: AFNI_SUMA_LINESIZE\n" ,
1559 "----------------------------\n" ,
1560 "This variable sets the thickness of the lines used when drawing a\n" ,
1561 "surface intersection overlay. The units are the width of the entire\n" ,
1562 "image; reasonable values are in the range 0..0.01; 0 means to draw the\n" ,
1563 "thinnest line possible. Since this is editable, you can experiment\n" ,
1564 "with it to see what looks good.\n" ,
1565 "\n" ,
1566 "-------------------------\n" ,
1567 "Variable: AFNI_NIML_START\n" ,
1568 "-------------------------\n" ,
1569 "If this YES/NO variable is set to YES, then NIML listening will be\n" ,
1570 "engaged from when AFNI starts. You can also enable NIML from the\n" ,
1571 "command line with the option \"-niml\", and from the Datamode->Misc menu\n" ,
1572 "item \"Start NIML\".\n" ,
1573 "\n" ,
1574 "NIML is the mechanism by which AFNI talks to other programs - it is\n" ,
1575 "the successor to plugouts. At this moment (Mar 2002), the only\n" ,
1576 "external NIML program is SUMA - the surface mapper.\n" ,
1577 "\n" ,
1578 "---------------------------\n" ,
1579 "Variable: AFNI_KEEP_PANNING (editable)\n" ,
1580 "---------------------------\n" ,
1581 "If this YES/NO variable is set to YES, then when the Zoom pan gets\n" ,
1582 "turned on in the AFNI image viewer, it will stay on until it is\n" ,
1583 "explicitly turned off. (The default behavior is to turn panning off\n" ,
1584 "after the user releases the mouse button.)\n" ,
1585 "\n" ,
1586 "-------------------------------\n" ,
1587 "Variable: AFNI_IMAGE_LABEL_MODE\n" ,
1588 "-------------------------------\n" ,
1589 "This integer determines the placement of the image coordinate labels\n" ,
1590 "drawn in the AFNI image viewer windows. The possible values are\n" ,
1591 " 0 = Labels are off\n" ,
1592 " 1 = Labels in upper left\n" ,
1593 " 2 = Labels in upper right\n" ,
1594 " 3 = Labels in lower left\n" ,
1595 " 4 = Labels in lower right\n" ,
1596 " 5 = Labels in upper middle\n" ,
1597 " 6 = Labels in lower middle\n" ,
1598 "You can also control the placement and size of the labels from the\n" ,
1599 "Button-3 (right-click) popup menu attached to the intensity bar to the\n" ,
1600 "right of the image sub-window.\n" ,
1601 "\n" ,
1602 "-------------------------------\n" ,
1603 "Variable: AFNI_IMAGE_LABEL_SIZE\n" ,
1604 "-------------------------------\n" ,
1605 "This integer determines the size of the image coordinate labels:\n" ,
1606 " 0 = Small\n" ,
1607 " 1 = Medium\n" ,
1608 " 2 = Large\n" ,
1609 " 3 = Huge\n" ,
1610 " 4 = Enormous\n" ,
1611 "\n" ,
1612 "--------------------------------\n" ,
1613 "Variable: AFNI_IMAGE_LABEL_COLOR (editable)\n" ,
1614 "--------------------------------\n" ,
1615 "This variable controls the color of the image coordinate labels.\n" ,
1616 "\n" ,
1617 "----------------------------------\n" ,
1618 "Variable: AFNI_IMAGE_LABEL_SETBACK (editable)\n" ,
1619 "----------------------------------\n" ,
1620 "This variable, a floating point value between 0 and 0.1, determines\n" ,
1621 "how far from the edge an image coordinate label will be drawn. The\n" ,
1622 "units are fractions of the image width/height.\n" ,
1623 "\n" ,
1624 "---------------------------------\n" ,
1625 "Variable: AFNI_IMAGE_LABEL_STRING (editable)\n" ,
1626 "---------------------------------\n" ,
1627 "This value of this variable is a string that is appended to the\n" ,
1628 "automatically generated image slice viewer overlay label -- the\n" ,
1629 "viewing of this label is controlled from the right-click popup menu\n" ,
1630 "attached to the intensity bar to the right of the image itself. This\n" ,
1631 "variable applies to any slice image viewer window into which the user\n" ,
1632 "has not specifically set a string for this purpose from the GUI menu\n" ,
1633 "item 'Label Append String'.\n" ,
1634 "\n" ,
1635 "------------------------------\n" ,
1636 "Variable: AFNI_IMAGE_LABEL_IJK (editable)\n" ,
1637 "------------------------------\n" ,
1638 "If this variable is YES, then the image label will be based on the\n" ,
1639 "slice index rather than the spatial (mm) coordinate. This variable can\n" ,
1640 "be set in the EditEnv AFNI GUI plugin (that is what 'editable' means).\n" ,
1641 "\n" ,
1642 "------------------------------\n" ,
1643 "Variable: AFNI_CROSSHAIR_LINES (editable) -- THIS VARIABLE IS NOW UNUSED\n" ,
1644 "------------------------------\n" ,
1645 "If this YES/NO variable is set to YES, then the image crosshairs will\n" ,
1646 "be drawn using lines rather than pixels. By default (this is the\n" ,
1647 "original AFNI way), crosshair lines are drawn the same way as\n" ,
1648 "functional overlays: by putting color pixels on top of the image. The\n" ,
1649 "new way draws lines on top of the image instead. The difference is\n" ,
1650 "quite visible when the image is zoomed; overlay by pixels shows the\n" ,
1651 "crosshair lines as fat blobs, but the lines are drawn as thin as\n" ,
1652 "possible, no matter what the image window size and zoom factor.\n" ,
1653 "\n" ,
1654 "Good points about crosshairs drawn with lines:\n" ,
1655 " - They are less obtrusive than pixel overlay, especially if you zoom\n" ,
1656 " or enlarge the image a lot\n" ,
1657 " - When doing a montage with Spacing=1, they'll look better in the\n" ,
1658 " orthogonal slices.\n" ,
1659 "Good points about crosshairs drawn with pixel overlay:\n" ,
1660 " - Pixel overlays can be rendered as translucent (on X11 TrueColor\n" ,
1661 " displays); geometrical overlays are always solid color.\n" ,
1662 "\n" ,
1663 "So you have to decide what you need most. You can change this item\n" ,
1664 "using the \"Edit Environment\" pseudo-plugin on the Datamode->Misc menu,\n" ,
1665 "so you can play with it interactively to get the features you want.\n" ,
1666 "\n" ,
1667 "----------------------------------\n" ,
1668 "Variable: AFNI_CROSSHAIR_THICKNESS\n" ,
1669 "----------------------------------\n" ,
1670 "This numeric variable lets you set the thickness of the lines used to\n" ,
1671 "draw the image viewer crosshairs. The default value is 0, which means\n" ,
1672 "thin lines. The units are fractions of the image size, and the legal\n" ,
1673 "range is 0 .. 0.05 (which will be very thick lines, I assure you).\n" ,
1674 "This variable was introduced in March 2015 for Corianne (if there is\n" ,
1675 "such a person).\n" ,
1676 "\n" ,
1677 "-----------------------------\n" ,
1678 "Variable: AFNI_CROSSHAIRS_OFF\n" ,
1679 "-----------------------------\n" ,
1680 "Set this variable to YES to turn off crosshairs for AFNI startup.\n" ,
1681 "\n" ,
1682 "----------------------------\n" ,
1683 "Variable: AFNI_CROP_ZOOMSAVE (editable)\n" ,
1684 "----------------------------\n" ,
1685 "When saving a zoomed image, the default is to save the entire zoomed\n" ,
1686 "image, not just the part you see. If this YES/NO variable is set to\n" ,
1687 "YES, then only the visible part will be saved.\n" ,
1688 "\n" ,
1689 "------------------------------\n" ,
1690 "Variable: AFNI_CROP_AUTOCENTER\n" ,
1691 "------------------------------\n" ,
1692 "If this variable is set to YES, then the image viewer windows will\n" ,
1693 "automatically re-center the cropping sub-window (if cropping is\n" ,
1694 "active) around the crosshair position -- as far as possible. You can\n" ,
1695 "also set this crop autocenter capability individually for each image\n" ,
1696 "viewer window from the intensity bar right-click popup menu.\n" ,
1697 "\n" ,
1698 "---------------------------\n" ,
1699 "Variables: AFNI_TLRC_BBOX_*\n" ,
1700 "---------------------------\n" ,
1701 "These variables let you choose the size of the \"Talairach Box\", into\n" ,
1702 "which +tlrc datasets are transformed. If defined, they should be\n" ,
1703 "positive values, in mm. The 5 variables (any or all of which may be\n" ,
1704 "used) are:\n" ,
1705 "\n" ,
1706 " AFNI_TLRC_BBOX_LAT = distance from midline to maximum left/right\n" ,
1707 " position [default=80]\n" ,
1708 " AFNI_TLRC_BBOX_ANT = distance from AC to most anterior point in box\n" ,
1709 " [default=80]\n" ,
1710 " AFNI_TLRC_BBOX_POS = distance from AC to most posterior point in box\n" ,
1711 " [default=110]\n" ,
1712 " AFNI_TLRC_BBOX_INF = distance from AC-PC line to most inferior point\n" ,
1713 " in box [default=55 for small box, 65 for big\n" ,
1714 " box]\n" ,
1715 " AFNI_TLRC_BBOX_SUP = distance from AC-PC line to most superior point\n" ,
1716 " in box [default=85]\n" ,
1717 "\n" ,
1718 "For example, \"setenv AFNI_TLRC_BBOX_INF 100\" lets you define the +tlrc\n" ,
1719 "box to extend 100 mm below the AC-PC line. Please note that virtually\n" ,
1720 "all the 3d* analysis programs (3dANOVA, etc.) do voxel-by-voxel\n" ,
1721 "analyses. This fact means that you will be unable to compare datasets\n" ,
1722 "created in +tlrc coordinates with different box sizes. Also, you will\n" ,
1723 "be unable to overlay regions from the Talairach Daemon database onto\n" ,
1724 "odd-sized +tlrc datasets. Therefore, I recommend that these variables\n" ,
1725 "be used only when strictly needed, and with caution.\n" ,
1726 "\n" ,
1727 "Lastly, try hard not to mix TLRC datasets created with various box\n" ,
1728 "sizes in the same session. Strange things may happen.\n" ,
1729 "\n" ,
1730 "---------------------------\n" ,
1731 "Variables: AFNI_ACPC_BBOX_*\n" ,
1732 "---------------------------\n" ,
1733 "The variables let you choose the size of the \"ACPC Box\", into which\n" ,
1734 "+acpc datasets are transformed. If defined, they should be positive\n" ,
1735 "values, in mm. The 6 variables (any or all of which may be used) are:\n" ,
1736 "\n" ,
1737 " AFNI_ACPC_BBOX_LAT = distance from midline to maximum left/right\n" ,
1738 " position [default=95]\n" ,
1739 " AFNI_ACPC_BBOX_ANT = distance from AC to most anterior point in box\n" ,
1740 " [default=95]\n" ,
1741 " AFNI_ACPC_BBOX_POS = distance from AC to most posterior point in box\n" ,
1742 " [default=140]\n" ,
1743 " AFNI_ACPC_BBOX_INF = distance from AC-PC line to most inferior point\n" ,
1744 " in box [default=70]\n" ,
1745 " AFNI_ACPC_BBOX_SUP = distance from AC-PC line to most superior point\n" ,
1746 " in box [default=100]\n" ,
1747 "\n" ,
1748 "Check example and heed ALL warnings for variables AFNI_TLRC_BBOX_*\n" ,
1749 "above.\n" ,
1750 "\n" ,
1751 "-------------------------\n" ,
1752 "Variable: AFNI_TTRR_SETUP\n" ,
1753 "-------------------------\n" ,
1754 "Name of a file to be loaded to define Talairach Atlas Colors, when the\n" ,
1755 "Atlas Colors control panel is first created. Format is the same as a\n" ,
1756 "file created from this control panel's \"Save\" button. This filename\n" ,
1757 "should be an absolute path (e.g., /home/yourname/.afni_ttcolors),\n" ,
1758 "since otherwise it will be read relative to the directory in which you\n" ,
1759 "start AFNI.\n" ,
1760 "\n" ,
1761 "-----------------------------\n" ,
1762 "Variable: AFNI_LOAD_PRINTSIZE\n" ,
1763 "-----------------------------\n" ,
1764 "AFNI will print (to stderr) a warning that it is loading a large\n" ,
1765 "dataset from disk. This value determines the meaning of \"large\". For\n" ,
1766 "example, setting this variable to \"40M\" means that loading a dataset\n" ,
1767 "larger than 40 Megabytes will trigger the warning. If not given, the\n" ,
1768 "default value is 100 Megabytes. The purpose of the warning is just to\n" ,
1769 "let the user know that it may be several seconds before the dataset is\n" ,
1770 "loaded (e.g., before the images appear). If you don't want this\n" ,
1771 "warning at all, set this variable to the string \"0\".\n" ,
1772 "\n" ,
1773 "-------------------------------\n" ,
1774 "Variable: AFNI_ANALYZE_DATASETS\n" ,
1775 "-------------------------------\n" ,
1776 "If this YES/NO variable is not set to NO, then ANALYZE-format files\n" ,
1777 "with name suffix .hdr will be read into the interactive AFNI program\n" ,
1778 "at startup, along with standard .HEAD/.BRIK datasets. That is, you\n" ,
1779 "have to set this variable explicitly to NO if you don't want\n" ,
1780 "ANALYZE-format files to be automatically recognized by the interactive\n" ,
1781 "AFNI program. This variable does not affect the ability of command\n" ,
1782 "line programs (3dSomething) to read .hdr input files.\n" ,
1783 "\n" ,
1784 "-----------------------------\n" ,
1785 "Variable: AFNI_ANALYZE_ORIENT\n" ,
1786 "-----------------------------\n" ,
1787 "ANALYZE .hdr files do not contain reliable information about the\n" ,
1788 "orientation of the data volumes. By default, AFNI assumes that these\n" ,
1789 "datasets are oriented in LPI order. You can set this variable to a\n" ,
1790 "different default order. See AFNI_ORIENT for details on the 3 letter\n" ,
1791 "format for this.\n" ,
1792 "\n" ,
1793 "---------------------------------\n" ,
1794 "Variable: AFNI_ANALYZE_AUTOCENTER\n" ,
1795 "---------------------------------\n" ,
1796 "ANALYZE .hdr files do not contain information about the origin of\n" ,
1797 "coordinates. The default AFNI approach mirrors that of FSL - the\n" ,
1798 "outermost corner of the first voxel in the dataset is set to (0,0,0).\n" ,
1799 "If you set this variable (AFNI_ANALYZE_AUTOCENTER) to YES, then\n" ,
1800 "instead (0,0,0) will be set to the center of the 3D ANALYZE array.\n" ,
1801 "This is the default that would be applied if you read the ANALYZE\n" ,
1802 "array into program to3d.\n" ,
1803 "\n" ,
1804 "----------------------------\n" ,
1805 "Variable: AFNI_VERSION_CHECK\n" ,
1806 "----------------------------\n" ,
1807 "If this YES/NO variable is set to NO, then AFNI will not try to check\n" ,
1808 "if its version is up-to-date when it starts. Otherwise, it will try\n" ,
1809 "to check the program version with the AFNI web server.\n" ,
1810 "\n" ,
1811 "-------------------------\n" ,
1812 "Variable: AFNI_MOTD_CHECK\n" ,
1813 "-------------------------\n" ,
1814 "Similarly, if this YES/NO variable is set to NO, then AFNI will not\n" ,
1815 "display and fetch the AFNI \"Message of the Day\" at startup. You can\n" ,
1816 "always check the MOTD by using the Datamode->Misc menu.\n" ,
1817 "\n" ,
1818 "-----------------------------------\n" ,
1819 "Variable: AFNI_SLICE_SPACING_IS_GAP\n" ,
1820 "-----------------------------------\n" ,
1821 "This YES/NO variable is designed to patch a flaw in some DICOM files,\n" ,
1822 "where the \"Spacing Between Slices\" attribute is erroneously set to the\n" ,
1823 "gap between the slices, rather than the center-to-center slice\n" ,
1824 "distance specified in the DICOM standard. If this variable is set to\n" ,
1825 "YES, then the \"Slice Thickness\" attribute will always be added to\n" ,
1826 "\"Spacing Between Slices\" to get the z voxel size (assuming both\n" ,
1827 "attributes are present in the DICOM file).\n" ,
1828 "\n" ,
1829 "To check if a DICOM file has this problem, you can read it into to3d\n" ,
1830 "with the command \"to3d suspect_file_name\". A warning will be printed\n" ,
1831 "to the terminal window if attribute \"Spacing Between Slices\" is less\n" ,
1832 "than attribute \"Slice Thickness\". Another way to check is with a\n" ,
1833 "command like so\n" ,
1834 "\n" ,
1835 " dicom_hdr suspect_file_name | grep \"Slice\"\n" ,
1836 "\n" ,
1837 "then check if the \"Spacing Between Slices\" and \"Slice Thickness\"\n" ,
1838 "values are correct for the given acquisition. We have only seen this\n" ,
1839 "problem in GE generated DICOM files, but that doesn't mean it won't\n" ,
1840 "occur elsewhere.\n" ,
1841 "\n" ,
1842 "If this variable is set to NO, then this patchup will never be made.\n" ,
1843 "The z voxel size will be set to \"Spacing Between Slices\" if present,\n" ,
1844 "otherwise to \"Slice Thickness\". This may be needed for some Phillips\n" ,
1845 "pulse sequences, which can report \"Spacing Between Slices\" < \"Slice\n" ,
1846 "Thickness\". In such a case, if this variable is not set, the wrong z\n" ,
1847 "voxel size will be assigned!\n" ,
1848 "\n" ,
1849 "If this variable is not set at all, AND if \"Spacing Between Slices\" is\n" ,
1850 "less less than 0.99 times \"Slice Thickness\", it will be treated as a\n" ,
1851 "gap; that is, the z voxel size will again be set to \"Spacing Between\n" ,
1852 "Slices\" + \"Slice Thickness\" if \"Spacing Between Slices\" < 0.99*\"Slice\n" ,
1853 "Thickness\". Otherwise, the z voxel size will be set to the larger of\n" ,
1854 "\"Spacing Between Slices\" and \"Slice Thickness\".\n" ,
1855 "\n" ,
1856 "N.B.: \"YES\", \"NO\", and \"not set\" have 3 different sets of behavior!\n" ,
1857 " In the summary below, if a variable isn't set, treat it as zero:\n" ,
1858 "\n" ,
1859 " YES => dz = Thickness + Spacing\n" ,
1860 " NO => dz = Spacing if present, otherwise Thickness\n" ,
1861 " not set => if( Spacing > 0 && Spacing < 0.99*Thickness )\n" ,
1862 " dz = Thickness + Spacing\n" ,
1863 " else\n" ,
1864 " dz = MAX( Thickness , Spacing )\n" ,
1865 "\n" ,
1866 "If neither variable is set, then dz=1 mm, which is probably wrong.\n" ,
1867 "\n" ,
1868 "Sorry about this complexity, but the situation with various\n" ,
1869 "manufacturers is complicated, murky, and confusingly maddening.\n" ,
1870 "\n" ,
1871 "---------------------------------------------------\n" ,
1872 "Variables: AFNI_DICOM_RESCALE and AFNI_DICOM_WINDOW\n" ,
1873 "---------------------------------------------------\n" ,
1874 "DICOM image files can contain rescaling and windowing \"tags\". If\n" ,
1875 "present, these values indicate to affinely modify the values stored in\n" ,
1876 "the file. As far as I can tell, \"rescale\" means that the values\n" ,
1877 "should always be modified, whereas \"window\" means the values should be\n" ,
1878 "modified for display purposes. If both are present, the rescale comes\n" ,
1879 "before window. These two YES/NO environment variables control whether\n" ,
1880 "the AFNI image input functions (used in to3d) should apply the rescale\n" ,
1881 "and window tags.\n" ,
1882 "\n" ,
1883 "It is my impression from the laconic, terse, and opaque DICOM manual\n" ,
1884 "that window tags are intended for display purposes only, and that they\n" ,
1885 "aren't needed for signal processing. But you'll have to examine your\n" ,
1886 "own data to decide whether to use these options -- manufacturers seem\n" ,
1887 "to differ. Plus, I don't have that much experience with DICOM data\n" ,
1888 "from many different sources.\n" ,
1889 "\n" ,
1890 "---------------------------------------------------\n" ,
1891 "Variable: AFNI_DICOM_VERBOSE\n" ,
1892 "---------------------------------------------------\n" ,
1893 "Set this YES/NO variable to YES to output extra details when reading\n" ,
1894 "DICOM images.\n" ,
1895 "\n" ,
1896 "---------------------------------------------------\n" ,
1897 "Variable: AFNI_DICOM_USE_LAST_ELEMENT\n" ,
1898 "---------------------------------------------------\n" ,
1899 "Set this YES/NO variable to YES to force the DICOM reading routines to\n" ,
1900 "set each DICOM element based on the last occurrence, not necessarily\n" ,
1901 "the first.\n" ,
1902 "\n" ,
1903 "-----------------------\n" ,
1904 "Variable: IDCODE_PREFIX\n" ,
1905 "-----------------------\n" ,
1906 "AFNI stores with each dataset a unique string, called an \"idcode\". An\n" ,
1907 "example is \"XYZ_MoNLqdNOwMNEYmKSBytfJg\". You can alter the first\n" ,
1908 "three characters of the idcode with this variable. For example,\n" ,
1909 " setenv IDCODE_PREFIX RWC\n" ,
1910 "sets the first 3 characters of newly generated idcodes to be the\n" ,
1911 "initials of AFNI's author. I find this a handy way to \"brand\" my\n" ,
1912 "datasets. Of course, there are only 17576 possible 3 letter\n" ,
1913 "combinations (140608 if you allow for case), so you should claim your\n" ,
1914 "prefix soon!!!\n" ,
1915 "\n" ,
1916 "Idcodes are used to store links between datasets. For example, when\n" ,
1917 "SUMA sends a surface to AFNI, it identifies the dataset to which the\n" ,
1918 "surface is to be associated with the dataset's idcode. Similarly,\n" ,
1919 "when AFNI sends a color overlay to SUMA, it uses the surface idcode to\n" ,
1920 "indicate which surface family the overlay is to be mapped onto.\n" ,
1921 "\n" ,
1922 "-------------------------\n" ,
1923 "Variable: AFNI_AGIF_DELAY\n" ,
1924 "-------------------------\n" ,
1925 "This is the time delay between frames when writing an animated GIF\n" ,
1926 "file from an image viewer window. The units are 100ths of seconds\n" ,
1927 "(centi-seconds!); the default value is 20 (= 5 frames per second).\n" ,
1928 "Note that this value is NOT editable in the Edit Environment control\n" ,
1929 "panel, so you have to set it up prior to starting AFNI (e.g., by using\n" ,
1930 "an option like '-DAFNI_AGIF_DELAY=10' on the command line when\n" ,
1931 "starting AFNI).\n" ,
1932 "\n" ,
