static char * readme_env[] = {
"Unix Environment Variables Used by AFNI\n" ,
"=======================================\n" ,
"The AFNI program allows you to use several Unix environment variables\n" ,
"to influence its behavior. The mechanics of setting an environment\n" ,
"variable depend on which shell you are using. To set an environment\n" ,
"variable named \"FRED\" to the string \"Elvis\":\n" ,
"\n" ,
" csh or tcsh: setenv FRED Elvis\n" ,
" bash or ksh: FRED=Elvis ; export FRED\n" ,
"\n" ,
"Normally, these commands would go in your .cshrc or .profile files,\n" ,
"so that they would be invoked when you login. If in doubt, consult\n" ,
"your local Unix guru. If you don't have one, well....\n" ,
"\n" ,
"You don't NEED to set any of these variables -- AFNI will still work\n" ,
"correctly. But they are an easy way to set up certain defaults to\n" ,
"make AFNI a little easier on your neocortex and hippocampus.\n" ,
"\n" ,
"N.B.: Changes to environment variables AFTER you start a program will\n" ,
" not be seen by that program, since each running program gets\n" ,
" a private copy of the entire set of environment variables when\n" ,
" it starts. This is a standard Unix feature, and is not specific\n" ,
" to AFNI. Some variables can be set internally in AFNI using\n" ,
" the \"Edit Environment\" control from the \"Datamode->Misc\" menu\n" ,
" or from the image window Button-3 popup menu. Such variables\n" ,
" are marked with \"(editable)\" in the descriptions below.\n" ,
"\n" ,
"N.B.: Some variables below are described as being of \"YES/NO\" type.\n" ,
" This means that they should either be set to the value \"YES\"\n" ,
" or to the value \"NO\".\n" ,
"\n" ,
"N.B.: You can now set environment variables on the 'afni' command\n" ,
" line; for example:\n" ,
" afni -DAFNI_EDGIZE_OVERLAY=YES -DAFNI_SESSTRAIL=3\n" ,
" This may be useful for a 'one time' situation, or as an alias.\n" ,
" -- RWCox - 22 Mar 2005\n" ,
"\n" ,
"N.B.: At the end of this file is a list of several environment variables\n" ,
" that affect the program 3dDeconvolve, rather than the interactive\n" ,
" AFNI program itself.\n" ,
"\n" ,
"********************************************************\n" ,
"June 1999: Setting environment variables in file .afnirc\n" ,
"********************************************************\n" ,
"You can now set environment variables for an interactive AFNI run in the\n" ,
"setup (.afnirc) file. This is provided as a convenience. An example:\n" ,
"\n" ,
"***ENVIRONMENT\n" ,
" AFNI_HINTS = YES\n" ,
" AFNI_SESSTRAIL = 3\n" ,
"\n" ,
"Note that the spaces around the \"=\" sign are required. See README.setup\n" ,
"for more information about the possible contents of .afnirc besides the\n" ,
"environment variables.\n" ,
"\n" ,
"A few other programs in the AFNI package also read the ***ENVIRONMENT\n" ,
"section of the .afnirc file. This is needed so that environment settings\n" ,
"that affect those programs (e.g., AFNI_COMPRESSOR for auto-compression of\n" ,
"output datasets) can be properly initialized in .afnirc.\n" ,
"\n" ,
"At the same time, the routine in AFNI that initializes certain internal\n" ,
"constants from X11 resources (usually in your .Xdefaults or .Xresources\n" ,
"file, and described in file AFNI.Xdefaults) has been modified to also\n" ,
"allow the same constants to be set from Unix environment variables.\n" ,
"For example, the gap (in pixels) between sub-graphs is set by the\n" ,
"X11 resource \"AFNI*graph_ggap\", and can now be set by the environment\n" ,
"variables \"AFNI_graph_ggap\" or \"AFNI_GRAPH_GGAP\", as in\n" ,
"\n" ,
" AFNI_graph_ggap = 6 // this is a comment\n" ,
"\n" ,
"If an X11 resource is actually set, it will take priority over the\n" ,
"environment variable. Some of the variables that can be set in this\n" ,
"way are:\n" ,
"\n" ,