1933 "-----------------------------\n" ,
1934 "Variable: AFNI_MPEG_FRAMERATE\n" ,
1935 "-----------------------------\n" ,
1936 "This value sets the frame rate (per second) of the MPEG-1 output\n" ,
1937 "animation from the image viewer window. The legal values allowed by\n" ,
1938 "MPEG-1 are 24, 25, 30, 50, and 60; 24 (the slowest) is the default.\n" ,
1939 "Note that the MPEG-1 standard does NOT allow arbitrary framerates,\n" ,
1940 "only these listed. To further slow down an MPEG-1 animation in AFNI,\n" ,
1941 "use the AFNI_ANIM_DUP variable, described below.\n" ,
1942 "\n" ,
1943 "-----------------------\n" ,
1944 "Variable: AFNI_ANIM_DUP (editable)\n" ,
1945 "-----------------------\n" ,
1946 "This value sets the frame duplication factor for AGIF or MPEG\n" ,
1947 "animation output. If this value 'd' is between 1 and 99, then each\n" ,
1948 "frame (image) will be written out 'd' times before being incorporated\n" ,
1949 "into the movie file. Note that AFNI_AGIF_DELAY can be used to slow\n" ,
1950 "down an AGIF file more efficiently, but that there is no other way\n" ,
1951 "(within AFNI) to slow down an MPEG file. (Some MPEG movie players\n" ,
1952 "will let you slow down the animation, but that's outside of AFNI's\n" ,
1953 "control.)\n" ,
1954 "\n" ,
1955 "You can control this variable directly from the Edit Environment\n" ,
1956 "control panel, or set its internal value in AFNI (or other image\n" ,
1957 "viewers) from the right-click popup menu attached to the intensity\n" ,
1958 "grayscale bar just to the right of the image sub-window in the viewer.\n" ,
1959 "Note that the duplication factor must be greater than 1 for any\n" ,
1960 "slowdown to occur. For example, if you want 6 frames per second in an\n" ,
1961 "MPEG file, then a duplication factor of 4 would work (24 fps / 4 = 6\n" ,
1962 "fps).\n" ,
1963 "\n" ,
1964 "For MPEG-1 files, AFNI will set up the frame temporal encoding pattern\n" ,
1965 "so that there is very little .mpg file size overhead for this frame\n" ,
1966 "duplication. The same is NOT true for animated GIF files, since these\n" ,
1967 "files do not have any compression along the time axis. Therefore, you\n" ,
1968 "should use AFNI_AGIF_DELAY to control the frame rate of animated GIF\n" ,
1969 "files, and not this frame duplication factor.\n" ,
1970 "\n" ,
1971 "----------------------------\n" ,
1972 "Variable: AFNI_STARTUP_SOUND\n" ,
1973 "----------------------------\n" ,
1974 "If this variable is set to YES, then when the AFNI GUI starts, a\n" ,
1975 "pair of notes will be played (softly). For this to happen, it is\n" ,
1976 "also necessary that\n" ,
1977 " a) the 'sox' sound software package be installed\n" ,
1978 " b) that the X11 display is local, not remote\n" ,
1979 " c) that no '-com' options are on the command line\n" ,
1980 "You can also try using the 'Play startup sound' button on the\n" ,
1981 "right-click popup menu attached to the logo space to the right\n" ,
1982 "of the GUI 'done' button. For that button to work, conditions\n" ,
1983 "a) and b) above must be true. On a Mac, you can install 'sox'\n" ,
1984 "using the 'brew' package (e.g.).\n" ,
1985 "\n" ,
1986 "---------------------------\n" ,
1987 "Variable: AFNI_SOUND_PLAYER\n" ,
1988 "---------------------------\n" ,
1989 "The 'p' and 'P' keys in the AFNI graph viewer can be used to generate\n" ,
1990 "sound from the graph data time series. However, AFNI itself does not\n" ,
1991 "play sound - it uses an external player program. By default, AFNI can\n" ,
1992 "use any one of these programs:\n" ,
1993 " play (part of sox) ; afplay (Mac) ; mplayer ; aplay (Linux)\n" ,
1994 "and it will search your path to find one of these (in that order).\n" ,
1995 "If you have some other player program you want to use, you can provide\n" ,
1996 "the full path to that program in this variable, as in '/usr/bin/afplay'.\n" ,
1997 "\n" ,
1998 "-------------------------\n" ,
1999 "Variable: AFNI_MUSIC_SIZE\n" ,
2000 "-------------------------\n" ,
2001 "This variable is the length of the random music sequence generated by\n" ,
2002 "the 'Play random music' button. The default value is 99; if you want\n" ,
2003 "it to be longer, increase this value. There are about 7 notes per\n" ,
2004 "seconds normally, so setting this value to 420 is about 1 minute.\n" ,
2005 "Music can only be played if a sound player program is installed on\n" ,
2006 "your computer, as described under AFNI_SOUND_PLAYER above.\n" ,
2007 "\n" ,
2008 "-----------------------------\n" ,
2009 "Variable: AFNI_STARTUP_SCRIPT\n" ,
2010 "-----------------------------\n" ,
2011 "If this is set, this is the name of an AFNI Script to run when AFNI\n" ,
2012 "first starts. (See the file README.driver for information about AFNI\n" ,
2013 "Scripts.) If this is not set, it defaults to \".afni.startup_script\".\n" ,
2014 "The program first tries to read this filename from the current working\n" ,
2015 "directory; if that fails, then it tries to read from your home\n" ,
2016 "directory. No error message is given if neither file can be read.\n" ,
2017 "\n" ,
2018 "You can save a file \".afni.startup_script\" that will recreate the\n" ,
2019 "window layout you currently have. Use the \"Datamode->Misc->Save\n" ,
2020 "Layout\" button and press \"Set\" on the popup control without entering\n" ,
2021 "any filename. Instead of a Layout file (cf. AFNI_LAYOUT_FILE above),\n" ,
2022 "you'll get a Script file if you leave the filename blank or enter any\n" ,
2023 "filename with the string \"script\" included (e.g., \"coolstuff.script\").\n" ,
2024 "\n" ,
2025 "The capabilities of Script files are expanded from time to time. Not\n" ,
2026 "all features of the AFNI window setup are currently save-able this\n" ,
2027 "way.\n" ,
2028 "\n" ,
2029 "You can load a Script file interactively during an AFNI run by using\n" ,
2030 "the button \"Datamode->Misc->Run Script\". As a 'secret' option, if you\n" ,
2031 "enter a line containing a blank in the filename dialog, that line\n" ,
2032 "will be executed as a single command, rather than be used as a script\n" ,
2033 "filename.\n" ,
2034 "\n" ,
2035 "------------------------------\n" ,
2036 "Variable: AFNI_DEFAULT_OPACITY\n" ,
2037 "------------------------------\n" ,
2038 "This should be set to an integer from 1..9, and controls the default\n" ,
2039 "opacity setting for the color overlay in image viewer windows.\n" ,
2040 "\n" ,
2041 "-----------------------------\n" ,
2042 "Variable: AFNI_DEFAULT_IMSAVE\n" ,
2043 "-----------------------------\n" ,
2044 "This should be set to the suffix of the image format to which you want\n" ,
2045 "to save from an image viewer. The suffixes AFNI knows about (as of 23\n" ,
2046 "Jan 2003) are\n" ,
2047 " ppm = Portable PixMap format = cat\n" ,
2048 " jpg = Joint Photographics Experts Group (JPEG) format = cjpeg\n" ,
2049 " gif = Compuserve Graphics Interchange File (GIF) format = ppmtogif\n" ,
2050 " tif = Tagged Image File Format (TIFF) = ppm2tiff\n" ,
2051 " or pnmtotiff\n" ,
2052 " bmp = Windows Bitmap (BMP) format = ppmtobmp\n" ,
2053 " eps = Encapsulated PostScript format = pnmtops\n" ,
2054 " pdf = Portable Document Format = epstopdf\n" ,
2055 " png = Portable Network Graphics format = pnmtopng\n" ,
2056 "The third column is the name of the external filter program that AFNI\n" ,
2057 "uses to write the format. If a filter is not present on your system,\n" ,
2058 "then that option is not available. Most of these filters are part of\n" ,
2059 "the netpbm package, which can be installed on MacOS X by using the\n" ,
2060 "brew package (for example).\n" ,
2061 "\n" ,
2062 "------------------------------\n" ,
2063 "Variable: AFNI_IMSAVE_WARNINGS\n" ,
2064 "------------------------------\n" ,
2065 "If this variable is not set, then if the program cannot find one\n" ,
2066 "of the output filter programs listed above, then a warning message\n" ,
2067 "will be printed to the terminal. However, if you set this variable\n" ,
2068 "to NO, then such warning messages will NOT be printed out. The\n" ,
2069 "purpose of this variable is to let you silence these messages\n" ,
2070 "once you get sick of seeing them.\n" ,
2071 "\n" ,
2072 "---------------------------\n" ,
2073 "Variable: AFNI_IMSAVE_DEBUG\n" ,
2074 "---------------------------\n" ,
2075 "If this variable is set to YES, then when you save an image from the\n" ,
2076 "image viewer, the various steps will be printed to the terminal\n" ,
2077 "as the process happens. As the variable name is implied, this\n" ,
2078 "capability is here for debugging, and has not actually been used\n" ,
2079 "for years (at least by the AFNI Imperial Command Team).\n" ,
2080 "\n" ,
2081 "-----------------------------\n" ,
2082 "Variables: AFNI_COLORSCALE_xx for xx=01, 02, ..., 99\n" ,
2083 "-----------------------------\n" ,
2084 "These variables let you name files to be read it at AFNI startup to\n" ,
2085 "define \"continuous\" colorscales for the \"**\" mode of the color pbar.\n" ,
2086 "These files will be looked for in the current directory when you start\n" ,
2087 "AFNI, or in your home directory (if they aren't in the current\n" ,
2088 "directory). A sample file:\n" ,
2089 "\n" ,
2090 " Yellow-Red-Blue\n" ,
2091 " 1.0 #ffff00\n" ,
2092 " 0.7 #ffaa00\n" ,
2093 " 0.5 #ff0000\n" ,
2094 " 0.3 #aa00aa\n" ,
2095 " 0.0 #0000ff\n" ,
2096 "\n" ,
2097 "The first line is the name of this colorscale, to go in the colorscale\n" ,
2098 "popup chooser. The succeeding lines each have a number and a color\n" ,
2099 "definition. The numbers should be decreasing, and indicate the\n" ,
2100 "location on the colorscale. The largest number corresponds to the top\n" ,
2101 "of the colorscale and the smallest to the bottom - intermediate\n" ,
2102 "numbers denote intermediate locations. The colors at each location\n" ,
2103 "are specified using X11 notation (cf. \"man XParseColor\"). In this\n" ,
2104 "example, I'm using hexadecimal colors, in the form #rrggbb, where each\n" ,
2105 "hex pair ranges from 00 to ff. Another color format is\n" ,
2106 "\"rgbi:rf/gf/bf\", where each value rf,gf,bf is a number between 0.0 and\n" ,
2107 "1.0 (inclusive); for example, yellow would be \"rgbi:1.0/1.0/0.0\".\n" ,
2108 "\n" ,
2109 "Colors are interpolated (linearly in RGB space) between the break\n" ,
2110 "locations given in the file. There are actually 128 color locations\n" ,
2111 "on a colorscale.\n" ,
2112 "\n" ,
2113 "An alternative format for the file is to omit the numbers indicating\n" ,
2114 "the break locations. In this case, the break locations will be taken\n" ,
2115 "to be equally spaced. For example:\n" ,
2116 "\n" ,
2117 " Yellow-Red-Blue\n" ,
2118 " #ffff00\n" ,
2119 " #ffaa00\n" ,
2120 " #ff0000\n" ,
2121 " #aa00aa\n" ,
2122 " #0000ff\n" ,
2123 "\n" ,
2124 "This example is not exactly the same as the other one, since the\n" ,
2125 "breakpoints are evenly spaced now (as if they had been given as 1.0,\n" ,
2126 "0.75, 0.5, 0.25, and 0.0). With this format, if you want to manually\n" ,
2127 "specify all 128 colors, you can do so, 1 color per line, remembering\n" ,
2128 "that the first line of the file is taken to be the colorscale title\n" ,
2129 "(no blanks allowed in the title!).\n" ,
2130 "\n" ,
2131 "---------------------------------\n" ,
2132 "Variable: AFNI_COLORSCALE_DEFAULT\n" ,
2133 "---------------------------------\n" ,
2134 "If set, this is the name of the default colorscale to use in setup.\n" ,
2135 "As a special case, if you DO NOT want a colorscale to be setup by\n" ,
2136 "default at all, then set this variable to the string \"NO\".\n" ,
2137 "\n" ,
2138 "N.B.: This variable only applies if you are using AFNI with a\n" ,
2139 "TrueColor X11 visual. If you are using a PseudoColor visual, then\n" ,
2140 "this variable is ignored!\n" ,
2141 "\n" ,
2142 "----------------------------\n" ,
2143 "Variable: AFNI_RESCAN_METHOD\n" ,
2144 "----------------------------\n" ,
2145 "On 28 Dec 2002, I modified the way that the \"Rescan\" operation in AFNI\n" ,
2146 "works when re-reading datasets from sessions. The old way would purge\n" ,
2147 "and replace all datasets; the new way just adds datasets that didn't\n" ,
2148 "exist before. There are some differences between these methods:\n" ,
2149 " \"Replace\" will detect changes to a dataset, so if you add a brick\n" ,
2150 " using 3dTcat -glueto (for example), this will be reflected in\n" ,
2151 " AFNI.\n" ,
2152 " \"Replace\" will cause troubles if you are using a dataset in a\n" ,
2153 " plugin; the two main examples are volume rendering and the drawing\n" ,
2154 " plugin. This problem will occur even if you didn't do anything to\n" ,
2155 " the dataset on disk, since the internal pointer to the dataset\n" ,
2156 " will have been changed by the rescan, but the plugins won't know\n" ,
2157 " that.\n" ,
2158 " \"Add\" will not detect changes to a dataset on disk, but it also\n" ,
2159 " won't affect the pointers to the existing datasets.\n" ,
2160 "You can choose to use the \"Replace\" method (the old style) by setting\n" ,
2161 "this environment variable to the string \"REPLACE\".\n" ,
2162 "\n" ,
2163 "---------------------------\n" ,
2164 "Variable: AFNI_OLD_PPMTOBMP\n" ,
2165 "---------------------------\n" ,
2166 "The old (before 21 Feb 2003) usage of netpbm program \"ppmtobmp\" was to\n" ,
2167 "write a color image quantized to 255 colors. The new usage is to\n" ,
2168 "write a 24-bit image, which is thus not color-quantized. If you want\n" ,
2169 "the old behavior, set this environment variable to YES. This setting\n" ,
2170 "(YES) will be necessary if you have an older version of ppmtobmp in\n" ,
2171 "your path, which doesn't support the \"-bpp\" option.\n" ,
2172 "\n" ,
2173 "------------------------------\n" ,
2174 "Variable: AFNI_1DPLOT_COLOR_xx\n" ,
2175 "------------------------------\n" ,
2176 "This variable lets you set the colors used in the 1dplot program (and\n" ,
2177 "other similar graphs). Here, \"xx\" is a number from \"01\" to \"19\". The\n" ,
2178 "value of the environment variable must be in the form \"rgbi:rf/gf/bf\",\n" ,
2179 "where each color intensity (rf, gf, bf) is a number between 0.0 and\n" ,
2180 "1.0. For example, \"rgbi:1.0/1.0/0.0\" is yellow. By default, the\n" ,
2181 "first 4 colors are defined as the equivalents of\n" ,
2182 " setenv AFNI_1DPLOT_COLOR_01 rgbi:0.0/0.0/0.0\n" ,
2183 " setenv AFNI_1DPLOT_COLOR_02 rgbi:0.9/0.0/0.0\n" ,
2184 " setenv AFNI_1DPLOT_COLOR_03 rgbi:0.0/0.7/0.0\n" ,
2185 " setenv AFNI_1DPLOT_COLOR_04 rgbi:0.0/0.0/0.9\n" ,
2186 "which are black, red, green, and blue, respectively. You can alter\n" ,
2187 "these colors, or leave them unchanged and start defining colors at 05.\n" ,
2188 "The largest color number you define will be the last color index used;\n" ,
2189 "if more line colors are needed, they will cycle back to color 01. If\n" ,
2190 "you leave a gap in the numbering (e.g., you define color 07 but not 05\n" ,
2191 "or 06), then the undefined colors will be fuliginous.\n" ,
2192 "\n" ,
2193 "[Dec 2007] You can now specify the colors by using the special names\n" ,
2194 "'green', 'red', 'blue', 'gold', 'pink', and 'purple'. Also, by using\n" ,
2195 "3 or 6 digit hexadecimal notation as in '#8888aa' for a blueish-gray\n" ,
2196 "color (6 digits) or '#0ac' for a cyanish color (3 digits). These are\n" ,
2197 "intended to make life a little simpler.\n" ,
2198 "\n" ,
2199 "--------------------------\n" ,
2200 "Variable: AFNI_1DPLOT_THIK (editable)\n" ,
2201 "--------------------------\n" ,
2202 "This numeric variable lets you control the thickness of lines drawn in\n" ,
2203 "the 1dplot-style windows. The units are in terms of the width of the\n" ,
2204 "entire plot, so that a value of 0.005 is 'reasonable'; 0.01 will be\n" ,
2205 "fairly thick lines, and 0.02 will be too thick for most purposes.\n" ,
2206 "\n" ,
2207 "----------------------------\n" ,
2208 "Variable: AFNI_1DPLOT_IMSIZE\n" ,
2209 "----------------------------\n" ,
2210 "This numeric variable sets the image size (in pixels across the\n" ,
2211 "screen) of images saved via the '-png' or '-jpg' options of 1dplot, or\n" ,
2212 "images saved when giving the '.png' or '.jpg' from 1dplot-style\n" ,
2213 "graphs. The default value is 1024. Values over 2048 may give odd\n" ,
2214 "looking results, and will be palpably slower to render.\n" ,
2215 "\n" ,
2216 "-----------------------------\n" ,
2217 "Variable: AFNI_1DPLOT_BOXSIZE\n" ,
2218 "-----------------------------\n" ,
2219 "This variable sets the size of the boxes that are plotted with the\n" ,
2220 "1dplot '-box' option. The units are in terms of the width of the\n" ,
2221 "entire plot; a value of 0.006 is the default. The largest allowed\n" ,
2222 "value is 0.02 and the smallest is 0.001.\n" ,
2223 "\n" ,
2224 "-------------------------------\n" ,
2225 "Variable: AFNI_1DPLOT_RENDEROLD\n" ,
2226 "-------------------------------\n" ,
2227 "On 30 Apr 2012, a new method of rendering the 1dplot graph into an X11\n" ,
2228 "window was introduced -- this method uses 'anti-aliasing' to produce\n" ,
2229 "smoother lines and characters. If you want the old coarser-looking\n" ,
2230 "rendering method, set this variable to YES.\n" ,
2231 "\n" ,
2232 "----------------------------\n" ,
2233 "Variable: AFNI_1DPLOT_RANBOX\n" ,
2234 "----------------------------\n" ,
2235 "When using '-noline' in 1dplot (to get a cloud of points without\n" ,
2236 "lines), and when there are multiple time series being plotted with\n" ,
2237 "option '-one', the normal state of affairs is that later time series\n" ,
2238 "boxes get plotted on top of earlier boxes. If there are a lot of\n" ,
2239 "points, then the earlier boxes get completely obscured. Setting\n" ,
2240 "this variable to YES means that the boxes will be plotted in a\n" ,
2241 "pseudo-random order, so that each color/shape of box has a chance\n" ,
2242 "to be seen in the cloud of data.\n" ,
2243 "\n" ,
2244 "---------------------------------\n" ,
2245 "Variable: AFNI_SIEMENS_INTERLEAVE\n" ,
2246 "---------------------------------\n" ,
2247 "The old (pre-DICOM) Siemens .ima image mosaic format sometimes stores\n" ,
2248 "the multi-slice EPI data in correct spatial order and sometimes in\n" ,
2249 "correct time acquisition order. In the latter case, the images are\n" ,
2250 "stored in a spatially-interleaved fashion. As far as I know, there is\n" ,
2251 "no way to tell this from the .ima file header itself. Therefore, if\n" ,
2252 "you have a problem with such files, set this variable to YES to\n" ,
2253 "un-interleave the images when to3d reads them. One way to tell if the\n" ,
2254 "images need to be un-interleaved is to do\n" ,
2255 " afni -im fred.ima\n" ,
2256 "then look at the images in an Axial image viewer. If the slices make\n" ,
2257 "up a single coherent volume, then they are NOT interleaved. If the\n" ,
2258 "slices look like they make up 2 separate brain volumes, then they need\n" ,
2259 "to be un-interleaved, and you need to set this variable to YES.\n" ,
2260 "\n" ,
2261 "-----------------------------\n" ,
2262 "Variable: AFNI_TRY_DICOM_LAST\n" ,
2263 "-----------------------------\n" ,
2264 "When to3d tries to read an image file, it guesses the format from the\n" ,
2265 "filename. However, this doesn't always work. In particular, DICOM\n" ,
2266 "files don't have any fixed filename suffix or prefix. If all else\n" ,
2267 "fails, to3d normally tries to read a file as a DICOM file, and as a\n" ,
2268 "last resort, as a flat binary file. However, if a file is NOT a DICOM\n" ,
2269 "file, the DICOM reading function will print out a lot of error\n" ,
2270 "messages, since there is also no standard internal marker in all DICOM\n" ,
2271 "files that identify them. Most people don't like all these messages\n" ,
2272 "(perhaps hundreds per file), even if the program then successfully\n" ,
2273 "reads their flat binary files.\n" ,
2274 "\n" ,
2275 "If this YES/NO variable is set to YES, then the normal last-resort\n" ,
2276 "order of reading described above is reversed. If to3d can't read the\n" ,
2277 "file any other way, it will try it as a flat binary file. If that\n" ,
2278 "fails, then DICOM will be the ultimate resort, instead of being the\n" ,
2279 "penultimate resort that it is by default. This may help elide some\n" ,
2280 "error messages. However, if you have a DICOM file that is exactly\n" ,
2281 "131072 bytes long (for example), then it will be interpreted as a\n" ,
2282 "headerless 256x256 image of shorts, instead of whatever it really is.\n" ,
2283 "So only set this variable to YES if necessary!\n" ,
2284 "\n" ,
2285 "-----------------------------\n" ,
2286 "Variable: AFNI_THRESH_BIGSTEP\n" ,
2287 "-----------------------------\n" ,
2288 "The AFNI threshold sliders (in the Define Overlay control panels and\n" ,
2289 "the Render Dataset plugins) are divided into 10000 steps from bottom\n" ,
2290 "to top. If you click in the trough or use the PageUp/PageDown keys,\n" ,
2291 "the default action is to move the slider 10 of the steps at once.\n" ,
2292 "(The up and down arrow keys move 1 step at a time.) You can change\n" ,
2293 "this big step from the default of 10 to any value between 1 and 1000\n" ,
2294 "by setting this environment variable; for example\n" ,
2295 " setenv AFNI_THRESH_BIGSTEP 100\n" ,
2296 "will move the slider 1% of its height per PageUp/PageDown key or mouse\n" ,
2297 "click.\n" ,
2298 "\n" ,
2299 "--------------------------\n" ,
2300 "Variable: AFNI_THRESH_AUTO (editable)\n" ,
2301 "--------------------------\n" ,
2302 "If this YES/NO variable is set to YES, then whenever you switch\n" ,
2303 "overlay datasets, the function threshold slider will automatically\n" ,
2304 "change to some value that MIGHT be appropriate for the values in the\n" ,
2305 "new dataset. [This is for Ziad!]\n" ,
2306 "\n" ,
2307 "-------------------------------\n" ,
2308 "Variable: AFNI_THRESH_TOP_EXPON\n" ,
2309 "-------------------------------\n" ,
2310 "This variable defines the maximum value for the '**' setting underneath\n" ,
2311 "the Overlay threshold slider. By default, this value is 5, but you\n" ,
2312 "can change that to 4 or 6 with this variable. [This is for Phil Kohn]\n" ,
2313 "\n" ,
2314 "--------------------------------\n" ,
2315 "Variable: AFNI_THRESH_INIT_EXPON\n" ,
2316 "--------------------------------\n" ,
2317 "This variable defines the initial power-of-ten scale for the '**'\n" ,
2318 "setting. By default, this value is 1 (thresholds run from 0 to 10),\n" ,
2319 "but you can change this to a value from 0 to 'TOP_EXPON'.\n" ,
2320 "\n" ,
2321 "-------------------------------\n" ,
2322 "Variable: AFNI_OLD_SHORT_THRESH\n" ,
2323 "-------------------------------\n" ,
2324 "When thresholding a dataset with a sub-brick that is stored as shorts\n" ,
2325 "(16 bit integers), the AFNI GUI uses floats, but the 3dmerge and\n" ,
2326 "Clusterize functions use shorts. The difference is that the\n" ,
2327 "user-supplied threshold in the latter case is rounded to the nearest\n" ,
2328 "short. Thus, a threshold of 2.2 would become 2, and then a value of 2\n" ,
2329 "would pass the 'greater than or equal to threshold' test -- which is\n" ,
2330 "probably not what the user meant. Again, this would happen in 3dmerge\n" ,
2331 "and Clusterize, but NOT in the AFNI GUI without Clusterize. This\n" ,
2332 "inconsistency has been fixed, and both sets of places now threshold\n" ,
2333 "using floats. However, IF you want to stick with the old method for\n" ,
2334 "some grotesquely un-imaginable reason, you need to set this variable\n" ,
2335 "to YES.\n" ,
2336 "\n" ,
2337 "------------------------------\n" ,
2338 "Variable: AFNI_SNAPFILE_PREFIX\n" ,
2339 "------------------------------\n" ,
2340 "Image files saved with the \"snapfile\" (or \"record to file\") by default\n" ,
2341 "have filenames of the form \"S_000001.ppm\". The prefix \"S\" can be\n" ,
2342 "altered by setting this environment variable; for example,\n" ,
2343 " setenv AFNI_SNAPFILE_PREFIX Elvis\n" ,
2344 "will save snapfiles with names like \"Elvis_000666.ppm\". You can view\n" ,
2345 "snapfiles with the \"aiv\" (\"AFNI Image Viewer\") utility, the \"xv\"\n" ,
2346 "program, or many other Unix utilities.\n" ,
2347 "\n" ,
2348 "-------------------------------\n" ,
2349 "Variable: AFNI_STARTUP_WARNINGS\n" ,
2350 "-------------------------------\n" ,
2351 "When the interactive AFNI program starts, it may pop up warnings about\n" ,
2352 "the programming environment for which it was compiled. At this time,\n" ,
2353 "there are two such warning messages possible:\n" ,
2354 " LessTiff: AFNI will work with LessTif, but works better with Motif.\n" ,
2355 " Button-3: On Solaris 2.8, Button-3 popup menus don't work quite\n" ,
2356 " properly.\n" ,
2357 "If you are tired of seeing these messages, set AFNI_STARTUP_WARNINGS\n" ,
2358 "to NO.\n" ,
2359 "\n" ,
2360 "----------------------\n" ,
2361 "Variable: AFNI_1D_TIME\n" ,
2362 "----------------------\n" ,
2363 "If this YES/NO variable is set to YES, then when a multicolumn .1D\n" ,
2364 "file is read in as an AFNI dataset, the column variable is taken to be\n" ,
2365 "time, and a time-dependent dataset is created. The default is to\n" ,
2366 "create a bucket dataset. Note that each row is taken to be a separate\n" ,
2367 "'voxel'.\n" ,
2368 "\n" ,
2369 "-------------------------\n" ,
2370 "Variable: AFNI_1D_TRANOUT\n" ,
2371 "-------------------------\n" ,
2372 "If this variable is set to YES, it affects the way 1D datasets are\n" ,
2373 "written out from 3d* programs that are being used to process 1D files\n" ,
2374 "as AFNI dataset. If this variable is YES, AND if the output dataset\n" ,
2375 "prefix ends in '.1D' or is the string '-' (meaning standard output),\n" ,
2376 "then the output 1D file will be transposed and written so that the\n" ,
2377 "time axis goes down the columns instead of across them. If this\n" ,
2378 "variable is NO, then the standard AFNI 1D-to-3D dataset convention is\n" ,
2379 "followed: each row is a single voxel time series. Example:\n" ,
2380 " 3dDetrend -polort 1 -prefix - 1D:'3 4 5 4 3'\\'\n" ,
2381 "will write to the screen\n" ,
2382 " -0.8\n" ,
2383 " 0.2\n" ,
2384 " 1.2\n" ,
2385 " 0.2\n" ,
2386 " -0.8\n" ,
2387 "if AFNI_1D_TRANOUT is YES, but will write\n" ,
2388 " -0.8 0.2 1.2 0.2 -0.8\n" ,
2389 "to stdout if AFNI_1D_TRANOUT is NO.\n" ,
2390 "\n" ,
2391 "-------------------------\n" ,
2392 "Variable: AFNI_1D_TIME_TR\n" ,
2393 "-------------------------\n" ,
2394 "If this is set, and AFNI_1D_TIME is YES, then this determines the TR\n" ,
2395 "(in seconds) of a .1D file read in as an AFNI dataset.\n" ,
2396 "\n" ,
2397 "---------------------------\n" ,
2398 "Variable: AFNI_1D_ZERO_TEXT\n" ,
2399 "---------------------------\n" ,
2400 "If this is set to 'YES', then non-commented text gets set to 0\n" ,
2401 "instead of causing a read failure. The default setting is 'No'\n" ,
2402 "\n" ,
2403 "------------------------\n" ,
2404 "Variable: AFNI_3D_BINARY\n" ,
2405 "------------------------\n" ,
2406 "If this is set to YES, then .3D files are written by AFNI programs in\n" ,
2407 "binary, rather than the default text mode. Binary files will be more\n" ,
2408 "compact (usually) and faster to read in.\n" ,
2409 "\n" ,
2410 "--------------------------\n" ,
2411 "Variable: AFNI_MAX_OPTMENU (editable)\n" ,
2412 "--------------------------\n" ,
2413 "This variable (default=255) sets the maximum number of entries allowed\n" ,
2414 "in an AFNI \"option menu\" -- these are the buttons that popup a menu\n" ,
2415 "of values from which to choose, and which also let you popup a text\n" ,
2416 "list chooser by right-clicking in the menu's label. (Example: the\n" ,
2417 "sub-brick option menus \"Anat\", \"Func\", \"Thr\" on the \"Define Overlay\"\n" ,
2418 "control panel.)\n" ,
2419 "\n" ,
2420 "Some computer systems may crash when an option menu gets too big.\n" ,
2421 "That's why there is a default limit in AFNI of 255 entries. However,\n" ,
2422 "if you have a bucket dataset with more than 255 sub-bricks, this makes\n" ,
2423 "it impossible to view the later data volumes. If this problem arises,\n" ,
2424 "you can try setting this environment variable to a larger limit (e.g.,\n" ,
2425 "99999 would take care of all currently imaginable cases).\n" ,
2426 "\n" ,
2427 "---------------------------------\n" ,
2428 "Variable: AFNI_VALUE_LABEL_DTABLE\n" ,
2429 "---------------------------------\n" ,
2430 "This variable sets a filename that holds a default value-label table\n" ,
2431 "for the Draw Dataset plugin. A sample file is shown below:\n" ,
2432 "\n" ,
2433 " <VALUE_LABEL_DTABLE\n" ,
2434 " ni_type=\"2*String\"\n" ,
2435 " ni_dimen=\"3\" >\n" ,
2436 " \"1\" \"elvis\"\n" ,
2437 " \"2\" \"presley\"\n" ,
2438 " \"3\" \"memphis\"\n" ,
2439 " </VALUE_LABEL_DTABLE>\n" ,
2440 "\n" ,
2441 "The 'ni_dimen' attribute is the number of value-label pairs; in the\n" ,
2442 " above example it is 3.\n" ,
2443 "Each value-label pair is shown on a separate line. The values and\n" ,
2444 " labels are strings, enclosed in quote characters. There should be\n" ,
2445 " exactly as many value-label pairs as specified in 'ni_dimen'.\n" ,
2446 "If you really want to put a double quote character \" in a label,\n" ,
2447 " you can enclose the label in single forward quotes ' instead.\n" ,
2448 "When you 'Save' a drawn dataset from the Draw Dataset plugin, the\n" ,
2449 " .HEAD file attribute VALUE_LABEL_DTABLE will contain a table in\n" ,
2450 " exactly this XML-based format.\n" ,
2451 "\n" ,
2452 "-------------------------------\n" ,
2453 "Variable: AFNI_STROKE_THRESHOLD (editable)\n" ,
2454 "-------------------------------\n" ,
2455 "If you press Button-1 in an image window, and then move it left or\n" ,
2456 "right (\"stroke it\") before releasing the button, the grayscale mapping\n" ,
2457 "changes in the same way as if you pressed the 'c' button up and the\n" ,
2458 "'b' button down. This variable sets the threshold for the stroking\n" ,
2459 "movement size in pixels; a movement of this number of pixels\n" ,
2460 "rightwards corresponds to one press of 'c' up and 'b' down, while a\n" ,
2461 "leftwards movement is like one press of 'c' down and 'b' up. Larger\n" ,
2462 "movements make larger adjustments.\n" ,
2463 "\n" ,
2464 "A larger threshold makes the stroking less sensitive; a smaller\n" ,
2465 "threshold makes it more sensitive. The value you choose will depend\n" ,
2466 "on your personal taste. The default is 32 pixels, which is the flavor\n" ,
2467 "I prefer. If you set this variable to 0, then the stroking function\n" ,
2468 "is disabled.\n" ,
2469 "\n" ,
2470 "-------------------------------\n" ,
2471 "Variable: AFNI_STROKE_AUTOPLOT (editable)\n" ,
2472 "-------------------------------\n" ,
2473 "If this variable is set to YES, then the graymap-versus-data value\n" ,
2474 "plot (manually controlled by \"Display Graymap Plot\") is automatically\n" ,
2475 "popped up when the grayscale mapping is altered by using the stroking\n" ,
2476 "feature described above. When the stroke is finished, the plot will\n" ,
2477 "pop down. N.B.: when the 'Draw Dataset' plugin is active, this option\n" ,
2478 "is disabled temporarily.\n" ,
2479 "\n" ,
2480 "-----------------------------\n" ,
2481 "Variable: AFNI_IMAGE_MINTOMAX (editable)\n" ,
2482 "-----------------------------\n" ,
2483 "If this variable is set to YES, then image viewer windows will be set\n" ,
2484 "to the \"Min-to-Max\" state rather than the default \"2%-to-98%\" state\n" ,
2485 "when they are opened. If you set this in the \"Edit Environment\"\n" ,
2486 "control, it only affects image viewer windows opened after that point.\n" ,
2487 "\n" ,
2488 "----------------------------\n" ,
2489 "Variable: AFNI_IMAGE_CLIPPED (editable)\n" ,
2490 "----------------------------\n" ,
2491 "If this variable is set to YES, then image viewer windows will be set\n" ,
2492 "to the \"Clipped\" state rather than the default \"2%-to-98%\" state\n" ,
2493 "when they are opened. If you set this in the \"Edit Environment\"\n" ,
2494 "control, it only affects image viewer windows opened after that point.\n" ,
2495 "\n" ,
2496 "----------------------------\n" ,
2497 "Variable: AFNI_IMAGE_CLIPBOT (editable)\n" ,
2498 "----------------------------\n" ,
2499 "In the \"Clipped\" mode, the top level of the grayscale image is\n" ,
2500 "computed as 3.11 times the 'cliplevel' as computed by the 3dClipLevel\n" ,
2501 "algorithm. The bottom level is then a fraction of this top level --\n" ,
2502 "by default, the fraction is 0.25, but you can change this default by\n" ,
2503 "setting this variable to a value between 0.0 and 0.5 (inclusive). You\n" ,
2504 "can also use variable AFNI_IMAGE_CLIPTOP to scale the default top\n" ,
2505 "level -- this variable can take values between 0.6 and 1.9 (inclusive)\n" ,
2506 "-- the default is 1.0.\n" ,
2507 "\n" ,
2508 "--------------------------------\n" ,
2509 "Variable: AFNI_IMAGE_GLOBALRANGE (editable)\n" ,
2510 "--------------------------------\n" ,
2511 "AFNI_IMAGE_GLOBALRANGE can be set to SLICE (default), VOLUME\n" ,
2512 "(SUBBRICK), or DSET. The GUI applies the lookup table to color the\n" ,
2513 "underlay with the range determined from the slice, sub-brick or the\n" ,
2514 "whole multi-sub-brick dataset,respectively, depending on this\n" ,
2515 "variable. Besides the .afnirc file, the GUI allows changes from the\n" ,
2516 "environment plugin menu, the right-click menu on the image viewer\n" ,
2517 "colorbar or by typing Control-m in an image viewer. The Control-m\n" ,
2518 "cycles among the global range types.\n" ,
2519 "\n" ,
2520 "Previous YES/NO definitions for this variable correspond to VOLUME and\n" ,
2521 "SLICE respectively and will continue to work as before. The lower\n" ,
2522 "right corner of the image viewer shows the current range setting:\n" ,
2523 "(2%-98%/Min2Max, Vol, Dset)\n" ,
2524 "\n" ,
2525 "If this variable is set to YES/VOLUME/SUBBRICK, then the image\n" ,
2526 "viewer windows will be set to scale the bottom gray level to the\n" ,
2527 "minimum value in the 3D volume and the top gray level to the maximum\n" ,
2528 "value in the 3D volume. Setting the variable to DSET similarly sets\n" ,
2529 "the minimum and maximum based on the range of the whole dataset.\n" ,
2530 "\n" ,
2531 "This setting overrides the \"Min-to-Max\" and \"2%-to-98%\" settings in\n" ,
2532 "the \"Disp\" control panel. This setting also applies to all image\n" ,
2533 "viewers. If you set this in the \"Edit Environment\" control, it will\n" ,
2534 "apply to all open image viewers immediately, as well as to any image\n" ,
2535 "viewers opened later.\n" ,
2536 " It is important to realize that if you use the 'Display Range'\n" ,
2537 "popup to set the bot-top range for the grayscale, these settings\n" ,
2538 "will override the global range UNTIL you switch datasets or switch\n" ,
2539 "sub-bricks within a dataset. At that point, the global range for\n" ,
2540 "the new volume will be enforced. This change can be confusing.\n" ,
2541 "Therefore, the info label beneath the slider shows the source of\n" ,
2542 "the bot-top grayscale values:\n" ,
2543 " [2%-98%] = from the 2% to 98% points on the slice histogram\n" ,
2544 " [Min2Max] = from the 0% to 100% points on the slice histogram\n" ,
2545 " [Vol] = set from the entire volume min and max values\n" ,
2546 " [Dset] = set from the min and max across all subbricks of a dataset\n" ,
2547 " [User] = set by the user from 'Display Range'\n" ,
2548 " absent = not applicable (e.g., underlay image is RGB)\n" ,
2549 "The popup 'hint' for the grayscale bar shows the current values\n" ,
2550 "of the bot-top range, if you want to know what numbers correspond\n" ,
2551 "to the image at which you are gazing so fondly.\n" ,
2552 " Finally, note that when a montage is built, the number-to-grayscale\n" ,
2553 "algorithm is applied to each slice separately, and then the montage\n" ,
2554 "is assembled. For [2%-98%] and [Min2Max], this fact means that each\n" ,
2555 "slice will (probably) have a separate grayscale conversion range.\n" ,
2556 "\n" ,
2557 "----------------------------\n" ,
2558 "Variable: AFNI_DRAW_UNDOSIZE (editable)\n" ,
2559 "----------------------------\n" ,
2560 "This variable sets the size (in units of Megabytes) of the Undo/Redo\n" ,
2561 "buffer in the Draw Dataset plugin. The default value is 6. If you\n" ,
2562 "are short on memory, you could set this to 1. If you are running out\n" ,
2563 "of undo levels, you could set this to a larger value; however, this\n" ,
2564 "would only be needed if you are drawing huge 3D swaths of data at a\n" ,
2565 "time (e.g., using the 3D sphere option with a large radius).\n" ,
2566 "\n" ,
2567 "----------------------------\n" ,
2568 "Variable: AFNI_DRAW_THRESH\n" ,
2569 "----------------------------\n" ,
2570 "This variable controls the clipping threshold for converting atlas\n" ,
2571 "regions into ROIs in the Draw Dataset plugin. The default value is 49\n" ,
2572 "percent unless set by this variable as a percentage greater than 0.0\n" ,
2573 "and at most 100.0 percent\n" ,
2574 "\n" ,
2575 "---------------------\n" ,
2576 "Variable: AFNI_SPEECH (editable)\n" ,
2577 "---------------------\n" ,
2578 "If this YES/NO variable is set to NO, then the AFNI speech synthesis\n" ,
2579 "is disabled. At the current time (Nov 2003), only the Mac OS X 10.3\n" ,
2580 "version of AFNI uses speech synthesis in any way. And that's just\n" ,
2581 "for fun.\n" ,
2582 "\n" ,
2583 "------------------------------\n" ,
2584 "Variable: AFNI_IMAGE_ZEROCOLOR\n" ,
2585 "------------------------------\n" ,
2586 "This variable, if set to the string name of one of the colors in the\n" ,
2587 "color chooser menus (e.g., \"Black\"), will result in voxels whose value\n" ,
2588 "is 0 being set to this color in the slice viewing windows (except when\n" ,
2589 "viewing RGB images). The main function is to avoid having to use the\n" ,
2590 "\"Choose Zero Color\" menu all the time, especially when you use the\n" ,
2591 "\"Swap\" feature to invert the grayscale map (e.g., to make a T2\n" ,
2592 "weighted image look sort of like a T1 weighted image).\n" ,
2593 "\n" ,
2594 "----------------------------\n" ,
2595 "Variable: AFNI_MPEG_DATASETS\n" ,
2596 "----------------------------\n" ,
2597 "This variable can be used to allow MPEG files to be read in as AFNI\n" ,
2598 "datasets. Such datasets are inherently 3 dimensional. How they will\n" ,
2599 "be organized inside AFNI depends on the setting of this variable. The\n" ,
2600 "options are:\n" ,
2601 " SPACE = the frame sequence number will be the z-axis\n" ,
2602 " TIME = the frame sequence number will be the time axis\n" ,
2603 " NO = MPEG files won't be read as AFNI datasets\n" ,
2604 " (they can still be read as images into to3d, aiv, etc.)\n" ,
2605 "If this variable is NOT set to anything, then it is the same as NO.\n" ,
2606 "\n" ,
2607 "MPEG filenames input to AFNI programs (as sources of images or as\n" ,
2608 "datasets) must end in \".mpg\", \".MPG\", \".mpeg\", or \".MPEG\". MPEG\n" ,
2609 "datasets will be read so that the individal images are displayed in an\n" ,
2610 "Axial image window.\n" ,
2611 "\n" ,
2612 "Note that decoding a long .mpg file that happens to be in your\n" ,
2613 "directory can slow down the AFNI startup considerably!\n" ,
2614 "\n" ,
2615 "---------------------------\n" ,
2616 "Variable: AFNI_MPEG_GRAYIZE\n" ,
2617 "---------------------------\n" ,
2618 "If this YES/NO variable is set to YES, then MPEG files read into AFNI,\n" ,
2619 "to3d, or aiv will be converted to grayscale, even if the images in\n" ,
2620 "the movie are in color.\n" ,
2621 "\n" ,
2622 "--------------------------\n" ,
2623 "Variable: AFNI_VIDEO_DELAY (editable)\n" ,
2624 "--------------------------\n" ,
2625 "This is the number of milliseconds the AFNI waits between drawing new\n" ,
2626 "images when the 'V' or 'v' keys are pressed in an image (or graph)\n" ,
2627 "window. The default value is 1, which is faster than video can be\n" ,
2628 "displayed anyway. Set this to a larger value (e.g, 100) to slow down\n" ,
2629 "the image redraw rate.\n" ,
2630 "\n" ,
2631 "----------------------------\n" ,
2632 "Variable: AFNI_IMAGE_ENTROPY (editable)\n" ,
2633 "----------------------------\n" ,
2634 "If this numeric variable is set, this is the entropy of an image below\n" ,
2635 "which the 2%-98% image scaling will be disabled, and min-to-max will\n" ,
2636 "be used instead. The units are bits/byte; a useful threshold seems to\n" ,
2637 "be in the range (0.2,0.5). For images that only have a few values\n" ,
2638 "different from 0, the 2%-98% scaling can produce weird artifacts. Such\n" ,
2639 "images will also have a very low entropy. Since this variable can be\n" ,
2640 "changed interactively from the Edit Environment controls, you can play\n" ,
2641 "with it to see how it affects your images.\n" ,
2642 "\n" ,
2643 "----------------------------\n" ,
2644 "Variable: AFNI_LOGO16 (etc.)\n" ,
2645 "----------------------------\n" ,
2646 "If this variable is set to YES, then the 'AFNI' background logo used in\n" ,
2647 "the controller and image windows will be enabled. By default, it is off.\n" ,
2648 "You can control the colors of this logo by the following variables:\n" ,
2649 " AFNI_LOGO16_FOREGROUND_x\n" ,
2650 " AFNI_LOGO16_BACKGROUND_x\n" ,
2651 "where 'x' is 'A', 'B', 'C', etc., for the various controller labels.\n" ,
2652 "If AFNI_LOGO16_BACKGROUND_x isn't set, then AFNI_LOGO16_BACKGROUND\n" ,
2653 "(with no suffix) is checked as an alternate. The values of these\n" ,