" AFNI_ncolors = number of gray levels to use\n" ,
" AFNI_gamma = gamma correction for image intensities\n" ,
" AFNI_graph_boxes_thick = 0=thin lines, 1=thick lines, for graph boxes\n" ,
" AFNI_graph_grid_thick = ditto for the graph vertical grid lines\n" ,
" AFNI_graph_data_thick = ditto for the data graphs\n" ,
" AFNI_graph_ideal_thick = ditto for the ideal graphs\n" ,
" AFNI_graph_ort_thick = ditto for the ort graphs\n" ,
" AFNI_graph_dplot_thick = ditto for the dplot graphs\n" ,
" AFNI_graph_ggap = initial spacing between graph boxes\n" ,
" AFNI_graph_matrix = initial number of sub-graphs\n" ,
" AFNI_fim_polort = polynomial detrending order for FIM\n" ,
" AFNI_fim_ignore = how many pts to ignore at start when doing FIM\n" ,
" AFNI_montage_periodic = True allows periodic montage wraparound\n" ,
" AFNI_purge = True allows automatic dataset memory purge\n" ,
" AFNI_resam_vox = dimension of voxel (mm) for resampled datasets\n" ,
" AFNI_resam_anat = One of NN, Li, Cu, Bk for Anat resampling mode\n" ,
" AFNI_resam_func = ditto for Func resampling mode\n" ,
" AFNI_resam_thr = ditto for Threshold resampling mode\n" ,
" AFNI_pbar_posfunc = True will start color pbar as all positive\n" ,
" AFNI_pbar_sgn_pane_count = # of panes to start signed color pbar with\n" ,
" AFNI_pbar_pos_pane_count = # of panes to start positive color pbar with\n" ,
"\n" ,
"Some other such variables are described in file AFNI.Xdefaults. Note that\n" ,
"values that actually affect the way the X11/Motif interface appears, such as\n" ,
"AFNI*troughColor, must be set via the X11 mechanism and cannot be set using\n" ,
"Unix environment variables. This is because they are interpreted by the\n" ,
"Motif graphics library when it starts and not by any actual AFNI code.\n" ,
"\n" ,
"The following example is from my own .afnirc file on the Linux system on\n" ,
"which I do most of the AFNI development. The first ones (in lower case)\n" ,
"are described in AFNI.Xdefaults. The later ones (all upper case) are\n" ,
"documented in this file. (You can tell from this file that I like to\n" ,
"have things line up. You would never be able to tell this from the\n" ,
"piles of paper in my office, though.)\n" ,
"\n" ,
" ***ENVIRONMENT\n" ,
"\n" ,
" AFNI_ncolors = 60 // number of gray levels\n" ,
" AFNI_gamma = 1.5 // adjust for proper display\n" ,
" AFNI_purge = True // purge datasets from memory when not used\n" ,
" AFNI_chooser_doubleclick = Apply // like Apply button; could also be Set\n" ,
" AFNI_chooser_listmax = 25 // max nonscrolling items in chooser lists\n" ,
" AFNI_graph_width = 512 // initial width of graph window (pixels)\n" ,
" AFNI_graph_height = 384 // initial height of graph window\n" ,
" AFNI_graph_data_thick = 1 // graph time series with thick lines\n" ,
" AFNI_fim_ignore = 2 // default value for FIM ignore\n" ,
" AFNI_graph_ggap = 7 // gap between sub-graphs (pixels)\n" ,
" AFNI_pbar_hide = True // hide color pbar when it changes size\n" ,
" AFNI_hotcolor = Violet // color to use on Done and Set buttons\n" ,
" AFNI_SESSTRAIL = 2 // see below for these ...\n" ,
" AFNI_RENDER_ANGLE_DELTA = 4.0 // |\n" ,
" AFNI_RENDER_CUTOUT_DELTA = 4.0 // |\n" ,
" AFNI_FIM_BKTHR = 25.0 // |\n" ,
" AFNI_SPLASHTIME = 3.0 // v\n" ,
"\n" ,
"------------------------------------\n" ,
"Variable: AFNI_DONT_SORT_ENVIRONMENT\n" ,
"------------------------------------\n" ,
"If this YES/NO variable is YES, then the Edit Environment controls will\n" ,
"NOT be sorted alphabetically. The default action is to sort them\n" ,
"alphabetically. If they are unsorted, the editable environment variables\n" ,
"will appear in the control panel in the order in which they were added to\n" ,
"the code (that is, in an order that makes no real sense).\n" ,
"\n" ,
"---------------------\n" ,
"Variable: AFNI_ORIENT (editable)\n" ,
"---------------------\n" ,
"This is a string used to control the display of coordinates in the AFNI\n" ,
"main control window. The string must be 3 letters, one each from the\n" ,
"pairs {R,L} {A,P} {I,S}. The first letter in the string gives the\n" ,
"orientation of the x-axis, the second the orientation of the y-axis,\n" ,
"the third the z-axis:\n" ,
"\n" ,
" R = right-to-left L = left-to-right\n" ,
" A = anterior-to-posterior P = posterior-to-anterior\n" ,
" I = inferior-to-superior S = superior-to-inferior\n" ,
"\n" ,
"If AFNI_ORIENT is undefined, the default is RAI. This is the order\n" ,
"used by DICOM, and means\n" ,
"\n" ,
" the -x axis is Right, the +x axis is Left,\n" ,
" the -y axis is Anterior, the +y axis is Posterior,\n" ,
" the -z axis is Inferior, the +z axis is Superior.\n" ,
"\n" ,
"As a special case, using the code 'flipped' is equivalent to 'LPI',\n" ,
"which is the orientation used in many neuroscience journals.\n" ,
"\n" ,
"This variable is also recognized by program 3dclust, which will report\n" ,
"the cluster coordinates in the (x,y,z) order given by AFNI_ORIENT.\n" ,
"Both AFNI and 3dclust also recognize the command line switch\n" ,
"\"-orient string\", where string is a 3 letter code that can be used\n" ,
"to override the value of AFNI_ORIENT.\n" ,
"\n" ,
"The plugin \"Coord Order\" (plug_coord.c) allows you to interactively\n" ,
"change the orientation of the variable display within AFNI.\n" ,
"\n" ,
"-------------------------\n" ,
"Variable: AFNI_PLUGINPATH\n" ,
"-------------------------\n" ,
"This variable should be the directory in which AFNI should search\n" ,
"for plugins. If there is more than one appropriate directory, they\n" ,
"can be separated by colons, as in\n" ,
"\n" ,
" setenv AFNI_PLUGINPATH /directory/one:/directory/two\n" ,
"\n" ,
"If this variable is not set, then AFNI will use the PATH variable\n" ,
"instead. This will waste time, since most directories in the PATH\n" ,
"will not have plugins. On some systems, using the PATH has been\n" ,
"known to cause problems when AFNI starts. I believe this is due to\n" ,
"bugs in the system library routines (e.g., dlopen) used to manage\n" ,
"dynamically loaded shared objects.\n" ,
"\n" ,
"------------------------\n" ,
"Variable: AFNI_NOPLUGINS\n" ,
"------------------------\n" ,
"If this YES/NO variable is set to YES, then AFNI will not try to\n" ,
"read plugins when it starts up. The command line switch \"-noplugins\"\n" ,
"will have the same effect.\n" ,
"\n" ,
"--------------------------\n" ,
"Variable: AFNI_YESPLUGOUTS\n" ,
"--------------------------\n" ,
"If this YES/NO variable is set to YES, then AFNI will try to listen\n" ,
"for plugouts when it starts. The command line switch \"-yesplugouts\"\n" ,
"will have the same effect. (Plugouts are an experimental feature\n" ,
"that allow external programs to exchange data with AFNI.) It is now\n" ,
"also possible to start plugout listening from the Datamode->Misc menu.\n" ,
"\n" ,
"---------------------\n" ,
"Variable: AFNI_TSPATH\n" ,
"---------------------\n" ,
"This variable should be set to any directory which you want to have\n" ,
"AFNI scan for timeseries files (*.1D -- see the AFNI manual). If\n" ,
"more than one directory is desired, then colons can be used to\n" ,
"separate them, as in AFNI_PLUGINPATH. Note that timeseries files\n" ,
"are read from all session directories, so directories provided by\n" ,
"AFNI_TSPATH are designed to contain extra timeseries files that\n" ,
"you want loaded no matter what AFNI sessions and datasets are being\n" ,
"viewed.\n" ,
"\n" ,
"------------------------\n" ,
"Variable: AFNI_MODELPATH\n" ,
"------------------------\n" ,
"This variable should be set to the directory from which you want AFNI\n" ,
"timeseries models to be loaded. These models are similar to plugins,\n" ,
"and are used by programs 3dNLfim, 3dTSgen, and the plugin plug_nlfit\n" ,