2654 "variables should be the names of one of the labels on the color chooser\n" ,
2655 "menus (e.g., the \"Xhairs Color\" menu). You can use these variables to\n" ,
2656 "make the windows for the various controllers somewhat distinct in\n" ,
2657 "appearance. If these color variables are not set at all, then AFNI\n" ,
2658 "uses some colors of my choosing for this purpose.\n" ,
2659 "\n" ,
2660 "----------------------------------\n" ,
2661 "Variable: AFNI_COLORIZE_CONTROLLER\n" ,
2662 "----------------------------------\n" ,
2663 "If this variable is set to YES, then the background of the AFNI\n" ,
2664 "controllers and image viewers will be colorized. The default state is\n" ,
2665 "that they are not colorized.\n" ,
2666 "\n" ,
2667 "--------------------------\n" ,
2668 "Variable: AFNI_THRESH_LOCK (editable)\n" ,
2669 "--------------------------\n" ,
2670 "This variable can be used to lock the Define Overlay threshold sliders\n" ,
2671 "together. There are three possibilities:\n" ,
2672 " NO (the default) => each controller's slider is independent\n" ,
2673 " VALUE => the numerical value on each slider will be the same\n" ,
2674 " P-VALUE => the p-value for each slider will be the same\n" ,
2675 "This locking only applies to AFNI controllers that are Lock-ed together\n" ,
2676 "(cf. AFNI_ALWAYS_LOCK and the Define Datamode->Lock menu). If p-values\n" ,
2677 "are locked, this lock will also only apply to controllers whose current\n" ,
2678 "Threshold sub-brick has a known statistical distribution.\n" ,
2679 "\n" ,
2680 "When you drag a locked threshold slider, the other one will only change\n" ,
2681 "when you release the mouse button -- they won't slide in tandem, but will\n" ,
2682 "just jump to the final value.\n" ,
2683 "\n" ,
2684 "------------------------\n" ,
2685 "Variable: AFNI_PBAR_LOCK (editable)\n" ,
2686 "------------------------\n" ,
2687 "If this variable is set to YES, then the Define Overlay color bars\n" ,
2688 "(the \"pbars\") of AFNI controllers that are Lock-ed together will be\n" ,
2689 "coordinated. Changes to one locked pbar will be reflected in the\n" ,
2690 "others immediately.\n" ,
2691 "\n" ,
2692 "------------------------\n" ,
2693 "Variable: AFNI_PBAR_AUTO (or AFNI_CMAP_AUTO)\n" ,
2694 "------------------------\n" ,
2695 "If this variable is set to NO, then the automatic color bar switching\n" ,
2696 "(that was introduced by Ziad Saad) will be turned off.\n" ,
2697 "\n" ,
2698 "-------------------------\n" ,
2699 "Variable: AFNI_PBAR_THREE\n" ,
2700 "-------------------------\n" ,
2701 "If this variable is set to YES, then the 'continuous' colorscale color\n" ,
2702 "bar in the AFNI GUI will have 3 panes rather than 1. The middle pane\n" ,
2703 "will have the continuously variable colorscale loaded. The upper and\n" ,
2704 "lower panes will have the upper and lower colors loaded, OR they can\n" ,
2705 "be turned off. The sashes that controls the position and size of the\n" ,
2706 "middle pane can be moved to separately set the top and bottom of the\n" ,
2707 "color-ization scale (rather than make bottom = -top or bottom = 0, as\n" ,
2708 "with the 1 pane color bar).\n" ,
2709 "\n" ,
2710 "------------------------\n" ,
2711 "Variable: AFNI_PBAR_TICK (editable)\n" ,
2712 "------------------------\n" ,
2713 "If this variable is set to NO, then the tick marks in the continuous\n" ,
2714 "colorscale bar in the AFNI GUI will not have tick marks added on the\n" ,
2715 "left and right edges. You can also set the number of tick marks this\n" ,
2716 "way, if you don't want the default number (9). The maximum number\n" ,
2717 "of tick marks allowed is 63, which should be enough.\n" ,
2718 "* If this variable is NOT set to NO (or 0), then 9 tick marks will\n" ,
2719 " be drawn in the image window intensity bar as well (dividing it\n" ,
2720 " into 10 intervals). For this bar, the number of tick marks is\n" ,
2721 " fixed: it is either 0 or 9.\n" ,
2722 "\n" ,
2723 "-----------------------------\n" ,
2724 "Variable: AFNI_PBAR_FULLRANGE [03 Jun 2014]\n" ,
2725 "-----------------------------\n" ,
2726 "If this variable is set to YES, then the color pbar in Define Overlay\n" ,
2727 "will reflect the range set by the user for the colorization process.\n" ,
2728 "At some point, this feature will become the default, and then you'll\n" ,
2729 "have to set this variable to NO to get the old behavior -- where the\n" ,
2730 "range set by the user is shown only at the bottom right of the Define\n" ,
2731 "Overlay panel, and it then multiplies the independently set top value\n" ,
2732 "of the pbar to get the colorization scale. In the new method, the top\n" ,
2733 "value of the pbar cannot be set by the user independently of the range\n" ,
2734 "(or autorange) parameter. The intention of this change is to make the\n" ,
2735 "number -> colors process somewhat more blatant. This variable's value\n" ,
2736 "must be set at startup (e.g., in .afnirc), and changing it later will\n" ,
2737 "have no effect. Also note that if this variable is YES, then setting\n" ,
2738 "AFNI_PBAR_LOCK to YES will imply AFNI_RANGE_LOCK is YES as well.\n" ,
2739 "\n" ,
2740 "-------------------------\n" ,
2741 "Variable: AFNI_RANGE_LOCK (editable)\n" ,
2742 "-------------------------\n" ,
2743 "If this variable is set to YES, then the OLay range values of\n" ,
2744 "different AFNI controllers that are Lock-ed together will be\n" ,
2745 "coordinated. Changes in one controller will be reflected in\n" ,
2746 "the others immediately.\n" ,
2747 "\n" ,
2748 "---------------------------\n" ,
2749 "Variable: AFNI_OPACITY_LOCK\n" ,
2750 "---------------------------\n" ,
2751 "This variable controls if changing the overlay opacity in one\n" ,
2752 "image viewer window (the 1-9 arrows at the viewer right edge)\n" ,
2753 "changes the opacity in all viewer windows. The default value\n" ,
2754 "is YES, but you can set this to NO if you don't like it.\n" ,
2755 "\n" ,
2756 "----------------------------\n" ,
2757 "Variable: AFNI_IMAGE_ZOOM_NN (editable)\n" ,
2758 "----------------------------\n" ,
2759 "If this variable is set to YES, then image viewer windows will use\n" ,
2760 "nearest neighbor interpolation for zooming. The default is linear\n" ,
2761 "interpolation, which produces smoother-looking images. However, some\n" ,
2762 "people want to see the actual data values represented in the window,\n" ,
2763 "not some fancy-schmancy interpolated values designed to look good but\n" ,
2764 "in fact making a mockery of a sham of a mockery of a travesty of two\n" ,
2765 "mockeries of a sham of reality.\n" ,
2766 "\n" ,
2767 "------------------------------\n" ,
2768 "Variable: AFNI_DISABLE_CURSORS\n" ,
2769 "------------------------------\n" ,
2770 "If this variable is set to YES, then AFNI will not try to change the\n" ,
2771 "X11 cursor shape. This feature is available because it seems that\n" ,
2772 "sometimes particular X11 installations choices of cursor and AFNI's\n" ,
2773 "choices don't work together well. If you have unpleasant cursors in\n" ,
2774 "AFNI (e.g., an X), try setting this variable to YES.\n" ,
2775 "\n" ,
2776 "-----------------------------\n" ,
2777 "Variable: AFNI_SLAVE_FUNCTIME (editable)\n" ,
2778 "-----------------------------\n" ,
2779 "When the underlay and overlay datasets both are time-dependent,\n" ,
2780 "switching the time index will change both the underlay and overlay\n" ,
2781 "sub-bricks. If you want the time index control to change ONLY the\n" ,
2782 "underlay sub-brick, then set this variable to NO.\n" ,
2783 "\n" ,
2784 "----------------------------\n" ,
2785 "Variable: AFNI_SLAVE_THROLAY\n" ,
2786 "----------------------------\n" ,
2787 "This variable allows you to control the INITIAL setting of the widgets\n" ,
2788 "that slave (or not) the threshold index to the overlay index. (These\n" ,
2789 "widgets are on the 'Index' right-click popup chooser and on the\n" ,
2790 "threshold slider right-click popup menu.) The values you can set for\n" ,
2791 "this variable, and their effects, are listed below (not case\n" ,
2792 "sensitive):\n" ,
2793 " 'OLay' *or* '==' *or* '0' ==> threshold index = overlay index\n" ,
2794 " 'OLay+1' *or* '+1' *or* '1' ==> threshold index = overlay index + 1\n" ,
2795 " ANYTHING ELSE ==> threshold index is free and wild\n" ,
2796 "This variable replaces the 2 variables listed below. Again, this only\n" ,
2797 "controls the INITIAL setting of the widgets -- you can change them in\n" ,
2798 "the AFNI GUI later at any time. Setting this variable after AFNI\n" ,
2799 "starts (e.g., from plugout_drive) will have little discernable effect.\n" ,
2800 "\n" ,
2801 "-------------------------\n" ,
2802 "Variable: AFNI_FUNC_ALPHA\n" ,
2803 "-------------------------\n" ,
2804 "Setting this string to YES will turn on Alpha fading of the functional\n" ,
2805 "overlay -- it is the same as setting the 'A' button on top of the\n" ,
2806 "threshold slider to the on stated.\n" ,
2807 "\n" ,
2808 "If Alpha is turned on, then the opacity of the overlay ranges from 1\n" ,
2809 "for above-threshold pixels down to 0. Note that the alpha (opacity)\n" ,
2810 "level at the pixel-wise level also is scaled by the global\n" ,
2811 "opacity '1-9' control on the right side of the image viewer,\n" ,
2812 "where '9' means that above-threshold pixels will be 100% opaque, and\n" ,
2813 "'6' means they will be 6/9=67% opaque -- and lower opacity pixels will\n" ,
2814 "be have their opacity scaled down by the same factor.\n" ,
2815 "\n" ,
2816 "The variable-opacity overlay usually looks better (less blocky) if you\n" ,
2817 "open 'Define Datamode' and set the resampling modes for the OLay and\n" ,
2818 "Stat to 'Li' (linear) rather than the default 'NN' (you can also do\n" ,
2819 "this via variables AFNI_resam_func and AFNI_resam_thr).\n" ,
2820 "\n" ,
2821 "Please note that the Alpha features described above only apply if the\n" ,
2822 "color scale is in the 'continuous' mode ('**'), not in the discrete\n" ,
2823 "panes mode. Sorry about this, but that's the situation for the nonce.\n" ,
2824 "\n" ,
2825 "-------------------------\n" ,
2826 "Variable: AFNI_FUNC_BOXED\n" ,
2827 "-------------------------\n" ,
2828 "Setting this string to YES will turn on outlining/boxing for the above\n" ,
2829 "threshold pixels in a functional image overlay. The outline is done over\n" ,
2830 "the pixels immediately OUTSIDE the above-threshold regions, in the\n" ,
2831 "overlay image as interpolated to the underlay resolution. If the\n" ,
2832 "underlay is on a coarse matrix (e.g., native EPI), these outlines\n" ,
2833 "will look blocky -- you can alter the underlay display grid dimension\n" ,
2834 "in 'Define Datamode' using the control 'Warp ULay on Demand', and then\n" ,
2835 "alter the way the datasets are interpolated to the underlay grid using\n" ,
2836 "'Resam Mode' menus. In this way, you can make blocky-looking EPI results\n" ,
2837 "fictionally look as if they are beautiful and high resolution.\n" ,
2838 "\n" ,
2839 "-------------------------------\n" ,
2840 "Variable: AFNI_FUNC_BOXED_COLOR (editable)\n" ,
2841 "-------------------------------\n" ,
2842 "Defines the color used for the boxed outline of above threshold\n" ,
2843 "regions, when Boxed ('B' button above threshold slided) is turned on.\n" ,
2844 "See AFNI_FUNC_BOXED for more information. The default color is\n" ,
2845 "black, which a few people find harsh. This variable replaces the former\n" ,
2846 "AFNI_EDGIZE_COLOR, which now has no effect. Colors can be set via X11\n" ,
2847 "names (e.g., \"yellow\", \"hotpink\", \"#1188ff\").\n" ,
2848 "\n" ,
2849 "----------------------------\n" ,
2850 "Variable: AFNI_SLAVE_THRTIME *** THIS VARIABLE IS NO LONGER USED ***\n" ,
2851 "----------------------------\n" ,
2852 "When the underlay and overlay datasets both are time-dependent,\n" ,
2853 "switching the time index will change both the underlay and overlay\n" ,
2854 "sub-bricks, but NOT the threshold sub-brick. If you want the time\n" ,
2855 "index control to change the threshold sub-brick, then set this\n" ,
2856 "variable to YES.\n" ,
2857 "\n" ,
2858 "--------------------------------\n" ,
2859 "Variable: AFNI_SLAVE_BUCKETS_TOO *** THIS VARIABLE IS NO LONGER USED ***\n" ,
2860 "--------------------------------\n" ,
2861 "Set this to YES if you want to make changing the time index in the\n" ,
2862 "underlay dataset change the sub-brick index in the overlay dataset\n" ,
2863 "even when the overlay is a 'bucket' dataset without a time axis.\n" ,
2864 "\n" ,
2865 "----------------------------\n" ,
2866 "Variable: AFNI_CLICK_MESSAGE\n" ,
2867 "----------------------------\n" ,
2868 "If this veriable is set to NO, then the string\n" ,
2869 " [---------------]\n" ,
2870 " [ Click in Text ]\n" ,
2871 " [ to Pop Down!! ]\n" ,
2872 "will NOT be appended to the very first popup message window that AFNI\n" ,
2873 "creates. This message was added because some people do not realize\n" ,
2874 "that the way to get rid of these popups (before they vanish on their\n" ,
2875 "own after 30 seconds) is to click in them. You know who you are.\n" ,
2876 "However, if you are advanced enough to read this file, then you\n" ,
2877 "probably aren't one of THEM.\n" ,
2878 "\n" ,
2879 "-----------------------------\n" ,
2880 "Variable: AFNI_X11_REDECORATE (editable)\n" ,
2881 "-----------------------------\n" ,
2882 "By default, AFNI tries to change some of the \"decorations\" (control\n" ,
2883 "buttons) on some of the windows it creates (e.g., removing resize\n" ,
2884 "handles). If you don't want this to happen, set this variable to NO.\n" ,
2885 "This variable only has an effect on windows created AFTER it is set,\n" ,
2886 "so if you change this interactively in the Edit Environment plugin, it\n" ,
2887 "will not affect existing windows. Normally, you would want to set\n" ,
2888 "this in your .afnirc file.\n" ,
2889 "\n" ,
2890 "-------------------------------\n" ,
2891 "Variable: AFNI_IMAGE_SAVESQUARE\n" ,
2892 "-------------------------------\n" ,
2893 "YES/NO: Forces images (from the image view \"Save\" button) to be saved\n" ,
2894 "with square pixels, even if they are stored with nonsquare pixels.\n" ,
2895 "\n" ,
2896 "-------------------------------\n" ,
2897 "Variable: AFNI_BUCKET_LABELSIZE\n" ,
2898 "-------------------------------\n" ,
2899 "THIS VARIABLE HAS BEEN REMOVED FROM AFNI.\n" ,
2900 "\n" ,
2901 "Formerly, it was used to set the width of the \"ULay\", \"OLay\", and\n" ,
2902 "\"Thr\" menu choosers on the \"Define Overlay\" control panel. As of 03\n" ,
2903 "May 2005, AFNI now calculates the default width based on the longest\n" ,
2904 "sub-brick label input for each dataset.\n" ,
2905 "\n" ,
2906 "-------------------------\n" ,
2907 "Variable: AFNI_MAX_1DSIZE\n" ,
2908 "-------------------------\n" ,
2909 "Sets the maximum size (in bytes) of each 1D file that will be\n" ,
2910 "automatically loaded when AFNI starts. The default is 123 Kbytes.\n" ,
2911 "The intention is to prevent loading of very large files that are not\n" ,
2912 "intended to be used for graphing/FIMming purposes. If you set this to\n" ,
2913 "0, you get the default size. If you set this to 1, no 1D files will\n" ,
2914 "be read at the AFNI GUI startup.\n" ,
2915 "\n" ,
2916 "---------------------------\n" ,
2917 "Variable: AFNI_TITLE_LABEL2 (editable)\n" ,
2918 "---------------------------\n" ,
2919 "If this YES/NO variable is YES, then the AFNI window titlebars will\n" ,
2920 "show the 'label2' field from the AFNI dataset .HEAD file, rather than\n" ,
2921 "the dataset filename. If the label2 field is set to a nontrivial\n" ,
2922 "value, that is. You can set the label2 field with the 3drefit\n" ,
2923 "command.\n" ,
2924 "\n" ,
2925 "----------------------------------\n" ,
2926 "Variable: AFNI_SKIP_ONETIME_POPUPS\n" ,
2927 "----------------------------------\n" ,
2928 "Some AFNI popup messages are 'onetime' -- that is, they show up only\n" ,
2929 "once for each user. This capability is there to announce changes that\n" ,
2930 "should be noticed. Each onetime message is logged into a file named\n" ,
2931 ".afni.recordings in the user's home directory, and if a record of such\n" ,
2932 "a message is found therein, it will not be shown again. To skip\n" ,
2933 "showing these messages at all, even once, set this variable to YES.\n" ,
2934 "\n" ,
2935 "-------------------------------\n" ,
2936 "Variable: AFNI_SHOW_SURF_POPUPS\n" ,
2937 "-------------------------------\n" ,
2938 "If this YES/NO variable is set to YES, then when AFNI receives surface\n" ,
2939 "nodes, triangles or normals from suma, a popup message will be\n" ,
2940 "displayed. Otherwise, the message will be send to stderr (on the\n" ,
2941 "terminal window).\n" ,
2942 "\n" ,
2943 "-------------------------------\n" ,
2944 "Variable: AFNI_KILL_SURF_POPUPS\n" ,
2945 "-------------------------------\n" ,
2946 "If this YES/NO variable is set to YES, then when AFNI receives surface\n" ,
2947 "nodes, triangles or normals from suma, no messages will be displayed,\n" ,
2948 "either in a popup or stderr. Note that if errors occur, popups will\n" ,
2949 "still be shown; this just turns off the normal information messages.\n" ,
2950 "N.B.: If AFNI_SHOW_SURF_POPUPS is YES, then it wins over\n" ,
2951 " AFNI_KILL_SURF_POPUPS being YES. If neither is set, then\n" ,
2952 " messages are displayed to stderr.\n" ,
2953 "\n" ,
2954 "-----------------------------\n" ,
2955 "Variable: AFNI_EDGIZE_OVERLAY ** This variable is no longer used **\n" ,
2956 "-----------------------------\n" ,
2957 "It has been replaced by AFNI_FUNC_BOXED.\n" ,
2958 "\n" ,
2959 "--------------------------\n" ,
2960 "Variable: AFNI_NIFTI_DEBUG (editable)\n" ,
2961 "--------------------------\n" ,
2962 "This integral variable determines the debug level used by the nifti_io\n" ,
2963 "library functions. If set to 0, only errors are reported by the\n" ,
2964 "library. The maximum debug level used is currently 4. Note that if\n" ,
2965 "this is changed from within AFNI, a 'Rescan: This' operation should\n" ,
2966 "probably be performed, which will force a re-reading of the datasets\n" ,
2967 "and so force an elicitation of the NIfTI debug messages (for .nii\n" ,
2968 "files, that is).\n" ,
2969 "\n" ,
2970 "------------------------------\n" ,
2971 "Variable: AFNI_NIFTI_TYPE_WARN\n" ,
2972 "------------------------------\n" ,
2973 "AFNI converts 'byte' NIFTI data types to 'short', and 'int' to\n" ,
2974 "'float'. Programs that do so will issue a warning each time such a\n" ,
2975 "conversion is carried out. When this variable is set to NO, as it is\n" ,
2976 "now by default, each program would issue just one warning at the first\n" ,
2977 "occurrence of a type conversion. Set this variable to YES if you want\n" ,
2978 "to see all conversion warnings.\n" ,
2979 "\n" ,
2980 "--------------------------\n" ,
2981 "Variable: AFNI_DEBUG_PLUG_VOL2SURF\n" ,
2982 "--------------------------\n" ,
2983 "Use this interger variable to initialize the debug level in\n" ,
2984 "plug_vol2surf. The current set of acceptable values is {0..5}.\n" ,
2985 "\n" ,
2986 "--------------------------\n" ,
2987 "Variable: AFNI_NIFTI_NOEXT\n" ,
2988 "--------------------------\n" ,
2989 "When writing a '.nii' (or '.nii.gz') file from an AFNI program,\n" ,
2990 "normally a NIfTI-1.1 extension field with some extra AFNI header\n" ,
2991 "information is written into the output file. If you set this variable\n" ,
2992 "to YES, then this extension is not written, which will make the output\n" ,
2993 "be a 'pure' NIfTI-1.1 file. Only use this if absolutely necessary.\n" ,
2994 "You can also use the 'nifti_tool' program to strip extension data from\n" ,
2995 "a NIfTI-1.1 dataset file.\n" ,
2996 "\n" ,
2997 "---------------------------\n" ,
2998 "Variable: AFNI_OVERLAY_ZERO (editable)\n" ,
2999 "---------------------------\n" ,
3000 "If set to YES, this variable indicates that voxels in the overlay\n" ,
3001 "dataset that have the numerical value of 0 will get colored when the\n" ,
3002 "Inten color scale on the Define Datamode panel indicates that 0 has a\n" ,
3003 "color that isn't \"none\". The default way that AFNI works is NOT to\n" ,
3004 "colorize voxels that are 0, even if they should otherwise get a color.\n" ,
3005 "\n" ,
3006 "---------------------------\n" ,
3007 "Variable: NIML_TRUSTHOST_xx\n" ,
3008 "---------------------------\n" ,
3009 "These environment variables ('xx' = '01', '02', ..., '99') set the\n" ,
3010 "names and/or addresses of external computer hosts to trust with NIML\n" ,
3011 "TCP/IP connections, which are how AFNI and SUMA communicate. Should\n" ,
3012 "only be necessary to use these if you are using AFNI and SUMA on\n" ,
3013 "different machines. Connections from machines not on the trusted list\n" ,