"(menu label \"NLfit & NLerr\") -- see documentation file 3dNLfim.ps.\n" ,
"If AFNI_MODELPATH is not given, then AFNI_PLUGINPATH will be used\n" ,
"instead.\n" ,
"\n" ,
"-----------------------------------------\n" ,
"Variable: AFNI_IMSIZE_* (or MCW_IMSIZE_*)\n" ,
"-----------------------------------------\n" ,
"These variables (named AFNI_IMSIZE_1 to AFNI_IMSIZE_99) allow you\n" ,
"to control how the AFNI programs read binary image files. The use of\n" ,
"these is somewhat complicated, and is explained in detail at the end\n" ,
"of the auxiliary programs manual (afni_aux.ps), in the section on \"3D:\"\n" ,
"file specifications, and is also explained in the AFNI FAQ list.\n" ,
"\n" ,
"------------------------\n" ,
"Variable: AFNI_SESSTRAIL (editable)\n" ,
"------------------------\n" ,
"This variable controls the number of directory levels shown when\n" ,
"choosing between session directories with the \"Switch Session\"\n" ,
"button. This variable should be set to a nonnegative integer.\n" ,
"If a session directory name were\n" ,
" this/is/a/directory/name/\n" ,
"then the \"Switch Session\" chooser would display the following:\n" ,
"\n" ,
" AFNI_SESSTRAIL Display\n" ,
" -------------- -------\n" ,
" 0 name/\n" ,
" 1 directory/name/\n" ,
" 2 a/directory/name/\n" ,
" 3 is/a/directory/name/\n" ,
" 4 this/is/a/directory/name/\n" ,
"\n" ,
"That is, AFNI_SESSTRAIL determines how many trailing levels of\n" ,
"the directory name are used for the display. If AFNI_SESSTRAIL\n" ,
"is not set, then it is equivalent to setting it to 0 (which\n" ,
"was the old method).\n" ,
"\n" ,
"--------------------\n" ,
"Variable: AFNI_HINTS\n" ,
"--------------------\n" ,
"This is a string controlling whether or not the popup \"hints\" are\n" ,
"displayed when AFNI starts. If the string is \"NO\", then the hints\n" ,
"are disabled when AFNI starts, otherwise they are enabled. In\n" ,
"either case, they can be turned off and on interactively from the\n" ,
"Define Datamode->Misc menu.\n" ,
"\n" ,
"Hints can be permanently disabled by setting the C macro\n" ,
"DONT_USE_HINTS in machdep.h and recompiling AFNI. They can also\n" ,
"be disabled at runtime by setting AFNI_HINTS to \"KILL\".\n" ,
"\n" ,
"-------------------------\n" ,
"Variable: AFNI_COMPRESSOR (cf. AFNI_AUTOGZIP) (editable)\n" ,
"-------------------------\n" ,
"This variable is used to control automatic compression of .BRIK files on\n" ,
"output. The legal values are \"COMPRESS\", \"GZIP\", and \"BZIP2\", which\n" ,
"respectively invoke programs \"compress\", \"gzip\", and \"bzip2\" (the program\n" ,
"must be in your path for compression to work). If AFNI_COMPRESSOR is\n" ,
"equal to one of these, then all AFNI programs will automatically pass\n" ,
".BRIK data through the appropriate compression program as it is written\n" ,
"to disk. Note that this will slow down dataset write operations. Note\n" ,
"also that compressed datasets cannot be mapped directly from disk into\n" ,
"memory ('mmap'), but must occupy actual memory (RAM) and swap space. For\n" ,
"more details, see file README.compression.\n" ,
"\n" ,
"Note that compressed (.BRIK.Z, .BRIK.gz, and .BRIK.bz2) datasets will\n" ,
"automatically be uncompressed on input, no matter what the setting of\n" ,
"this variable. AFNI_COMPRESSOR only controls how the datasets are\n" ,
"written.\n" ,
"\n" ,
"------------------------\n" ,
"Variable: AFNI_BYTEORDER\n" ,
"------------------------\n" ,
"This variable is used to control the byte order for output files.\n" ,
"If you use it, the two legal values are \"LSB_FIRST\" and \"MSB_FIRST\".\n" ,
"If you don't use it, the default order on your CPU will be used.\n" ,
"The main purpose of this would be if you were using a mixture of\n" ,
"CPU types reading shared disks (i.e., using NFS). If the majority\n" ,
"of the systems were MSB_FIRST (e.g., SGI, HP, Sun), but there were\n" ,
"a few LSB_FIRST systems (e.g., Intel, DEC Alpha), then you might\n" ,
"want to do 'setenv AFNI_BYTEORDER MSB_FIRST' on all of the MSB_FIRST\n" ,
"systems to make sure that the datasets that they write out are\n" ,
"readable by the other computers.\n" ,
"\n" ,
"Note that AFNI programs can now check the .HEAD file for the byte\n" ,
"order of a dataset, and will swap the bytes on input, if needed.\n" ,
"If you wish to mark all of the datasets on a given system as\n" ,
"being in a particular order, the following command should work:\n" ,
"\n" ,
" find /top/dir -name \\*.HEAD -exec 3drefit -byteorder NATIVE_ORDER {} \\;\n" ,
"\n" ,
"Here, '/top/dir' is the name of the top level directory under\n" ,
"which you wish to search for AFNI datasets. The string NATIVE_ORDER\n" ,
"means to set all datasets to the CPU default order, which is probably\n" ,
"what you are using now. (You can use the program 'byteorder' to\n" ,
"find out the native byte ordering of your CPU.)\n" ,
"\n" ,
"------------------------------\n" ,
"Variable: AFNI_BYTEORDER_INPUT\n" ,
"------------------------------\n" ,
"This variable is used to control the byte order for input files.\n" ,
"If you use it, the two legal values are \"LSB_FIRST\" and \"MSB_FIRST\".\n" ,
"The value of this variable is only used for old datasets that do\n" ,
"not have the byte order encoded in their headers. If this variable\n" ,
"is not present, then the CPU native byte order is used. If this\n" ,
"variable is present, and its value differs from the native byte\n" ,
"order, then 2 byte dataset BRIKs (short) are 2-swapped (as in\n" ,
"\"ab\" -> \"ba\") when they are read from disk, and 4 byte datasets\n" ,
"(float, complex) are 4-swapped (\"abcd\" -> \"dcba\").\n" ,
"\n" ,
"[per the request of John Koger]\n" ,
"\n" ,
"---------------------\n" ,
"Variable: AFNI_NOMMAP\n" ,
"---------------------\n" ,
"This YES/NO variable can be used to turn off the mmap feature by which\n" ,
"AFNI can load datasets into memory using the map-file-to-memory\n" ,
"functionality of Unix. (Dataset .BRIK files will only be mmap-ed if\n" ,
"they are not compressed and are in the native byte order of the CPU.)\n" ,
"On some systems, mmap doesn't seem to work very well (e.g., Linux kernel\n" ,
"version 1.2.13). You can disable mmap by 'setenv AFNI_NOMMAP YES'.\n" ,
"\n" ,
"The penalty for disabling mmap is that all datasets must be loaded\n" ,
"into actual RAM. AFNI does not have the ability to load a dataset\n" ,
"only partially, so if a 20 Megabyte .BRIK file is accessed, all of\n" ,
"it will be loaded into RAM. With mmap, the Unix operating system will\n" ,
"decide how much of the file to load. In this way, it is possible to\n" ,
"deal with more files than you have swap space on your computer\n" ,
"(since .BRIK files are mmap-ed in readonly mode).\n" ,
"\n" ,
"The moral of the story: buy more memory, it's cheap. At the time\n" ,
"I write this line [Aug 1998], I have a PC with 384 MB of RAM, and\n" ,
"it is great to use with AFNI.\n" ,
"\n" ,
"[Feb 2004] I now have a Mac G5 with 8 GB of RAM, and it is even greater!\n" ,
"\n" ,
"----------------------\n" ,
"Variable: AFNI_PSPRINT (editable)\n" ,
"----------------------\n" ,
"This variable is used to define a command that will print the\n" ,
"standard input (stdin) to a PostScript printer. If it is defined,\n" ,
"the \"->printer\" button on the timeseries \"Plot\" windows will work.\n" ,
"For some Unix systems, the following should work:\n" ,
" setenv AFNI_PSPRINT \"lp -\"\n" ,
"For others, this may work\n" ,
" setenv AFNI_PSPRINT \"lpr -\"\n" ,
"It all depends on the printer software setup you have. To send the\n" ,
"output into GhostView\n" ,
" setenv AFNI_PSPRINT \"ghostview -landscape -\"\n" ,
"\n" ,