3014 "will be rejected, for the sake of security. The 'localhost' or\n" ,
3015 "127.0.0.1 address and local class B network 192.168.0.* addresses are\n" ,
3016 "always trusted.\n" ,
3017 "\n" ,
3018 "---------------------------\n" ,
3019 "Variable: AFNI_DONT_LOGFILE\n" ,
3020 "---------------------------\n" ,
3021 "Most AFNI programs write a copy of their command line to a file in\n" ,
3022 "your home directory named \".afni.log\". If you do NOT want the log to\n" ,
3023 "be kept, set this environment variable to YES. The purpose of the log\n" ,
3024 "is for you to be able to look back and see what AFNI commands you used\n" ,
3025 "in the past. However, if you are doing a vast number of commands\n" ,
3026 "inside a script, the log file might eventually become gigantic (the\n" ,
3027 "Kevin Murphy effect).\n" ,
3028 "\n" ,
3029 "-------------------------------\n" ,
3030 "Variable: AFNI_ECHO_COMMANDLINE\n" ,
3031 "-------------------------------\n" ,
3032 "If this is YES, then the command line logger will also echo the\n" ,
3033 "command line of each AFNI program to stderr, as it starts up. This\n" ,
3034 "feature is explicitly for Daniel Handwerker, and may well eventually\n" ,
3035 "be considered his ultimate claim to fame in the Macrocosmic All.\n" ,
3036 "\n" ,
3037 "-------------------------\n" ,
3038 "Variable: AFNI_WRITE_NIML\n" ,
3039 "-------------------------\n" ,
3040 "If this variable is set to YES, then AFNI .HEAD files will be written\n" ,
3041 "in the new NIML (XML subset) format, rather than the 'classic' format.\n" ,
3042 "The volumetric image data is still in the pure binary .BRIK file, not\n" ,
3043 "XML-ified in any way. At present (Jun 2005) this format is\n" ,
3044 "experimental, but will someday soon become the default.\n" ,
3045 "\n" ,
3046 "---------------------------------\n" ,
3047 "Variable: AFNI_ALLOW_MILLISECONDS\n" ,
3048 "---------------------------------\n" ,
3049 "The TR value (time step) in 3D+time datasets created with to3d can be\n" ,
3050 "flagged as being in units of milliseconds (ms) or seconds (s). This\n" ,
3051 "situation is unfortunate, as some AFNI programs assume that the units\n" ,
3052 "are always s, which doesn't work well when the TR is actually in ms.\n" ,
3053 "On 15 Aug 2005, AFNI dataset I/O was modified to only write out TR in\n" ,
3054 "s units, and to convert ms units to s units on input. If you\n" ,
3055 "absolutely need to store TR in ms, then you must set this environment\n" ,
3056 "variable to YES. I strongly recommend against such a setting, but\n" ,
3057 "recall the AFNI philosophy: \"provide mechanism, not policy\" -- in\n" ,
3058 "other words, if you want to shoot yourself in the foot, go right\n" ,
3059 "ahead. This variable is just the safety on the revolver.\n" ,
3060 "\n" ,
3061 "--------------------------\n" ,
3062 "Variable: AFNI_AUTO_RESCAN\n" ,
3063 "--------------------------\n" ,
3064 "If this YES/NO variable is set to YES, then the interactive AFNI\n" ,
3065 "program will rescan all session directories every 15 seconds for new\n" ,
3066 "datasets. Basically, this is just a way for you to avoid pressing the\n" ,
3067 "'Rescan' buttons. Note that if AFNI_AUTO_RESCAN is enabled, then the\n" ,
3068 "rescan method will be 'Add', not 'Replace', no matter what you set\n" ,
3069 "variable AFNI_RESCAN_METHOD to.\n" ,
3070 "\n" ,
3071 "-------------------------------\n" ,
3072 "Variable: AFNI_RESCAN_AT_SWITCH\n" ,
3073 "-------------------------------\n" ,
3074 "If this YES/NO variable is set to YES, then the interactive AFNI\n" ,
3075 "program will rescan all session directories everytime you click on\n" ,
3076 "either of the 'Overlay' or 'Underlay' buttons. Basically, this is just\n" ,
3077 "another way for you to avoid pressing the 'Rescan' buttons. (Unlike\n" ,
3078 "with AFNI_AUTO_RESCAN, the AFNI_RESCAN_METHOD settings are respected.)\n" ,
3079 "\n" ,
3080 "---------------------------\n" ,
3081 "Variable: AFNI_ALL_DATASETS [02 Jun 2016]\n" ,
3082 "---------------------------\n" ,
3083 "By default, AFNI creates a session (internal to the program) that\n" ,
3084 "contains all the input datasets -- if you input more than one session\n" ,
3085 "directory, that is. This session is called 'All_Datasets' in the\n" ,
3086 "'DataDir Switch' popup chooser, and should be the last session listed\n" ,
3087 "in that list. If you do NOT want this session created, then set\n" ,
3088 "AFNI_ALL_DATASETS to NO.\n" ,
3089 "\n" ,
3090 "--------------------------\n" ,
3091 "Variable: AFNI_WEB_BROWSER\n" ,
3092 "--------------------------\n" ,
3093 "This variable should be set to the full executable path to a Web\n" ,
3094 "browser, as in\n" ,
3095 " setenv AFNI_WEB_BROWSER /usr/bin/mozilla\n" ,
3096 "If it is not set, AFNI will scan your path to see if it can find a\n" ,
3097 "browser, looking for \"firefox\", \"mozilla\", \"netscape\", and \"opera\" (in\n" ,
3098 "that order). If a browser is found, or set, then the 'hidden' popup\n" ,
3099 "menu (in the blank square to the right of the 'done' button) will have\n" ,
3100 "a menu item to open it.\n" ,
3101 "\n" ,
3102 "--------------------------\n" ,
3103 "Variable: AFNI_SELENIUM\n" ,
3104 "--------------------------\n" ,
3105 "If this YES/NO variable is set to YES, then the Selenium webdriver\n" ,
3106 "will be used to open a browser window in the places where AFNI uses\n" ,
3107 "webpages (whereami, help,...) The AFNI_WEB_BROWSER should be set to\n" ,
3108 "the browser of choice (Chrome,Firefox,Safari). The default browser\n" ,
3109 "will be chrome if the AFNI_WEB_BROWSER variable is not set. If\n" ,
3110 "AFNI_SELENIUM is not set or set to NO, AFNI will open the standard\n" ,
3111 "browser using a system command. Selenium may be installed with \"pip\n" ,
3112 "install -U selenium\" on a Mac or \"sudo yum install selenium\" on\n" ,
3113 "Linux. If you need to get pip, it is available from\n" ,
3114 "https://pypi.python.org/pypi/pip .\n" ,
3115 "\n" ,
3116 "-----------------------------\n" ,
3117 "Variable: AFNI_WEB_DOWNLOADER\n" ,
3118 "-----------------------------\n" ,
3119 "This variable should be set to the full executable path to a Web\n" ,
3120 "downloader, as in\n" ,
3121 " setenv AFNI_WEB_DOWNLOADER /usr/bin/curl\n" ,
3122 "If it is not set, AFNI will scan your path to see if it can find a\n" ,
3123 "downloader, looking for \"curl\" and \"wget\" (in that order).\n" ,
3124 "\n" ,
3125 "----------------------------\n" ,
3126 "Variable: AFNI_JPEG_COMPRESS\n" ,
3127 "----------------------------\n" ,
3128 "This variable determines the compression quality of JPEG files saved\n" ,
3129 "in the AFNI GUI and 3dDeconvolve. Its value can be set to an integer\n" ,
3130 "from 1 to 100. If not set, the default value is 95%.\n" ,
3131 "\n" ,
3132 "---------------------------\n" ,
3133 "Variable: AFNI_NLFIM_METHOD\n" ,
3134 "---------------------------\n" ,
3135 "Can be used to set the optimization method using in the NLfit plugin\n" ,
3136 "(not in 3dNLfim). The methods available are\n" ,
3137 " SIMPLEX (the default)\n" ,
3138 " POWELL (the NEWUOA method)\n" ,
3139 " BOTH (use both methods, choose the 'best' result)\n" ,
3140 "\n" ,
3141 "----------------------------\n" ,
3142 "Variable: AFNI_OVERLAY_ONTOP\n" ,
3143 "----------------------------\n" ,
3144 "If this variable is set to YES, then the 'Overlay' button will be\n" ,
3145 "above the 'Underlay' button on the AFNI control panel. The default,\n" ,
3146 "from the olden days, is to have the 'Underlay' button above the\n" ,
3147 "'Overlay' button, which some people find confusing.\n" ,
3148 "\n" ,
3149 "-----------------------------\n" ,
3150 "Variable: AFNI_DATASET_BROWSE (editable)\n" ,
3151 "-----------------------------\n" ,
3152 "If this variable is set to YES, then when you 'browse' through a\n" ,
3153 "dataset chooser ('Overlay' or 'Underlay' list) with the mouse or arrow\n" ,
3154 "keys, then as a dataset is selected in the list, AFNI will immediately\n" ,
3155 "switch to viewing that dataset. This can be convenient for scrolling\n" ,
3156 "through datasets, but can also consume memory and CPU time very\n" ,
3157 "quickly.\n" ,
3158 "\n" ,
3159 "------------------------------\n" ,
3160 "Variable: AFNI_DISABLE_TEAROFF\n" ,
3161 "------------------------------\n" ,
3162 "If this variable is set to YES, then the AFNI GUI will not allow popup\n" ,
3163 "or popdown menus to be 'torn off'. The default is to enable tear off\n" ,
3164 "for most menus, but this may cause bad things on some platforms (like\n" ,
3165 "program death).\n" ,
3166 "\n" ,
3167 "-------------------------------\n" ,
3168 "Variable: AFNI_PLUGOUT_TCP_BASE (BETTER USE AFNI_PORT_OFFSET)\n" ,
3169 "-------------------------------\n" ,
3170 "This integer will override the base TCP port used by afni to listen for\n" ,
3171 "plugouts. This allows multiple instances of afni on one machine, where\n" ,
3172 "each can listen for plugouts. Valid port numbers are 1024..65535.\n" ,
3173 "\n" ,
3174 "--------------------------\n" ,
3175 "Variable: AFNI_PORT_OFFSET\n" ,
3176 "--------------------------\n" ,
3177 "This integer provides an offset for the range of port numbers used by\n" ,
3178 "AFNI and its ilk. This allows multiple instances of communicating\n" ,
3179 "programs on one machine. Valid port offset numbers are 1024..65000.\n" ,
3180 "See related options -np in afni -help. See also AFNI_PORT_BLOC.\n" ,
3181 "\n" ,
3182 "--------------------------\n" ,
3183 "Variable: AFNI_PORT_BLOC\n" ,
3184 "--------------------------\n" ,
3185 "This integer selects a bloc of port numbers to be used by\n" ,
3186 "AFNI and its ilk. Much like AFNI_PORT_OFFSET, it allows multiple instances\n" ,
3187 "of communicating programs on one machine. However it is easier to use.\n" ,
3188 "Acceptable integer values range from 0 to a couple of thousands.\n" ,
3189 "See related option -npb, -max_port_bloc in afni -help.\n" ,
3190 "This environment variable takes precedence over AFNI_PORT_OFFSET.\n" ,
3191 "\n" ,
3192 "-----------------------------------\n" ,
3193 "Variable: AFNI_IMAGE_TICK_DIV_IN_MM (editable)\n" ,
3194 "-----------------------------------\n" ,
3195 "If this YES/NO variable is set to YES, then the Tick Div. value in an\n" ,
3196 "image window will be interpreted as a separation distance, in mm, as\n" ,
3197 "opposed to the number of tick divisions along each edge. In the YES\n" ,
3198 "case, a larger value would produce fewer ticks, as they would be\n" ,
3199 "farther apart. In the NO case, a larger value will produce more tick\n" ,
3200 "marks. Tick marks are controlled from the Button 3 popup menu\n" ,
3201 "attached to the grayscale intensity bar in an image viewer.\n" ,
3202 "\n" ,
3203 "----------------------------\n" ,
3204 "Variable: AFNI_IMAGRA_CLOSER\n" ,
3205 "----------------------------\n" ,
3206 "If this YES/NO variable is set to YES, then when you click in an\n" ,
3207 "'Image' or 'Graph' button for a viewer window that is already open (so\n" ,
3208 "the button is displayed in inverted colors), then the corresponding\n" ,
3209 "viewer window will close. The default action is to try to raise the\n" ,
3210 "viewer window to the front, but some window managers (I'm looking at\n" ,
3211 "you, FC5) don't allow this action. So this provides a way to kill the\n" ,
3212 "window, at least, if you've lost it in desktop hell somewhere.\n" ,
3213 "\n" ,
3214 "-------------------------\n" ,
3215 "Variable: AFNI_DECONFLICT\n" ,
3216 "-------------------------\n" ,
3217 "When AFNI programs write datasets to disk, they will check whether the\n" ,
3218 "output filename already exists. If it does, the AFNI programs will act\n" ,
3219 "based on the possible values of AFNI_DECONFLICT as follows:\n" ,
3220 " NO/<none> : do not modify the name or overwrite the file, but\n" ,
3221 " inform the user of the conflict, and exit\n" ,
3222 " YES : modify the filename, as stated below\n" ,
3223 " OVERWRITE : do not modify the filename, overwrite the dataset\n" ,
3224 "If AFNI_DECONFLICT is YES, then the filename will be changed to one that\n" ,
3225 "does not conflict with any existing file. For example 'fred+orig' could\n" ,
3226 "be changed to 'fred_AA1+orig'.\n" ,
3227 "\n" ,
3228 "The default behavior is as 'NO', not to deconflict, but to exit.\n" ,
3229 "Some programs supply their own default.\n" ,
3230 "\n" ,
3231 "---------------------------------------\n" ,
3232 "Variable: AFNI_GUI_WRITE_AS_DECONFLICT\n" ,
3233 "---------------------------------------\n" ,
3234 "When you use the 'Write' buttons under 'Define Datamode' Panel, the\n" ,
3235 "default is to overwrite existing datasets. However, if\n" ,
3236 "AFNI_GUI_WRITE_AS_DECONFLICT is set to YES, then the decision follows\n" ,
3237 "the value of AFNI_DECONFLICT\n" ,
3238 "\n" ,
3239 "The default value for this variable is NO, which means interactive\n" ,
3240 "'Write' operates in overwrite mode.\n" ,
3241 "\n" ,
3242 "--------------------------\n" ,
3243 "Variable: AFNI_SEE_OVERLAY\n" ,
3244 "--------------------------\n" ,
3245 "If this variable is set to YES, then the 'See Overlay' button will be\n" ,
3246 "turned on when a new AFNI controller is opened.\n" ,
3247 "\n" ,
3248 "------------------------------\n" ,
3249 "Variable: AFNI_INDEX_SCROLLREV\n" ,
3250 "------------------------------\n" ,
3251 "If this variable is set to YES, then the default direction of image\n" ,
3252 "slice and time index scrolling will be reversed in the image and graph\n" ,
3253 "viewers, respectively.\n" ,
3254 "\n" ,
3255 "-----------------------------\n" ,
3256 "Variable: AFNI_CLUSTER_PREFIX\n" ,
3257 "-----------------------------\n" ,
3258 "This variable sets the prefix for 'Save' timeseries 1D files from the\n" ,
3259 "'Clusterize' report panel. The default string is \"Clust\". The value\n" ,
3260 "of this variable will be loaded into the cluster Rpt window text entry\n" ,
3261 "field, and the prefix can be edited there by the users when it comes\n" ,
3262 "time to save files.\n" ,
3263 "\n" ,
3264 "-----------------------------\n" ,
3265 "Variable: AFNI_CLUSTER_SCROLL\n" ,
3266 "-----------------------------\n" ,
3267 "If this variable is NO, then the 'Clusterize' report will not be given\n" ,
3268 "scrollbars. The default is to give it scroll bars (i.e., YES).\n" ,
3269 "\n" ,
3270 "---------------------------\n" ,
3271 "Variable: AFNI_CLUSTER_EBAR\n" ,
3272 "---------------------------\n" ,
3273 "If this variable is YES, then the Clusterize 'Mean' and 'Medn' Plot\n" ,
3274 "graphs will have error bars plotted.\n" ,
3275 "\n" ,
3276 "-----------------------------\n" ,
3277 "Variable: AFNI_CLUSTER_REPMAX (editable)\n" ,
3278 "-----------------------------\n" ,
3279 "This numeric variable (between 10 and 9999, inclusive) sets the\n" ,
3280 "maximum number of clusters that will be reported in a 'Clusterize'\n" ,
3281 "report panel, if scroll bars are turned off by\n" ,
3282 "AFNI_CLUSTER_SCROLL. The default value is 15. If scroll bars are\n" ,
3283 "turned on, then the maximum number of clusters shown defaults to 999,\n" ,
3284 "but can be increased to 9999 if you are completely mad, or are named\n" ,
3285 "Shruti. If scroll bars are turned off, then you probably don't want\n" ,
3286 "to make this very big, since the report window would become taller\n" ,
3287 "than your monitor, and that would be hard to deal with.\n" ,
3288 "\n" ,
3289 "------------------------------\n" ,
3290 "Variable: AFNI_CLUSTER_WAMIMAX (editable)\n" ,
3291 "------------------------------\n" ,
3292 "This variable should be set to a number indicating the maximum number\n" ,
3293 "of clusters to get a 'whereami' report when the 'WamI' button is\n" ,
3294 "pressed. Since the querying the diverse atlas datasets is slow,\n" ,
3295 "increasing this value much past its default value of 20 is not usually\n" ,
3296 "a good plan.\n" ,
3297 "\n" ,
3298 "-----------------------------\n" ,
3299 "Variable: AFNI_CLUSTERIZE_OLD\n" ,
3300 "-----------------------------\n" ,
3301 "As of Halloween 2018, the 'Clusterize' control panel in the AFNI GUI\n" ,
3302 "uses program 3dClusterize for outputting tables and masks. One good\n" ,
3303 "point of this program is that it can do bi-sided clustering, as the\n" ,
3304 "GUI does. The older program 3dclust cannot do this type of clustering.\n" ,
3305 "However, if for some bizarre deranged maniacal reason (e.g., testing)\n" ,
3306 "you want to use 3dclust for these reporting purposes, then set this\n" ,
3307 "variable to YES. Note that the internal clustering of the AFNI GUI\n" ,
3308 "does not use either program - the external program is used only for\n" ,
3309 "the purpose of mask saving. If you use bi-sided clustering, then\n" ,
3310 "to get the saved mask have the same results as the AFNI GUI, you\n" ,
3311 "should NOT set this variable to YES.\n" ,
3312 "\n" ,
3313 "----------------------------\n" ,
3314 "Variable: AFNI_STRLIST_INDEX\n" ,
3315 "----------------------------\n" ,
3316 "If this variable is set to NO, then the new [12 Oct 2007] 'Index'\n" ,
3317 "selector at the bottom of a string-list chooser (e.g., the 'Overlay'\n" ,
3318 "button popup window) will NOT be shown.\n" ,
3319 "\n" ,
3320 "-----------------------------\n" ,
3321 "Variable: AFNI_HISTOG_MAXDSET\n" ,
3322 "-----------------------------\n" ,
3323 "If this variable is set to a numeric value between 4 and 9\n" ,
3324 "(inclusive), then the number of Source datasets in the 'Histogram:\n" ,
3325 "Multi' plugin will be set to this value. The default number of Source\n" ,
3326 "datasets is 3 -- this variable allows you to increase that setting.\n" ,
3327 "\n" ,
3328 "--------------------------------\n" ,
3329 "Variable: AFNI_HISTOG_CUMULATIVE (editable)\n" ,
3330 "--------------------------------\n" ,
3331 "This YES/NO variable lets you control if the 'Histogram: Multi' plugin\n" ,
3332 "plots the cumulative distribution as well as the density histogram.\n" ,
3333 "Mostly this was added to subserve the nefarious conspiracies of the\n" ,
3334 "dreaded Dr Cox, but if you find it useful ....\n" ,
3335 "\n" ,
3336 "----------------------------\n" ,
3337 "Variable: AFNI_SIGQUIT_DELAY\n" ,
3338 "----------------------------\n" ,
3339 "This numeric variable (between 1 and 30) sets the number of seconds\n" ,
3340 "AFNI will delay before exiting after a SIGQUIT signal is delivered to\n" ,
3341 "the process. The default delay is 5 seconds. If you deliver a\n" ,
3342 "SIGALRM signal, AFNI will exit immediately. If you don't know what\n" ,
3343 "Unix signals are, then don't pay any attention to this subject!\n" ,
3344 "\n" ,
3345 "--------------------------------\n" ,
3346 "Variable: AFNI_NEVER_SAY_GOODBYE\n" ,
3347 "--------------------------------\n" ,
3348 "If this variable is set to YES, then the AFNI 'goodbye' messages won't\n" ,
3349 "be printed when the program exits. For the grumpy people out there\n" ,
3350 "(you know who I'm talking about, don't you, Daniel?).\n" ,
3351 "\n" ,
3352 "--------------------------------\n" ,
3353 "Variable: AFNI_NEWSESSION_SWITCH\n" ,
3354 "--------------------------------\n" ,
3355 "If this variable is set to NO, then AFNI will not automatically switch\n" ,
3356 "to a new session after that session is read in using the 'Read Sess'\n" ,
3357 "button on the Datamode control panel.\n" ,
3358 "\n" ,
3359 "-------------------------------\n" ,
3360 "Variable: AFNI_FLASH_VIEWSWITCH\n" ,
3361 "-------------------------------\n" ,
3362 "If you switch sessions, underlay, or overlay, it can happen that the\n" ,
3363 "coordinate system might be forced to switch from +orig to +tlrc\n" ,
3364 "(for example) because there is no dataset to view in the +orig system.\n" ,
3365 "If you set this variable to YES, AFNI flashes the view switch buttons\n" ,
3366 "on and off a few times to let you know this is happening\n" ,
3367 "(this is the Adam Thomas feature).\n" ,
3368 " ** Formerly, this feature was on by default, but now you have **\n" ,
3369 " ** to explicitly turn it on (this is the Ziad Saad fixup). **\n" ,
3370 "\n" ,
3371 "-------------------------\n" ,
3372 "Variable: AFNI_SHELL_GLOB\n" ,
3373 "-------------------------\n" ,
3374 "'Globbing' is the Unix jargon for filename wildcard expansion. AFNI\n" ,
3375 "programs do globbing at various points, using an adaptation of a\n" ,
3376 "function from the csh shell. This function has been reported to fail\n" ,
3377 "on Mac OS X Server 10.5 on network mounted directories. If you set\n" ,
3378 "this variable to YES, then globbing will instead be done using the\n" ,
3379 "shell directly (via popen and ls). You should only set this variable\n" ,
3380 "if you really need it, and understand the issue! [For Graham Wideman]\n" ,
3381 "\n" ,
3382 "-----------------------------\n" ,
3383 "Variable: AFNI_GLOB_SELECTORS\n" ,
3384 "-----------------------------\n" ,