"In the (very far distant) future, other windows (e.g., image and graph\n" ,
"displays) may get the ability to print to a PostScript file or printer.\n" ,
"\n" ,
"---------------------------\n" ,
"Variable: AFNI_LEFT_IS_LEFT (editable)\n" ,
"---------------------------\n" ,
"Setting this YES/NO variable to YES tells AFNI to display images with\n" ,
"the left side of the subject on the left side of the window. The default\n" ,
"mode is to display the right side of the subject on the left side of\n" ,
"the window - the radiology convention. This \"handedness\" can also be\n" ,
"controlled with the \"-flipim\" and \"-noflipim\" command line options to AFNI.\n" ,
"\n" ,
"--------------------------\n" ,
"Variable: AFNI_ALWAYS_LOCK\n" ,
"--------------------------\n" ,
"Setting this YES/NO variable to YES tells AFNI to start up with all\n" ,
"the controller windows locked together. If you mostly use multiple\n" ,
"controllers to view datasets in unison, then this will be useful.\n" ,
"Notice that the Time Lock feature is not automatically enabled\n" ,
"by this -- you must still actuate it manually from the Lock menu\n" ,
"on the Define Datamode panel.\n" ,
"\n" ,
"------------------------\n" ,
"Variables: AFNI_RENDER_* (editable)\n" ,
"------------------------\n" ,
"These variables set some defaults in the \"Render Dataset\" (volume\n" ,
"rendering) plugin. The first two variables are\n" ,
"\n" ,
" AFNI_RENDER_ANGLE_DELTA = stepsize for viewing angles, in degrees\n" ,
" AFNI_RENDER_CUTOUT_DELTA = stepsize for cutout dimensions, in mm\n" ,
"\n" ,
"These stepsizes control how much the control parameters change when\n" ,
"one of their up- or down-arrows is pressed. Both of these stepsize\n" ,
"values default to 5.0.\n" ,
"\n" ,
"The third variable is\n" ,
"\n" ,
" AFNI_RENDER_PRECALC_MODE = \"Low\", \"Medium\", or \"High\"\n" ,
"\n" ,
"This is used to set the initial precalculation mode for the renderer\n" ,
"(this mode can be altered interactively, unlike the stepsizes).\n" ,
"\n" ,
"The fourth variable is\n" ,
"\n" ,
" AFNI_RENDER_SHOWTHRU_FAC = some number between 0.0 and 1.0\n" ,
"\n" ,
"This is used to control the way in which the \"ShowThru\" Color Opacity\n" ,
"option renders images. See the rendering plugin Help window for more\n" ,
"information.\n" ,
"\n" ,
"-------------------------\n" ,
"Variable: AFNI_NOREALPATH\n" ,
"-------------------------\n" ,
"Normally, when AFNI reads a list of session directories, it converts\n" ,
"their names to the \"real path\" form, which follows symbolic links, and\n" ,
"removes '/./' and '/../' components. These converted names are used\n" ,
"for display purposes in the \"Switch Session\" chooser and in other\n" ,
"places. If you wish to have the names NOT converted to the \"real path\"\n" ,
"format, set this YES/NO environment variable to YES, as in\n" ,
"\n" ,
" setenv AFNI_NOREALPATH YES\n" ,
"\n" ,
"(For more information on the \"real path\" conversion, see the Unix\n" ,
"man page for the realpath() function.) Note that if you use this\n" ,
"feature, then the effect of AFNI_SESSTRAIL will be limited to what\n" ,
"you type on the command line, since it is the realpath() function\n" ,
"that provides the higher level hierarchies of the session names.\n" ,
"\n" ,
"----------------------------\n" ,
"Variable: AFNI_NO_MCW_MALLOC\n" ,
"----------------------------\n" ,
"AFNI uses a set of \"wrapper\" macros and functions to let itself keep\n" ,
"track of the memory allocated and freed by the C malloc() library.\n" ,
"This is useful for debugging purposes (see the last items on the 'Misc'\n" ,
"menu in the AFNI 'Define Datamode' control panel), but carries a small\n" ,
"overhead (both in memory and speed). Setting this YES/NO environment\n" ,
"variable to YES provides one way to disable this facility, as in\n" ,
"\n" ,
" setenv AFNI_NO_MCW_MALLOC YES\n" ,
"\n" ,