3385 "If this variable is 'YES', then internal wildcard expansion (in AFNI\n" ,
3386 "programs that support this capability) will NOT use the '[]' , '{}' ,\n" ,
3387 "or '<>' selectors. Note that '[]' is a standard shell wildcard, so\n" ,
3388 "using this variable will restrict your wildcard-ing. On the other\n" ,
3389 "hand, it lets you do something like\n" ,
3390 " 3dTcat -prefix ALL_rest0.nii -relabel -verb 'rest_*.nii[0]'\n" ,
3391 "which will create a dataset from the #0 sub-brick of every dataset\n" ,
3392 "that matches the wildcard 'rest_*.nii'.\n" ,
3393 "\n" ,
3394 "----------------------------------\n" ,
3395 "Variable: AFNI_IGNORE_BRICK_FLTFAC\n" ,
3396 "----------------------------------\n" ,
3397 "Under some very rare circumstances, you might want to ignore the brick\n" ,
3398 "scaling factors. Set this variable to YES to do so. WARNING: this is\n" ,
3399 "dangerous, so be sure to unset this variable when you are done.\n" ,
3400 "Sample usage:\n" ,
3401 " 3dBrickStat -DAFNI_IGNORE_BRICK_FLTFAC=YES -max fred+orig\n" ,
3402 "\n" ,
3403 "----------------------------------------\n" ,
3404 "Variable: AFNI_ALLOW_ARBITRARY_FILENAMES\n" ,
3405 "----------------------------------------\n" ,
3406 "Normally, AFNI checks output filenames for 'bad' characters, which are\n" ,
3407 "defined as control characters and ASCII characters that will cause\n" ,
3408 "trouble on the Unix command line ('*', '$', etc.). 'Bad' filenames\n" ,
3409 "will not be allowed by most AFNI programs. If, for some reason, you\n" ,
3410 "want to use such filenames, set this variable to YES. Don't blame\n" ,
3411 "me if you get into trouble with such filenames!\n" ,
3412 "\n" ,
3413 "----------------------------\n" ,
3414 "Variable: AFNI_INSTACORR_FDR (editable)\n" ,
3415 "----------------------------\n" ,
3416 "If you want AFNI's InstaCorr feature to compute the FDR curve for the\n" ,
3417 "on-the-fly correlation coefficient sub-brick created interactively,\n" ,
3418 "then set this variable to YES. Since the FDR computations are the\n" ,
3419 "slowest part of the operation, the default (if this variable is not\n" ,
3420 "YES) is that FDR curves are NOT computed.\n" ,
3421 "\n" ,
3422 "---------------------------------\n" ,
3423 "Variable: AFNI_INSTACORR_SEEDBLUR\n" ,
3424 "---------------------------------\n" ,
3425 "The InstaCorr controls let you use extra spatial smoothing when\n" ,
3426 "selecting the seed voxel time series. By default, this extra\n" ,
3427 "smoothing is a flat average over a sphere of the chosen radius:\n" ,
3428 "\"SeedRad\". However, if this environment variable is set to YES, then\n" ,
3429 "the extra smoothing is done by Gaussian blurring with the chosen FWHM:\n" ,
3430 "\"SeedBlur\". This variable cannot be set interactively, but can be set\n" ,
3431 "on the AFNI command line with the usual -DAFNI_INSTACORR_SEEDBLUR=YES\n" ,
3432 "method.\n" ,
3433 "\n" ,
3434 "-----------------------------\n" ,
3435 "Variable: AFNI_INSTACORR_JUMP (editable)\n" ,
3436 "-----------------------------\n" ,
3437 "When using the Shift+Ctrl+Click method to set the InstaCorr seed, the\n" ,
3438 "usual operation is to jump the crosshairs focus point to the location\n" ,
3439 "where the click happened, and then do the InstaCorr seed set. If you\n" ,
3440 "set this environment variable to NO (the default value is YES), then\n" ,
3441 "the crosshair jumping will not happen, but the seed will be set at\n" ,
3442 "the clicked point.\n" ,
3443 "One use case for this setting is when you have setup a Montage layout\n" ,
3444 "and don't want it to automatically jump to a new slice when you set\n" ,
3445 "the InstaCorr seed -- you like the layout of what you are seeing, and\n" ,
3446 "don't want it to change underneath you just because you are moving\n" ,
3447 "the seed location. [For Phil Kohn, Sep 2021]\n" ,
3448 "\n" ,
3449 "--------------------------------\n" ,
3450 "Variable: AFNI_INSTACORR_XYZ_LPI\n" ,
3451 "--------------------------------\n" ,
3452 "In 3dGroupInCorr's batch mode, the XYZ method of operation sets the\n" ,
3453 "seed coordinates using AFNI's standard RAI (DICOM) order. If you\n" ,
3454 "set this variable to YES, then the coordinates given will be\n" ,
3455 "interpreted as being in LPI (AKA 'neurological') order; that is,\n" ,
3456 "the given x and y values will be negated before being used inside\n" ,
3457 "3dGroupInCorr to pick the seed voxel.\n" ,
3458 "\n" ,
3459 "----------------------------------\n" ,
3460 "Variable: AFNI_BLUR_INTS_AS_OLD\n" ,
3461 "----------------------------------\n" ,
3462 "As of 15 June 2009, the FIR (finite implulse response) method is\n" ,
3463 "applid to byte and short data. Previously, 3dmerge had used FIR only\n" ,
3464 "on float data, meaning shorts and floats would be applied via Fourier\n" ,
3465 "interpolation. Setting AFNI_BLUR_INTS_AS_OLD to YES will revert to\n" ,
3466 "the Fourier method for such data.\n" ,
3467 "\n" ,
3468 "-----------------------------\n" ,
3469 "Variable: AFNI_IMAGE_CROPSTEP (editable)\n" ,
3470 "-----------------------------\n" ,
3471 "Numeric value sets the size of the panning step using in the image\n" ,
3472 "viewer, when you are adjusting the cropping region using the\n" ,
3473 "Shift+Arrow keys on the keyboard. Defaults to 1. Legal values are\n" ,
3474 "-9..9 (inclusive). Positive values means pressing Shift+LeftArrow\n" ,
3475 "causes the image in the crop window to appear to move to the left;\n" ,
3476 "negative values cause the crop window to move in the opposite\n" ,
3477 "direction, so the visible part of the image appears to move to the\n" ,
3478 "right. (Mutatis mutandum for the other directions, of course.)\n" ,
3479 "\n" ,
3480 "-------------------------------\n" ,
3481 "Variable: AFNI_IMAGE_COLORANGLE (editable) ** OBSOLETE **/\n" ,
3482 "-------------------------------\n" ,
3483 "This value, a number between 90 and 360 (inclusive) describes the\n" ,
3484 "amount of the AJJ color circle used by the 'Colr' button in an\n" ,
3485 "AFNI image viewer. If no value is given, the default is 240.\n" ,
3486 "Changing this number to 360 means the color circle is continuous\n" ,
3487 "from top to bottom -- an effect that is obvious if you use the 'r'\n" ,
3488 "arrow buttons (on the right of the image viewer) to rotate the\n" ,
3489 "color circle. The default value of 240 is purely for historical\n" ,
3490 "reasons, dating back to the old FD program from Medieval Times.\n" ,
3491 "\n" ,
3492 "-------------------------------\n" ,
3493 "Variable: AFNI_IMAGE_COLORSCALE\n" ,
3494 "-------------------------------\n" ,
3495 "This variable defines the colorscale used by the 'Colr' button\n" ,
3496 "at the top right of the AFNI image viwer window to colorize\n" ,
3497 "the Underlay image -- the Overlay colorization is controlled\n" ,
3498 "from the colorscale on the 'Define Overlay' control pane.\n" ,
3499 "At this time [Oct 2019], only the following four color scales\n" ,
3500 "can be used for this purpose:\n" ,
3501 " magma plasma viridis googleturbo\n" ,
3502 "If you do not define AFNI_IMAGE_COLORSCALE, or you define it\n" ,
3503 "to something besides one of these names (case insensitive),\n" ,
3504 "then 'googleturbo' is used.\n" ,
3505 " https://ai.googleblog.com/2019/08/turbo-improved-rainbow-colormap-for.html\n" ,
3506 "Note that the color scale can be modified somewhat by using the\n" ,
3507 "'g' (gamma) arrow buttons on the right edge of the image viewer.\n" ,
3508 "\n" ,
3509 "It is possible to change this image viewer underlay colorscale by\n" ,
3510 "changing this environment variable interactively, using the driving\n" ,
3511 "feature of the AFNI GUI (e.g., program plugout_drive).\n" ,
3512 "\n" ,
3513 "--------------------------------------\n" ,
3514 "Variable: AFNI_IMAGE_SCROLLWHEEL_TMASK\n" ,
3515 "--------------------------------------\n" ,
3516 "This variable lets you control which keyboard modifier keys are\n" ,
3517 "checked when the mouse scroll wheel is used inside the image.\n" ,
3518 "If one (or more) of the selected keys is pressed while the\n" ,
3519 "scroll wheel is moved, then the AFNI controller 'Define Overlay'\n" ,
3520 "threshold slider moves -- otherwise (the normal case), the image\n" ,
3521 "slice slider moves. The value of this variable should be contain\n" ,
3522 "one or more of these strings (NOT case sensitive):\n" ,
3523 " Shift = Shift key pressed\n" ,
3524 " Ctrl or Control = Control key pressed\n" ,
3525 " Mod1 = Alt key pressed (Linux)\n" ,
3526 " Mod2 = Command key pressed (Mac)\n" ,
3527 "If you do NOT set this variable, it is like setting it to the\n" ,
3528 "value 'Mod1+Mod2' (so that Alt and Command work on Linux and\n" ,
3529 "Mac OS X, respectively). However, some Linux systems seem to\n" ,
3530 "always have the Mod2 mask set for the scroll wheel, and so\n" ,
3531 "the wheel ALWAYS change the threshold slider and not the slice.\n" ,
3532 "To prevent this sad thing from happening, set this variable to\n" ,
3533 "just 'Mod1'. Furthermore, if you include the string 'Debug'\n" ,
3534 "in this variable, when the scroll wheel is used over the image\n" ,
3535 "sub-window, some information will be printed out about what the\n" ,
3536 "program detects, which might help you set things up correctly.\n" ,
3537 "On my Mac, I get the following output when using the scroll wheel\n" ,
3538 "twice -- once with no key pressed and once with the Command key:\n" ,
3539 " ++ Scrollwheel (imag): button=5 ; state mask=0x\n" ,
3540 " + (mask: shift=1x ctrl=4x mod1=8x mod2=10x mod3=20x mod4=40x mod5=80x)\n" ,
3541 " + change slice\n" ,
3542 " ++ Scrollwheel (imag): button=5 ; state mask=10x\n" ,
3543 " + (mask: shift=1x ctrl=4x mod1=8x mod2=10x mod3=20x mod4=40x mod5=80x)\n" ,
3544 " + change threshold\n" ,
3545 "The second use shows that the 'state mask' (which shows the modifier\n" ,
3546 "keys) was hexadecimal '10x', which corresponds to the 'mod2' value.\n" ,
3547 "\n" ,
3548 "----------------------------\n" ,
3549 "Variable: AFNI_DUMMY_DATASET\n" ,
3550 "----------------------------\n" ,
3551 "The old 'frivolous' AFNI dummy dataset was replaced with a\n" ,
3552 "low-resolution edition of the N27 dataset on 12 Feb 2010. If for some\n" ,
3553 "absurd reason you want the old dummy dataset back, then set this\n" ,
3554 "variable to OLD. (Recall that the dummy dataset is only created if\n" ,
3555 "you start the AFNI GUI without any input datasets at all -- AFNI is so\n" ,
3556 "constructed that it needs SOME dataset present to be able to operate:\n" ,
3557 "hence, the dummy dataset concept.)\n" ,
3558 "\n" ,
3559 "----------------------------\n" ,
3560 "Variable: AFNI_DONT_COMMAIZE\n" ,
3561 "----------------------------\n" ,
3562 "When AFNI programs print out informative (and fun) messages about the\n" ,
3563 "size of files, memory space, etc., by default commas are inserted,\n" ,
3564 "as in \"8,765,432\". If you want these numbers printed as \"8765432\"\n" ,
3565 "(for whatever hideous and twisted reason), set this variable to YES.\n" ,
3566 "\n" ,
3567 "----------------------------\n" ,
3568 "Variable: AFNI_FILE_COORDS_x\n" ,
3569 "----------------------------\n" ,
3570 "If this variable is set (where 'x' is A, B, C, ...), then for AFNI\n" ,
3571 "controller 'x', whenever the crosshair viewpoint changes, the DICOM\n" ,
3572 "order (x,y,z) coordinates and the dataset 3D index (i,j,k) will be\n" ,
3573 "written to the file whose name is given by the value of this variable.\n" ,
3574 "As a special case, if the filename is 'stdout', then the coordinates\n" ,
3575 "are written to standard output. A sample command\n" ,
3576 "\n" ,
3577 " afni -DAFNI_FILE_COORDS_A=stdout\n" ,
3578 "\n" ,
3579 "If the file already exists when afni starts, it will be over-written;\n" ,
3580 "that is, it is opened in \"w\" mode.\n" ,
3581 "\n" ,
3582 "This feature may be referred to as the Jen Evans special.\n" ,
3583 "\n" ,
3584 "------------------------------\n" ,
3585 "Variable: AFNI_AUTORANGE_POWER -- this variable is now obsolete\n" ,
3586 "------------------------------\n" ,
3587 "If this variable is set to a value between 0 and 1 (exclusive),\n" ,
3588 "then the functional overlay 'autoRange' value will be set to\n" ,
3589 "the largest value in the dataset raised to this power. By default,\n" ,
3590 "the autoRange value is computed as if this power is 1.\n" ,
3591 "\n" ,
3592 "-----------------------------\n" ,
3593 "Variable: AFNI_AUTORANGE_PERC - experimental at this moment\n" ,
3594 "-----------------------------\n" ,
3595 "If this variable is set to a value P between 2 and 99 (inclusive),\n" ,
3596 "then it indicates that the functional overlay 'autoRange' value\n" ,
3597 "will be set the P-th percentile point on the cumulative histogram\n" ,
3598 "of the absolute values of the nonzero entries in the Overlay\n" ,
3599 "dataset sub-brick being viewed. To be less confusing, if P=95\n" ,
3600 "(for example), then the nonzero absolute values are tabulated\n" ,
3601 "into histogram bins from smallest (percentile=0) to largest\n" ,
3602 "(percentile=100), and the value at the 95th percentile will\n" ,
3603 "be chosen -- so that only 5 percent of the values in the\n" ,
3604 "dataset are larger than this autoRange value. The reason for\n" ,
3605 "doing this is to avoid allowing a few large values to distort\n" ,
3606 "the overlay color scale.\n" ,
3607 "\n" ,
3608 "---------------------------\n" ,
3609 "Variable: AFNI_IDEAL_COLORS (editable)\n" ,
3610 "---------------------------\n" ,
3611 "This variable, if set, allows you to specify the set of colors used\n" ,
3612 "for the FIM Ideal overlay in the graph viewer window. Separate color\n" ,
3613 "names by colons, as in \"red:green:blue\". The first column in the\n" ,
3614 "Ideal 1D file gets the first color; the second column gets the second\n" ,
3615 "color, and so on. The variable AFNI_ORT_COLORS can similarly be used\n" ,
3616 "to specify the colors for the FIM Ort overlay.\n" ,
3617 "\n" ,
3618 "-------------------------------\n" ,
3619 "Variable: AFNI_DONT_USE_HTMLWIN\n" ,
3620 "-------------------------------\n" ,
3621 "If this variable is set to NO, then the 'AFNI Tips' button will not\n" ,
3622 "use the HTML window to display the requested information -- a plain\n" ,
3623 "text window will be used. You should only need to use this variable\n" ,
3624 "if the AFNI Tips window crashes on your system.\n" ,
3625 "\n" ,
3626 "-----------------------------\n" ,
3627 "Variable: AFNI_UNFONTIZE_HTML\n" ,
3628 "-----------------------------\n" ,
3629 "If this variable is set to YES, then font-changing HTML tags will be\n" ,
3630 "deleted before opening the 'AFNI Tips' HTML window. Try this first\n" ,
3631 "to avoid crashes, before using the previous variable to turn off the\n" ,
3632 "HTML tips entirely.\n" ,
3633 "\n" ,
3634 "------------------------\n" ,
3635 "Variable: AFNI_USE_FGETS\n" ,
3636 "------------------------\n" ,
3637 "The function fgets() is the Unix standard for reading text lines from\n" ,
3638 "a file. However, it assumes that the text file lines end in the Unix\n" ,
3639 "standard end-of-line character (ASCII 0xA). Files created on\n" ,
3640 "Microsoft platforms use a different end-of-line character (ASCII 0xD).\n" ,
3641 "The result is that Microsoft-ized text files don't work well with\n" ,
3642 "fgets(). AFNI uses its own function, cleverly called afni_fgets(), to\n" ,
3643 "read text lines, to avoid this problem. However, this function is 4-5\n" ,
3644 "times slower than the system fgets() function, so if speed if crucial\n" ,
3645 "-- as when reading a giant 1D file -- then set AFNI_USE_FGETS to YES\n" ,
3646 "to make AFNI programs use the system fgets() function. The best way\n" ,
3647 "to do this would be on the command line, as in the simple example\n" ,
3648 "below:\n" ,
3649 " 1dcat -DAFNI_USE_FGETS=YES bigfileA.1D bigfileB.1D > bigfileAB.1D\n" ,
3650 "In such an example, you won't see a 4-5 times speedup, since actually\n" ,
3651 "most of the time is spent decoding the text in the file into numbers\n" ,
3652 "and then writing them back out -- you'll probably see a speedup of\n" ,
3653 "about 1.2-1.4 instead -- not trivial, but not exhilarating.\n" ,
3654 "\n" ,
3655 "------------------------\n" ,
3656 "Variables: AFNI_WSINC5_*\n" ,
3657 "------------------------\n" ,
3658 "These variables affect the way the '3dAllineate -final wsinc5' windowed\n" ,
3659 "since interpolation option works. See the output of the command\n" ,
3660 " 3dAllineate -HELP\n" ,
3661 "for the details. You can control the width of the sinc window, the\n" ,
3662 "tapering function, and a couple of other useless options.\n" ,
3663 "** N.B.: You can turn off the message that the wsinc5 code prints out\n" ,
3664 "detailing the parameter setup by setting AFNI_WSINC5_SILENT to YES.\n" ,
3665 "\n" ,
3666 "--------------------------------\n" ,
3667 "Variable: AFNI_3dAllineate_final\n" ,
3668 "--------------------------------\n" ,
3669 "The default '-final' option for 3dAllineate is 'cubic'. You can change\n" ,
3670 "this default to any other legitimate value, such as 'wsinc5' or 'NN'.\n" ,
3671 "This variable is provided to allow you to force the final interpolation\n" ,
3672 "mode into a script that doesn't allow any easy way to affect it, such\n" ,
3673 "as that generated by afni_proc.py.\n" ,
3674 "\n" ,
3675 "-------------------------\n" ,
3676 "Variable: AFNI_INDEX_STEP\n" ,
3677 "-------------------------\n" ,
3678 "This numeric variable (between 1 and 9, inclusive) sets the step size\n" ,
3679 "used when you press the up/down arrows on the 'Index' control in the\n" ,
3680 "left column of the main AFNI controller. Setting this value to 2 (say)\n" ,
3681 "let's you scroll through an image time series seeing alternate time\n" ,
3682 "points. This feature can be useful when looking at datasets where\n" ,
3683 "sub-bricks alternate in type -- for example, from 3dttest++, where the\n" ,
3684 "even-numbered volumes are effect size estimates, and the odd-numbered\n" ,
3685 "volumes are the corresponding t-statistics. (This value can also be\n" ,
3686 "set interactively from a popup chooser activated by right-clicking\n" ,
3687 "on the 'Index' label to the left of the up/down arrows.)\n" ,
3688 "\n" ,
3689 "-----------------------------\n" ,
3690 "Variable: AFNI_SCATPLOT_LINES\n" ,
3691 "-----------------------------\n" ,
3692 "The ScatterPlot plugin lets you graph the data in one sub-brick along\n" ,
3693 "the x-axis and the data in another sub-brick along the y-axis. It also\n" ,
3694 "computes some straight line y=ax+b fits to the graph. By default, it\n" ,
3695 "does 2 different fits, with least sum of squares (L2) and least sum\n" ,
3696 "of absolutes (L1) criteria. The L2 line is plotted in red (and thus\n" ,
3697 "corresponds to the Pearson R also shown in red), and the L1 line is\n" ,
3698 "plotted in blue (and corresponds to the Spearman rho shown in blue).\n" ,
3699 "With this variable, you can turn off the plotting of either or both\n" ,
3700 "of these lines, which are often very nearly the same. If the value\n" ,
3701 "of this variable contains the string 'NOL1', then the L1 line won't\n" ,
3702 "be shown, and if the value of this variable contains 'NOL2', then\n" ,
3703 "the L2 line won't be shown. Thus, if the value of this variable is\n" ,
3704 "'NOL1+NOL2', neither line will be plotted.\n" ,
3705 "\n" ,
3706 "----------------------------\n" ,
3707 "Variable: AFNI_SCATPLOT_FRAC\n" ,
3708 "----------------------------\n" ,
3709 "This variable lets you choose the size of the boxes plotted in the\n" ,
3710 "ScatterPlot plugin. The units are fractions of the plot width,\n" ,
3711 "so the reasonable range for this value is 0.0 to 0.01 (not inclusive).\n" ,
3712 "If this variable is not set, or the value is outside of this range,\n" ,
3713 "then the size of the boxes is set based on the number of points\n" ,
3714 "being plotted. The only reason for using this variable is if you\n" ,
3715 "wish to create a sequence of scatterplots and ensure that the points\n" ,
3716 "plotted in different graphs have a uniform size of boxes.\n" ,
3717 "\n" ,
3718 "-------------------------\n" ,
3719 "Variable: AFNI_GIFTI_VERB\n" ,
3720 "-------------------------\n" ,
3721 "This integer sets the verbose level in the gifti I/O library routines.\n" ,
3722 "Level 1 is the default, 0 is \"quiet\", and values go up to 7.\n" ,
3723 "\n" ,
3724 "----------------------------\n" ,
3725 "Variable: AFNI_DATASETN_NMAX\n" ,
3726 "----------------------------\n" ,
3727 "This numeric variable, if set, lets you expand the number of dataset\n" ,
3728 "lines in the 'Dataset#N' plugin from the default of 9 up to a max of 49.\n" ,
3729 "(This one is for Shruti.)\n" ,
3730 "\n" ,
3731 "---------------------------------\n" ,
3732 "Variable: AFNI_WRITE_1D_AS_PREFIX\n" ,
3733 "---------------------------------\n" ,
3734 "If this variable is set to YES, then 1D formatted files will be\n" ,
3735 "written to the file based on the given prefix, rather than to an\n" ,
3736 "automatic 1D file. This allows writing surface files to NIfTI format,\n" ,
3737 "for example.\n" ,
3738 "\n" ,
3739 "-----------------------------------\n" ,
3740 "Variable: AFNI_PATH_SPACES_OK\n" ,
3741 "-----------------------------------\n" ,
3742 "If this variable is set to YES, dataset names with spaces in them will\n" ,
3743 "go through \"normal\" reading routines, rather than using\n" ,
3744 "THD_open_tcat() to try to combine multiple datasets.\n" ,
3745 "\n" ,
3746 "----------------------\n" ,
3747 "Variable: AFNI_CREEPTO\n" ,
3748 "----------------------\n" ,
3749 "If set to YES, then the AFNI GUI 'Jump to (xyz)' behavior is altered to\n" ,
3750 "move the crosshairs to the chosen location incrementally, rather than\n" ,
3751 "in one big jump. The reasons for using this feature are (a) to help\n" ,
3752 "get a feel for the transit, and (b) just plain fun.\n" ,
3753 "\n" ,
3754 "---------------------------\n" ,
3755 "Variable: AFNI_HISTORY_NAME\n" ,
3756 "---------------------------\n" ,
3757 "The value of this variable will alter the 'username@machine' listing\n" ,
3758 "in the history notes generated by AFNI programs. If this variable\n" ,
3759 "is NOT set, then your user login name and machine ID are put in the\n" ,
3760 "header; otherwise, the value of this string is used. You can set this\n" ,
3761 "string to the null string '' if you wish to hide your identity totally.\n" ,
3762 "\n" ,
3763 "---------------------------\n" ,
3764 "Variable: AFNI_INCLUDE_HISTORY\n" ,
3765 "---------------------------\n" ,
3766 "If this variable is set to YES, output datasets will have a\n" ,
3767 "HISTORY_NOTE which can be seen via 3dinfo, for example. If set to NO,\n" ,
3768 "output datasets will not have any HISTORY. This is one method for\n" ,
3769 "making datasets anonymous.\n" ,
3770 "\n" ,
3771 "---------------------------------------------------------\n" ,
3772 "Variables: AFNI_XCLUSTSIM_GLOBAL and AFNI_XCLUSTSIM_LOCAL\n" ,
3773 "---------------------------------------------------------\n" ,
3774 "These variables control the setting of the 'global' and 'local' ETAC\n" ,
3775 "calculations, and are equivalent to using the '-ETAC_global' and\n" ,
3776 "'-ETAC_local' command line switches to 3dttest++. If you set a\n" ,
3777 "variable to YES, then that commands the relevant ETAC thresholds\n" ,
3778 "to be calculated; if you set a variable to NO, it turns off the\n" ,
3779 "relevant calculation. If you do not set a variable, and you do\n" ,
3780 "not use the 3dttest++ command line option, you will get whatever\n" ,
3781 "the default ETAC method(s) are enabled.\n" ,
3782 "\n" ,
3783 "----------------------------\n" ,
3784 "Variable: AFNI_CLUSTSIM_MEGA\n" ,
3785 "----------------------------\n" ,
3786 "Set this variable to YES to force the use of the '-MEGA' option\n" ,
3787 "in 3dClustSim. The primary reason for this usage is to force\n" ,
3788 "'3dttest -Clustsim' to use '-MEGA' rather than the default '-LOTS'.\n" ,
3789 "\n" ,
3790 "=============================================\n" ,
3791 "| Robert W Cox, PhD |\n" ,
3792 "| Scientific and Statistical Computing Core |\n" ,
3793 "| National Institute of Mental Health |\n" ,
3794 "| National Institutes of Health |\n" ,
3795 "| Department of Health & Human Services |\n" ,
3796 "| United States of America |\n" ,
3797 "| Earth, United Federation of Planets |\n" ,
3798 "| Alpha Quadrant, Milky Way Galaxy |\n" ,
3799 "| Local Group, Virgo Supercluster |\n" ,
3800 "=============================================\n" ,
3801 "\n" ,
3802 "-------------------------\n" ,
3803 "Variable: AFNI_LINKRBRAIN\n" ,
3804 "-------------------------\n" ,
3805 "If you do NOT want to see the 'linkRbrain' button in the Clusterize\n" ,
3806 "GUI, then set this variable to NO.\n" ,
3807 "\n" ,
3808 "------------------------------\n" ,
3809 "Variable: AFNI_LINKRBRAIN_SITE\n" ,
3810 "------------------------------\n" ,
3811 "This variable sets the name of the linkRbrain server to use. The default\n" ,
3812 "server is 'linkrbrain.eu'.\n" ,
3813 "\n" ,
3814 "#########################################\n" ,
3815 "### Vars for realtime functionality ###\n" ,
3816 "#########################################\n" ,
3817 "\n" ,
3818 "--------------------------\n" ,
3819 "Variables: AFNI_REALTIME_*\n" ,
3820 "--------------------------\n" ,
3821 "This set of variables allows you to control the initial setup of the\n" ,
3822 "realtime data acquisition plugin (menu item \"RT Options\"). Normally,\n" ,
3823 "this plugin is active only if AFNI is started with the \"-rt\" command\n" ,
3824 "line option. (It will consume CPU time continually as it polls for\n" ,
3825 "an incoming data connection, which is why you don't want it running\n" ,
3826 "by default.) The following variables can be used to initialize the\n" ,
3827 "plugin's options:\n" ,
3828 "\n" ,
3829 "AFNI_REALTIME_Activate = This is a YES/NO variable, and allows you\n" ,
3830 " to have the realtime plugin active without\n" ,
3831 " using the \"-rt\" command line option. If\n" ,
3832 " this variable is set to YES, then you can\n" ,
3833 " disable the realtime plugin with \"-nort\".\n" ,
3834 "\n" ,
3835 "The variables below are used to set the initial status of the widgets\n" ,
3836 "in the realtime plugin's control window. Each one has the same name as\n" ,
3837 "the labels in the control window, with blanks replaced by underscores.\n" ,
3838 "The values to set for these variables are exact copies of the inputs\n" ,
3839 "you would specify interactively (again, with blanks replaced by\n" ,
3840 "underscores). For details as to the meaning of these options, see\n" ,
3841 "the plugin's Help window.\n" ,
3842 "\n" ,
3843 "AFNI_REALTIME_Images_Only = \"No\" or \"Yes\"\n" ,
3844 "AFNI_REALTIME_Root = name for datasets to be created\n" ,
3845 "AFNI_REALTIME_Update = an integer from 0 to 19\n" ,
3846 "AFNI_REALTIME_Function = \"None\" or \"FIM\" (cf. AFNI_FIM_IDEAL below)\n" ,
3847 "AFNI_REALTIME_Verbose = \"No\", \"Yes\", or \"Very\"\n" ,
3848 "AFNI_REALTIME_Registration = \"None\", \"2D:_realtime\", \"2D:_at_end\",\n" ,
3849 " \"3D:_realtime\", \"3D:_at_end\",\n" ,
3850 " or \"3D:_estimate\"\n" ,
3851 "AFNI_REALTIME_Resampling = \"Cubic\", \"Quintic\", \"Heptic\", \"Fourier\",\n" ,
3852 " or \"Hept+Four\"\n" ,
3853 "AFNI_REALTIME_Reg_Base_Mode= \"Current_Run\", \"Current_Run_Keep\", or\n" ,
3854 " \"External_Dataset\"\n" ,
3855 "AFNI_REALTIME_Base_Image = an integer from 0 to 9999\n" ,
3856 "AFNI_REALTIME_Graph = \"No\", \"Yes\", or \"Realtime\"\n" ,
3857 "AFNI_REALTIME_NR = an integer from 5 to 9999\n" ,
3858 "AFNI_REALTIME_YR = a floating point number from 0.1 to 10.0\n" ,
3859 "\n" ,
3860 "AFNI_REALTIME_External_Dataset = name of dataset to use as external\n" ,
3861 " basis for registration\n" ,
3862 " * if this variable is set, then the plugin assumes that\n" ,
3863 " AFNI_REALTIME_Reg_Base_Mode is \"External_Dataset\"\n" ,
3864 " * but AFNI_REALTIME_Base_Image is ignored\n" ,
3865 " * instead, you can use a sub-brick selector here, if desired;\n" ,
3866 " for example: setenv AFNI_REALTIME_External_Dataset 'X+orig[3]'\n" ,
3867 " * to be brutally clear, you can give the name of a dataset that is\n" ,
3868 " NOT in the current directory -- unlike when using the plugin GUI\n" ,
3869 " * the plugin GUI will NOT show the choice of external dataset given\n" ,
3870 " via this environment variable!\n" ,
3871 "\n" ,
3872 "AFNI_REALTIME_Mask_Vals = String (one of the listed strings)\n" ,
3873 "\n" ,
3874 " This allows the user to set the \"Vals to Send\" field from the RT\n" ,
3875 " plugin's \"Mask\" line. It determines what data are sent to the remote\n" ,
3876 " MP program (e.g. serial_helper). Valid strings are:\n" ,
3877 "\n" ,
3878 " None - send nothing\n" ,
3879 " Motion_Only - send only the 6 registration parameters\n" ,
3880 " ROI_means - send the mean EPI value per mask ROI (value) per TR\n" ,
3881 " All_Data - send each voxel value (in mask) per TR\n" ,
3882 "\n" ,
3883 "AFNI_REALTIME_Mask_Dset = String (the name of a dataset)\n" ,
3884 "\n" ,
3885 " This option allows the user to set the Mask dataset, used to\n" ,
3886 " send ROI and motion data to a program listening at a socket.\n" ,
3887 " This environment variable overrides the variable set in the\n" ,
3888 " plugin interface, allowing it to change per run.\n" ,
3889 "\n" ,
3890 " Set the variable to None to either clear the mask or to allow\n" ,
3891 " the interface mask to apply. Note that this can be done via a\n" ,
3892 " drive afni command, allowing changes after afni is already\n" ,
3893 " running, e.g. plugout_drive -com 'SETENV\n" ,
3894 " AFNI_REALTIME_MASK_DSET None' -quit\n" ,
3895 "\n" ,
3896 "AFNI_REALTIME_WRITEMODE = Number\n" ,
3897 " This variable controls writing individual volumes as they are acquired\n" ,
3898 " by the realtime plugin. Valid Numbers and their effects are:\n" ,
3899 " 0 = Off : do nothing [default]\n" ,
3900 " 1 = Acquired : write each volume as it is acquired\n" ,
3901 " 2 = Registered : write each registered volume\n" ,
3902 " 3 = Merged : write each merged volume (merged across channels)\n" ,
3903 "\n" ,
3904 "\n" ,
3905 "N.B.: The following internal controls can only be set using these environment\n" ,
3906 " variables (there is no GUI to set these values):\n" ,
3907 "\n" ,
3908 "AFNI_REALTIME_volreg_maxite = an integer >= 1 [default = 9]\n" ,
3909 "AFNI_REALTIME_volreg_maxite_est = an integer >= 1 [default = 1]\n" ,
3910 "AFNI_REALTIME_volreg_graphgeom = something like 320x320+59+159\n" ,
3911 "\n" ,
3912 "AFNI_REALTIME_reset_output_index = YES/NO\n" ,
3913 "\n" ,
3914 " By default, output files will be named with a prefix,\n" ,
3915 " PREFIX__NNN, where PREFIX is given by the AFNI_REALTIME_Root\n" ,
3916 " variable or the Root in the interface, and where NNN\n" ,
3917 " increments per run.\n" ,
3918 "\n" ,
3919 " If this variable is set to YES, then the plugin will try to\n" ,
3920 " use NNN=001 each run.\n" ,
3921 "\n" ,
3922 "AFNI_REALTIME_CHILDWAIT = max wait time (in sec) for child info process\n" ,
3923 " [default = 66.6]; not needed if child info process is not used\n" ,
3924 "\n" ,
3925 "AFNI_REALTIME_WRITEWAIT = if the image data pauses for this number of\n" ,
3926 " seconds, then the datasets being constructed will be written\n" ,
3927 " to disk [default=37.954]; since this output may take several\n" ,
3928 " seconds, you may need to adjust this if you are in fact doing\n" ,
3929 " imaging with a very long TR.\n" ,
3930 " Note that after this wait, the plugin can still receive image\n" ,
3931 " data -- even if the image source program is silent for a very\n" ,
3932 " long time, AFNI will still be waiting patiently for data.\n" ,
3933 "\n" ,
3934 "AFNI_GRAPH_AUTOGRID = By default, if the number of time points in an\n" ,
3935 " AFNI graph viewer changes, the density of vertical grid lines\n" ,
3936 " changes. If you don't want this to happen, set this variable\n" ,
3937 " to NO.\n" ,
3938 "\n" ,
3939 "AFNI_REALTIME_MP_HOST_PORT = HOST:PORT\n" ,
3940 "\n" ,
3941 " When this variable is set, the realtime plugin will attempt to\n" ,
3942 " open a tcp socket to the corresponding host and port, and will\n" ,
3943 " send the six registration correction parameters for each 3D\n" ,
3944 " volume received by the plugin. This applies only to the case\n" ,
3945 " of graphing 3D registration. The socket will be opened at the\n" ,
3946 " start of each run, and will be closed at the end. A simple\n" ,
3947 " example of what to set this variable to is localhost:53214.\n" ,
3948 " See 'serial_helper -help' for more details.\n" ,
3949 "\n" ,
3950 "AFNI_REALTIME_SEND_VER = Y/N\n" ,
3951 "\n" ,
3952 " If AFNI_REALTIME_MP_HOST_PORT is set, the RT plugin has 3 choices\n" ,
3953 " of what to send to that port (possibly to serial_helper):\n" ,
3954 " 0. the motion parameters\n" ,
3955 " 1. motion params, along with average EPI values over each ROI\n" ,
3956 " in the mask dataset (if set)\n" ,
3957 " 2. motion params, along with all voxel values over the mask\n" ,
3958 " dataset (including index, i,j,k and x,y,z values)\n" ,
3959 " If AFNI_REALTIME_SEND_VER is set to YES, then the plugin will\n" ,
3960 " offset the last byte of the communication HELLO string by the\n" ,
3961 " version number (0, 1 or 2). In the case of versions 1 or 2,\n" ,
3962 " the plugin will send the number of ROIs/voxels in a 4-byte int\n" ,
3963 " after the HELLO string.\n" ,
3964 "\n" ,
3965 "AFNI_REALTIME_SHOW_TIMES = Y/N\n" ,
3966 "\n" ,
3967 " If set, the RT plugin will output CPU times whenever motion\n" ,
3968 " parameters are sent to the remote program, allowing evaluation\n" ,
3969 " of timing. The times are modulo one hour, and are at a\n" ,
3970 " millisecond resolution.\n" ,
3971 "\n" ,
3972 "AFNI_REALTIME_MAX_CONTROLLERS = Number\n" ,
3973 "\n" ,
3974 " If set, this is the maximum number of controllers that AFNI will\n" ,
3975 " open for multi-channel acquisition display. If more channels\n" ,
3976 " than this are sent, only the first ones will be displayed.\n" ,
3977 " ** If this variable is not set, its value defaults to 2.\n" ,
3978 "\n" ,
3979 "AFNI_REALTIME_DATAMODE = Number\n" ,
3980 "\n" ,
3981 " If set, this variable controls the initial setting of the\n" ,
3982 " \"DataWriting\" control, where 0=Off, 1=Acquired, etc. If not\n" ,
3983 " set, the default value is 0.\n" ,
3984 "\n" ,
3985 "AFNI_REALTIME_CHMERMODE = Number\n" ,
3986 "\n" ,
3987 " If set, this variable controls the initial setting of the\n" ,
3988 " \"ChannelMerge\" control, where 0=none, 1=sum, 2=L1 norm, 3=L2norm.\n" ,
3989 " If not set, the default value is 0.\n" ,
3990 "\n" ,
3991 "AFNI_REALTIME_CM_REG_MODE = Number\n" ,
3992 "\n" ,
3993 " If set, this variable controls the ChannelMerge registration mode.\n" ,
3994 " Here: 0=none : no merge registration\n" ,
3995 " 1=reg_merge : register merged dastaset\n" ,
3996 " 2=reg_chan : apply merge xform to all channels\n" ,
3997 " The default is 0.\n" ,
3998 "\n" ,
3999 "AFNI_REALTIME_MRG_CHANLIST = String\n" ,
4000 "\n" ,
4001 " If set, this variable specifies a list of 0-based channels to\n" ,
4002 " merge, rather than using all channels. The format is akin to\n" ,
4003 " sub-brick selection. For example '0..$' means all and\n" ,
4004 " '0,5..7' means 0,5,6,7.\n" ,
4005 "\n" ,
4006 "\n" ,
4007 "For detailed information about how the realtime plugin works, read the\n" ,
4008 "file README.realtime.\n" ,
4009 "\n" ,
4010 "Also see \"Dimon -help\" (example E \"for testing complete real-time system\").\n" ,
4011 "Also see \"serial_helper -help\".\n" ,
4012 "Also see program rtfeedme.c and \"rtfeedme -help\".\n" ,
4013 "\n" ,
4014 "###################################\n" ,
4015 "### Vars specific to NIML I/O ###\n" ,
4016 "###################################\n" ,
4017 "\n" ,
4018 "-----------------------------------\n" ,
4019 "Variable: AFNI_NIML_DEBUG\n" ,
4020 "-----------------------------------\n" ,
4021 "This integer sets the debugging level in some niml I/O routines,\n" ,
4022 "particularly those in thd_niml.c. Currently used values range from 0\n" ,
4023 "to 3.\n" ,
4024 "\n" ,
4025 "-----------------------------------\n" ,
4026 "Variable: AFNI_NSD_ADD_NODES\n" ,
4027 "-----------------------------------\n" ,
4028 "If this YES/NO variable is set to YES, then when a NI_SURF_DSET\n" ,
4029 "dataset is written to disk, if it has no node list attribute, a\n" ,
4030 "default list will be created.\n" ,
4031 "\n" ,
4032 "-----------------------------------\n" ,
4033 "Variable: AFNI_NSD_TO_FLOAT\n" ,
4034 "-----------------------------------\n" ,
4035 "If this YES/NO variable is set to NO, then any necessary conversion of\n" ,
4036 "NI_SURF_DSET datasets to type float will be blocked. Otherwise, all such\n" ,
4037 "datasets will be written as float.\n" ,
4038 "\n" ,
4039 "-----------------------------------\n" ,
4040 "Variable: AFNI_NIML_TEXT_DATA\n" ,
4041 "-----------------------------------\n" ,
4042 "If this YES/NO variable is set to YES, then NI_SURF_DSET datasets will\n" ,
4043 "be written with data in text format. Otherwise, data will be in\n" ,
4044 "binary.\n" ,
4045 "\n" ,
4046 "-----------------------------\n" ,
4047 "Variable: AFNI_SIMPLE_HISTORY\n" ,
4048 "-----------------------------\n" ,
4049 "A few programs (particularly 3dcalc) create a complicated history note\n" ,
4050 "in the output dataset header, by including the history of all inputs.\n" ,
4051 "This history can become inordinately long and pointless when 3calc is\n" ,
4052 "run in a long chain of calculations. Setting this variable to YES\n" ,
4053 "will turn off this cumulation of all histories, and may make your\n" ,
4054 "dataset headers more manageable.\n" ,
4055 "\n" ,
4056 "-------------------------------------------\n" ,
4057 "Variable: AFNI_NIML_BUFSIZE or NIML_BUFSIZE\n" ,
4058 "-------------------------------------------\n" ,
4059 "This variable sets the number of bytes used as a memory buffer for\n" ,
4060 "NIML dataset input. If you are inputting gigantic headers or gigantic\n" ,
4061 "String data components (I'm looking at YOU, Ziad), then you may want\n" ,
4062 "to increase this past its default size of 255*1024=261120.\n" ,
4063 "\n" ,
4064 "###############################\n" ,
4065 "### Vars for 3dDeconvolve ###\n" ,
4066 "###############################\n" ,
4067 "\n" ,
4068 "---------------------------\n" ,
4069 "Variable: AFNI_INDEX_PREFIX\n" ,
4070 "---------------------------\n" ,
4071 "3dDeconvolve and 3dREMLfit create statistics datasets that have sub-brick\n" ,
4072 "labels of the form 'NAME#0_Coef', where 'NAME' is the task name set up\n" ,
4073 "when running the program. This environment variable lets you replace\n" ,
4074 "'#' character with another character; for example (in tcsh):\n" ,
4075 " setenv AFNI_INDEX_PREFIX _\n" ,
4076 "which will create labels of the form 'NAME_0_Coef' instead. The single\n" ,
4077 "character value you supply must be a printable character - not a space,\n" ,
4078 "not a control character, and not the '~' character (which is special).\n" ,
4079 "\n" ,
4080 "Please note that in the future, the default '#' may be replaced by\n" ,
4081 "some other character in the AFNI setup. When that happens, datasets\n" ,
4082 "created after that date will not be exactly compatible (as far as\n" ,
4083 "the sub-brick labels) with datasets created earlier. The purpose of this\n" ,
4084 "environment variable is to allow you to make these programs backward\n" ,
4085 "compatible, if necessary. [11 Jul 2019]\n" ,
4086 "\n" ,
4087 "-----------------------------------\n" ,
4088 "Variable: AFNI_3dDeconvolve_GOFORIT\n" ,
4089 "-----------------------------------\n" ,
4090 "If this variable is set to YES, then 3dDeconvolve behaves as if you\n" ,
4091 "used the '-GOFORIT' option on the command line -- that is, it will\n" ,
4092 "continue to run even if it detects serious non-fatal problems with the\n" ,
4093 "problem setup.\n" ,
4094 "\n" ,
4095 "--------------------------------\n" ,
4096 "Variable: AFNI_3dDeconvolve_NIML\n" ,
4097 "--------------------------------\n" ,
4098 "3dDeconvolve outputs the regression matrix 'X' into a file formatted in\n" ,
4099 "the 'NIML' .1D format -- with an XML-style header in '#' comments at the\n" ,
4100 "start of the file. If you DON'T want this format, just plain numbers,\n" ,
4101 "set this variable to NO.\n" ,
4102 "\n" ,
4103 "----------------------------------\n" ,
4104 "Variable: AFNI_3dDeconvolve_extend\n" ,
4105 "----------------------------------\n" ,
4106 "If you input a stimulus time series (via the -stim_file option) to\n" ,
4107 "3dDeconvolve that is shorter than needed for the regression analysis,\n" ,
4108 "the program will normally print a warning message and extend the time\n" ,
4109 "series with zero values to the needed length. If you would rather\n" ,
4110 "have the program stop if it detects this problem (the behavior before\n" ,
4111 "22 Oct 2003), then set this environment variable to NO.\n" ,
4112 "\n" ,
4113 "---------------------------------\n" ,
4114 "Variable: AFNI_3dDeconvolve_nodup\n" ,
4115 "---------------------------------\n" ,
4116 "If this variable is set to YES, then if the 3dDeconvolve program\n" ,
4117 "detects duplicate input stimulus filenames or duplicate regressors,\n" ,
4118 "the program will fail (with an error message) rather than attempt to\n" ,
4119 "continue.\n" ,
4120 "\n" ,
4121 "-----------------------------------------\n" ,
4122 "Variable: AFNI_3dDeconvolve_nodata_extras\n" ,
4123 "-----------------------------------------\n" ,
4124 "When using the -nodata option in 3dDeconvolve, the default printout\n" ,
4125 "gives the 'normalized standard deviation' for each stimulus parameter.\n" ,
4126 "If you set this variable to YES, then the printout will include the\n" ,
4127 "-polort baseline parameters as well, and also the L2 norm of each\n" ,
4128 "column in the regression matrix.\n" ,
4129 "\n" ,
4130 "-----------------------------------\n" ,
4131 "Variable: AFNI_3dDeconvolve_oneline\n" ,
4132 "-----------------------------------\n" ,
4133 "3dDeconvolve outputs a command line for running the cognate 3dREMLfit\n" ,
4134 "program. By default, this command line is line broken with '\\'\n" ,
4135 "characters for printing beauty. If you want this command line\n" ,
4136 "to be all on one physical output line, for convenience in automatic\n" ,
4137 "extraction (e.g., via grep), then set this variable to YES before\n" ,
4138 "running the program.\n" ,
4139 "\n" ,
4140 "----------------------------------\n" ,
4141 "Variable: AFNI_3dDeconvolve_rawAM2\n" ,
4142 "----------------------------------\n" ,
4143 "Normally, when you use the -stim_times_AM2 option, the regression\n" ,
4144 "against the covariates is 'centered' around the mean of the values\n" ,
4145 "given. If you want the regression to proceed directly with the\n" ,
4146 "covariate values as given, set this option to YES. Please do NOT do\n" ,
4147 "this unless you understand what this means!!!\n" ,
4148 "\n" ,
4149 "--------------------------\n" ,
4150 "Variable: AFNI_XJPEG_COLOR\n" ,
4151 "--------------------------\n" ,
4152 "Determines the color of the lines drawn between the column boxes in\n" ,
4153 "the output from the -xjpeg option to 3dDeconvolve. The color format\n" ,
4154 "is \"rgbi:rf/gf/bf\", where each value rf,gf,bf is a number between 0.0\n" ,
4155 "and 1.0 (inclusive); for example, yellow would be \"rgbi:1.0/1.0/0.0\".\n" ,
4156 "As a special case, if this value is the string \"none\" or \"NONE\", then\n" ,
4157 "these lines will not be drawn.\n" ,
4158 "\n" ,
4159 "-------------------------\n" ,
4160 "Variable: AFNI_XJPEG_IMXY\n" ,
4161 "-------------------------\n" ,
4162 "This variable determines the size of the image saved when via the\n" ,
4163 "-xjpeg option to 3dDeconvolve. It should be in the format AxB, where\n" ,
4164 "'A' is the number of pixels the image is to be wide (across the matrix\n" ,
4165 "rows) and 'B' is the number of pixels high (down the columns); for\n" ,
4166 "example:\n" ,
4167 " setenv AFNI_XJPEG_IMXY 768x1024\n" ,
4168 "which means to set the x-size (horizontal) to 768 pixels and the\n" ,
4169 "y-size (vertical) to 1024 pixels. These values are the default, by\n" ,
4170 "the way.\n" ,
4171 "\n" ,
4172 "If the first value 'A' is negative and less than -1, its absolute\n" ,
4173 "value is the number of pixels across PER ROW. If the second value 'B'\n" ,
4174 "is negative, its absolute value is the number of pixels down PER ROW.\n" ,
4175 "(Usually there are many fewer columns than rows.)\n" ,
4176 "\n" ,
4177 "-------------------------\n" ,
4178 "Variable: AFNI_XSAVE_TEXT\n" ,
4179 "-------------------------\n" ,
4180 "If this YES/NO variable is set to YES, then the .xsave file created by\n" ,
4181 "the \"-xsave\" option to 3dDeconvolve will be saved in text format. The\n" ,
4182 "default is a binary format, which preserves the full accuracy of the\n" ,
4183 "matrices stored therein. However, if you want to look at the .xsave\n" ,
4184 "file yourself, the binary format is hard to grok. Note that the two\n" ,
4185 "forms are not quite equivalent, since the binary format stores the\n" ,
4186 "exact matrices used internally in the program, whereas the ASCII format\n" ,
4187 "stores only a decimal approximation of these matrices.\n" ,
4188 "\n" ,
4189 "---------------------------\n" ,
4190 "Variable: AFNI_GLTSYM_PRINT\n" ,
4191 "---------------------------\n" ,
4192 "If this YES/NO variable is set to YES, then the GLT matrices generated\n" ,
4193 "in 3dDeconvolve by the \"-gltsym\" option will be printed to the screen\n" ,
4194 "when the program starts up.\n" ,
4195 "\n" ,
4196 "-----------------------\n" ,
4197 "Variable: AFNI_FLOATIZE\n" ,
4198 "-----------------------\n" ,
4199 "If this YES/NO variable is set to YES, then 3dDeconvolve and 3dcalc\n" ,
4200 "will write their outputs in floating point format (unless they are\n" ,
4201 "forced to do otherwise with the '-datum short' type of option). In\n" ,
4202 "the future, other programs may also be affected by this variable.\n" ,
4203 "Later [18 Nov 2008]: Now 3dANOVA, 3dANOVA2, and 3dANOVA3 will also\n" ,
4204 "use this flag to determine if their outputs should be written in\n" ,
4205 "float format. For example:\n" ,
4206 " 3dANOVA -DAFNI_FLOATIZE=YES ... other options ...\n" ,
4207 "\n" ,
4208 "----------------------------\n" ,
4209 "Variable: AFNI_AUTOMATIC_FDR\n" ,
4210 "----------------------------\n" ,
4211 "If this variable is set to NO, then the automatic computation of FDR\n" ,
4212 "curves into headers output by 3dDeconvolve, 3dANOVA, 3dttest, and\n" ,
4213 "3dNLfim will NOT be done. Otherwise, the automatic FDR-ization of\n" ,
4214 "these datasets will performed when the datasets are written to disk.\n" ,
4215 "(You can always use '3drefit -addFDR' to add FDR curves to a dataset\n" ,
4216 "header, for those sub-bricks marked as statistical parameters.)\n" ,
4217 "\n" ,
4218 "------------------------------\n" ,
4219 "Variable: AFNI_DONT_ADJUST_FDR\n" ,
4220 "------------------------------\n" ,
4221 "If this variable is set to YES, then the adjustment of FDR q-values\n" ,
4222 "downwards by allowing for the estimate of the number of true\n" ,
4223 "negatives (e.g., as discussed by Storey, Benjamini, and others)\n" ,
4224 "will NOT be carried out. As of 26 Mar 2009, this adjustment of\n" ,
4225 "q-values is the default in AFNI programs. If you want the old\n" ,
4226 "behavior, set this variable to YES.\n" ,
4227 "\n" ,
4228 "----------------------------------\n" ,
4229 "Variable: AFNI_NON_INDEPENDENT_FDR\n" ,
4230 "----------------------------------\n" ,
4231 "If this variable is set to YES, then the FDR calculation is made using\n" ,
4232 "the non-independent assumption, as in the '-cdep' option for program\n" ,
4233 "3dFDR. This setting will affect the calculation of FDR curves via\n" ,
4234 "program 3drefit, et cetera.\n" ,
4235 "\n" ,
4236 "----------------------------\n" ,
4237 "Variable: AFNI_SKIP_SATCHECK\n" ,
4238 "----------------------------\n" ,
4239 "If you want 3dDeconvolve to check the input dataset time series for\n" ,
4240 "initial saturation transients (a somewhat time consuming process),\n" ,
4241 "set this variable to NO. You can also use program 3dSatCheck for\n" ,
4242 "this purpose. Or just look at your data (please!).\n" ,
4243 "\n" ,
4244 "###########################################\n" ,
4245 "### ATLAS and WHEREAMI env variables ###\n" ,
4246 "###########################################\n" ,
4247 "\n" ,
4248 "N.B.: These variables control how AFNI and whereami make use of\n" ,
4249 " various atlases and template spaces. The variables may also\n" ,
4250 " affect how other AFNI programs use atlases as input datasets.\n" ,
4251 "\n" ,
4252 "-------------------------\n" ,
4253 "Variable: AFNI_ATLAS_LIST\n" ,
4254 "-------------------------\n" ,
4255 "This list contains the names of the atlases that should be queried\n" ,
4256 "when no specific atlas has been requested. For example, the afni GUI\n" ,
4257 "and whereami, by default, do not load all the atlases specified in the\n" ,
4258 "AFNI_atlas_spaces.niml file. If this variable is not set, the\n" ,
4259 "TT_Daemon atlas and the cytoarchitectonic Eickhoff-Zilles in MNI_ANAT\n" ,
4260 "space are loaded. If the variable is set to a list like\n" ,
4261 "\"TT_Daemon,DD_Desai_PM\", then only these two atlases are loaded. The\n" ,
4262 "list of atlas names may be separated by commas or semicolons. A\n" ,
4263 "special case of \"ALL\" may be set, and all the available atlases will\n" ,
4264 "be loaded.\n" ,
4265 "\n" ,
4266 "----------------------------------\n" ,
4267 "Variable: AFNI_TEMPLATE_SPACE_LIST\n" ,
4268 "----------------------------------\n" ,
4269 "This list contains the names of the template spaces that are shown\n" ,
4270 "when whereami reports the coordinates among various spaces. By\n" ,
4271 "default, the list contains \"TLRC,MNI,MNI_ANAT\". As with\n" ,
4272 "AFNI_ATLAS_LIST, this list may also be set to \"ALL\".\n" ,
4273 "\n" ,
4274 "----------------------------\n" ,
4275 "Variable: AFNI_ATLAS_COLORS (editable)\n" ,
4276 "----------------------------\n" ,
4277 "This variable sets which atlas to use in the AFNI GUI for \"Atlas\n" ,
4278 "Colors\", \"Go to Atlas location\", \"Draw Dataset\" and \"Renderer\"\n" ,
4279 "functions.\n" ,
4280 "\n" ,
4281 "----------------------------\n" ,
4282 "Variable: AFNI_JUMPTO_SPACE (editable)\n" ,
4283 "----------------------------\n" ,
4284 "This variable sets which space to use in the AFNI GUI for \"Jump to\n" ,
4285 "(spacename)\" function where this would default to \"MNI\". Choose a\n" ,
4286 "valid spacename from the current list of spaces in \"whereami\n" ,
4287 "-show_spaces\". The jump function transforms the user input coordinates\n" ,
4288 "from that space to the space of the dataset.\n" ,
4289 "\n" ,
4290 "----------------------------\n" ,
4291 "Variable: AFNI_ATLAS_PATH\n" ,
4292 "----------------------------\n" ,
4293 "This variable sets which directory or directories to search for AFNI\n" ,
4294 "atlas datasets that have been defined in the AFNI_atlas_spaces.niml or\n" ,
4295 "CustomAtlases.niml file. For all afni programs and scripts that use\n" ,
4296 "atlas and template datasets, the program will preferentially use (in\n" ,
4297 "order) the file path included in the dataset filename definition, the\n" ,
4298 "AFNI_ATLAS_PATH, the AFNI_PLUGINPATH or the standard PATH values.\n" ,
4299 "\n" ,
4300 "-------------------------\n" ,
4301 "Variable: AFNI_PLUGINPATH\n" ,
4302 "-------------------------\n" ,
4303 "Described above, this variable is used for several purposes. For\n" ,
4304 "whereami, this variable sets the directory to load atlases and NIML\n" ,
4305 "files if not in the current directory. If this variable does not exist\n" ,
4306 "or the referred file does not exist, then the atlas is searched in the\n" ,
4307 "user's current PATH setting. If this is set, atlases will be found\n" ,
4308 "more quickly than searching all the directories of the entire\n" ,
4309 "PATH. Searches of the PATH variable for whereami usage stop at the\n" ,
4310 "first occurrence of the searched file, so placing the AFNI directory\n" ,
4311 "earlier in the PATH will dramatically increase the speed that the file\n" ,
4312 "is found.\n" ,
4313 "\n" ,
4314 "----------------------------------\n" ,
4315 "Variable: AFNI_WHEREAMI_DEC_PLACES (editable)\n" ,
4316 "----------------------------------\n" ,
4317 "Sets precision for whereami output. Higher field data and animal\n" ,
4318 "atlases require higher precision. The default value used for focus\n" ,
4319 "point among template spaces is still 0 decimal places (closest mm),\n" ,
4320 "but animal data requires three decimal places. Value may range from 0\n" ,
4321 "to 10.\n" ,
4322 "\n" ,
4323 "-------------------------\n" ,
4324 "Variable: AFNI_WAMI_DEBUG\n" ,
4325 "-------------------------\n" ,
4326 "This variable controls the output of detailed messages about various\n" ,
4327 "tasks involved in loading atlases, transformations and composing query\n" ,
4328 "results. By default, this information is not shown. This integer sets\n" ,
4329 "the debugging level in whereami routines. Currently used values range\n" ,
4330 "from 0 to 3.\n" ,
4331 "\n" ,
4332 "------------------------------\n" ,
4333 "Variable: AFNI_TTATLAS_DATASET\n" ,
4334 "------------------------------\n" ,
4335 "This variable may also specify the default location of AFNI atlases. This\n" ,
4336 "variable is maintained mostly for backward compatibility. By default, this\n" ,
4337 "is not set.\n" ,
4338 "\n" ,
4339 "-------------------------------\n" ,
4340 "Variable: AFNI_WHEREAMI_NO_WARN\n" ,
4341 "-------------------------------\n" ,
4342 "Turns off warnings about various whereami features - like queries that\n" ,
4343 "have reached their limit of returned results. By default, warnings are\n" ,
4344 "displayed only the first time a particular message is encountered.\n" ,
4345 "\n" ,
4346 "--------------------------------\n" ,
4347 "Variable: AFNI_WHEREAMI_MAX_FIND (editable)\n" ,
4348 "--------------------------------\n" ,
4349 "By default, only the first nine structures are displayed within a\n" ,
4350 "particular atlas. You may increase or decrease this to show more or\n" ,
4351 "fewer structures in the whereami results.\n" ,
4352 "\n" ,
4353 "-------------------------------\n" ,
4354 "Variable: AFNI_WHEREAMI_MAX_SEARCH_RAD (editable)\n" ,
4355 "-------------------------------\n" ,
4356 "\n" ,
4357 "By default, whereami searches a radius of 7.5 mm. Set a radius up to\n" ,
4358 "9.5 mm.\n" ,
4359 "\n" ,
4360 "-------------------------------\n" ,
4361 "Variable: AFNI_WHEREAMI_PROB_MIN\n" ,
4362 "-------------------------------\n" ,
4363 "Minimum probability AFNI considers in probabilistic atlases\n" ,
4364 "\n" ,
4365 "--------------------------------\n" ,
4366 "Variable: AFNI_DEFAULT_STD_SPACE\n" ,
4367 "--------------------------------\n" ,
4368 "The default template space is assumed to be TLRC. This is used for\n" ,
4369 "coordinate input to whereami, the whereami GUI and for TLRC view\n" ,
4370 "datasets without a template space explicitly set in the dataset\n" ,
4371 "header.\n" ,
4372 "\n" ,
4373 "--------------------------------\n" ,
4374 "Variable: AFNI_NIFTI_VIEW\n" ,
4375 "--------------------------------\n" ,
4376 "The default view extension used for output when creating AFNI format\n" ,
4377 "datasets from NIFTI datasets.This variable is only applicable for\n" ,
4378 "sform and qform codes that do not have clearly defined views\n" ,
4379 "(sform/qform code = 2). Set to \"tlrc\" or \"orig\". See also\n" ,
4380 "AFNI_DEFAULT_STD_SPACE and AFNI_NIFTI_PRIORITY. Note sform/qform code=5\n" ,
4381 "can be used for spaces other than MNI or TLRC including MNI_ANAT or D99\n" ,
4382 "spaces.\n" ,
4383 "\n" ,
4384 "--------------------------------\n" ,
4385 "Variable: AFNI_NIFTI_PRIORITY\n" ,
4386 "--------------------------------\n" ,
4387 "Sets preference for NIFTI files to use sform or qform codes and\n" ,
4388 "matrices to determine space, origin and orientation. Set to 'S' or 'Q'\n" ,
4389 "for sform or qform respectively. If not set, NIFTI files are read\n" ,
4390 "using the non-zero form code or the sform code if both are set.\n" ,
4391 "\n" ,
4392 "-------------------------------------------\n" ,
4393 "Variable: AFNI_SUPP_ATLAS, AFNI_LOCAL_ATLAS\n" ,
4394 "-------------------------------------------\n" ,
4395 "These variables allow the addition of more atlas definitions to the\n" ,
4396 "global list of atlases, templates, spaces and transformations. The\n" ,
4397 "variable should be set to the name of a NIML file with the same format\n" ,
4398 "of the AFNI_atlas_spaces.niml file. These can be customized by site\n" ,
4399 "(supplemental) or by subject (local) and follow the same search order\n" ,
4400 "as the AFNI_atlas_spaces.niml file. In order to be included in default\n" ,
4401 "searches, additional atlases or template spaces would also need to be\n" ,
4402 "added to AFNI_ATLAS_SPACE_LIST and the AFNI_TEMPLATE_SPACE_LIST,\n" ,
4403 "unless those are set to \"ALL\".\n" ,
4404 "\n" ,
4405 "-------------------------------------------\n" ,
4406 "Variable: AFNI_SUPP_ATLAS_DIR\n" ,
4407 "-------------------------------------------\n" ,
4408 "Allows the addition of atlas definitions to the global list of\n" ,
4409 "atlases, templates,spaces and transformations. The variable should be\n" ,
4410 "set to the name of a directory that contains a SessionAtlases.niml\n" ,
4411 "file with the same format as the AFNI_atlas_spaces.niml file. Also see\n" ,
4412 "AFNI_SUPP_ATLAS, AFNI_LOCAL_ATLAS, AFNI_ATLAS_SPACE_LIST,\n" ,
4413 "AFNI_TEMPLATE_SPACE_LIST.\n" ,
4414 "\n" ,
4415 "------------------------------\n" ,
4416 "Variable: AFNI_TTATLAS_CAUTION (editable)\n" ,
4417 "------------------------------\n" ,
4418 "If this YES/NO variable is set to NO, then the warning about the\n" ,
4419 "potential errors in the \"Where am I?\" popup will not appear. (This is\n" ,
4420 "purely for cosmetic purposes, Ziad.)\n" ,
4421 "\n" ,
4422 "-------------------------------\n" ,
4423 "Variable: AFNI_TTATLAS_FONTSIZE (editable)\n" ,
4424 "-------------------------------\n" ,
4425 "If this variable is not set, the default font size is used in the\n" ,
4426 "'Where am I?' popup window.\n" ,
4427 "If this variable is set to 'BIG', then a larger font size is used.\n" ,
4428 "\n" ,
4429 "-------------------------------\n" ,
4430 "Variable: AFNI_ATLAS_NAME_TYPE\n" ,
4431 "-------------------------------\n" ,
4432 "Atlas region labels can be shown as either as a short name or with a\n" ,
4433 "longer, more descriptive name. Note that most atlases have only the\n" ,
4434 "short name available. The whereami GUI and command line can show either\n" ,
4435 "or both labels with this variable set to \"longname\", \"both\" or \"name\",\n" ,
4436 "where \"name\" is only the short, standard version. The overlay panel\n" ,
4437 "and image viewers can show this label too. The names are separated by\n" ,
4438 "a vertical pipe symbol if both are in the atlas header.\n" ,
4439 "The default is to show both names if they are available.\n" ,
4440 "\n" ,
4441 "-------------------------\n" ,
4442 "Variable: AFNI_WEBBY_WAMI\n" ,
4443 "-------------------------\n" ,
4444 "When set to YES, the Where Am I GUI becomes 'web-enabled', i.e. the\n" ,
4445 "report becomes clickable to open web pages from the output. Most\n" ,
4446 "features are still experimental. See AFNI_NEUROSYNTH and AFNI_SUMSDB\n" ,
4447 "below for examples. The default value is 'NO'.\n" ,
4448 "\n" ,
4449 "-------------------------\n" ,
4450 "Variable: AFNI_NEUROSYNTH\n" ,
4451 "-------------------------\n" ,
4452 "When set to YES, provides link for MNI coordinate in Where Am I GUI to\n" ,
4453 "the Neurosynth site. Requires AFNI_WEBBY_WAMI to also be set to\n" ,
4454 "YES. The default value is 'NO'.\n" ,
4455 "\n" ,
4456 "---------------------\n" ,
4457 "Variable: AFNI_SUMSDB\n" ,
4458 "---------------------\n" ,
4459 "When set to YES, provides link for MNI coordinate in Where Am I GUI to\n" ,
4460 "the SumsDB site. Requires AFNI_WEBBY_WAMI to also be set to YES. The\n" ,
4461 "default value is 'NO'.\n" ,
4462 "\n" ,
4463 "#####################################################\n" ,
4464 "### Interacting with other progs and miscellany ###\n" ,
4465 "#####################################################\n" ,
4466 "\n" ,
4467 "-------------------------------\n" ,
4468 "Variable: AFNI_NO_OPTION_HINT\n" ,
4469 "-------------------------------\n" ,
4470 "If this variable is set, do NOT make suggestions if a program parsing\n" ,
4471 "error is encountered.\n" ,
4472 "\n" ,
4473 "--------------------------\n" ,
4474 "Variable: AFNI_GUI_EDITOR\n" ,
4475 "--------------------------\n" ,
4476 "Set this variable to your favorite GUI text editor.\n" ,
4477 "\n" ,
4478 "----------------------------\n" ,
4479 "Variable: AFNI_IMAGE_VIEWER\n" ,
4480 "----------------------------\n" ,
4481 "Set this variable to your favorite image viewer.\n" ,
4482 "\n" ,
4483 "----------------------------\n" ,
4484 "Variable: AFNI_PDF_VIEWER\n" ,
4485 "----------------------------\n" ,
4486 "Set this variable to your favorite pdf viewer.\n" ,
4487 "\n" ,
4488 "------------------------------------\n" ,
4489 "Variable: AFNI_LOG_BEST_PROG_OPTION\n" ,
4490 "------------------------------------\n" ,
4491 "If set to YES, allow approximate searching functions to log their\n" ,
4492 "behavior in a file named ~/.afni/help/aps.log.txt\n" ,
4493 "\n" ,
4494 "------------------------------------\n" ,
4495 "Variable: AFNI_HISTDB_SCRIPT\n" ,
4496 "------------------------------------\n" ,
4497 "If set to a non-empty string, an attribute called HISTDB_SCRIPT is\n" ,
4498 "added to the header of AFNI datasets at write time. The value of the\n" ,
4499 "attribute is that of the variable AFNI_HISTDB_SCRIPT.\n" ,
4500 "At the moment, this variable is solely for Tom Ross's nefarious\n" ,
4501 "history databasing schemes.\n" ,
4502 "\n" ,
4503 "------------------------------------\n" ,
4504 "Variable: AFNI_ICORR_UBER_USER\n" ,
4505 "------------------------------------\n" ,
4506 "If set to YES, enable distance measures that are not ready for prime\n" ,
4507 "time in the instacorr interface.\n" ,
4508 NULL } ;
4509 #define NUM_readme_env 4505
4510