"Another way to permanently disable this capability (so that it isn't\n" ,
"even compiled) is outlined in the file machdep.h. Also, the interactive\n" ,
"AFNI program takes the command line switch \"-nomall\", which will turn\n" ,
"off these functions for the given run.\n" ,
"\n" ,
"N.B.: Setting this variable in the .afnirc file will have no effect,\n" ,
" since the decision whether to use the routines in mcw_malloc.c\n" ,
" is made at the very start of the program, before .afnirc is\n" ,
" scanned. Therefore, to use this variable, you must set it\n" ,
" externally, perhaps in your .cshrc or .profile initialization\n" ,
" file.\n" ,
"\n" ,
"------------------------\n" ,
"Variable: AFNI_FIM_BKTHR\n" ,
"------------------------\n" ,
"This sets the threshold for the elimination of the background voxels\n" ,
"during the interactive FIM calculations. The average intensity of\n" ,
"all voxels in the first 3D volume used in the correlation is calculated.\n" ,
"Voxels with intensity below 0.01 * AFNI_FIM_BKTHR * (this average)\n" ,
"will not have the correlation computed. The default value is 10.0, but\n" ,
"values as large as 50.0 may be useful. This parameter may be changed\n" ,
"interactively from the FIM->Edit Ideal submenu in a graph viewer.\n" ,
"\n" ,
"------------------------\n" ,
"Variable: AFNI_FLOATSCAN (editable)\n" ,
"------------------------\n" ,
"If this YES/NO variable is set to YES, then floating point bricks\n" ,
"are checked for illegal values (NaN and Infinity) when they are\n" ,
"read into an AFNI program -- illegal values will be replaced by\n" ,
"zeros. If a dataset brick contains such illegal values that go\n" ,
"undetected, AFNI programs will probably fail miserably, and have\n" ,
"been known to go into nearly-infinite loops.\n" ,
"\n" ,
"Setting this variable implies setting AFNI_NOMMAP to YES, since\n" ,
"only in-memory bricks can be altered (mmap-ed bricks are readonly).\n" ,
"\n" ,
"The command line program 'float_scan' can be used to check and\n" ,
"patch floating point files.\n" ,
"\n" ,
"[14 Sep 1999] The program to3d will scan input float and complex\n" ,
"files for illegal values, and patch illegal input numbers with\n" ,
"zeros in the output dataset. If this behavior is not desired for\n" ,
"some bizarre reason, the '-nofloatscan' command line option to\n" ,
"to3d must be used.\n" ,
"\n" ,
"-----------------------\n" ,
"Variable: AFNI_NOSPLASH\n" ,
"-----------------------\n" ,
"If this YES/NO variable is set to YES, then the AFNI splash screen\n" ,
"will not be displayed when the program starts. I'm not sure WHY\n" ,
"you would want to disable this thing of beauty (which is a joy\n" ,
"forever), but if your soul is thusly degraded, so be it.\n" ,
"\n" ,
"------------------------\n" ,
"Variable: AFNI_SPLASH_XY\n" ,
"------------------------\n" ,
"If set, this variable should be in the form \"100:37\" (two integers\n" ,
"separated by a colon). These values specify the (x,y) screen location\n" ,
"where the splash window's upper left corner will be placed. If not\n" ,
"set, x will be set to center the splash window on the display and\n" ,
"y will be 100.\n" ,
"\n" ,
"-------------------------\n" ,
"Variable: AFNI_SPLASHTIME\n" ,
"-------------------------\n" ,
"The value of this variable determines how long the AFNI splash screen\n" ,
"will stay popped up, in seconds (default value = 5.0). The splash\n" ,
"screen will always stay up until the first AFNI controller window is\n" ,
"ready for use. If the time from program start to this ready condition\n" ,
"is less than AFNI_SPLASHTIME, the splash screen will stay up until\n" ,
"AFNI_SPLASHTIME has elapsed; otherwise, the splash screen will be\n" ,
"removed as soon as AFNI is ready to go. By setting AFNI_SPLASHTIME\n" ,
"to 0.0, you can have the splash screen removed as soon as possible\n" ,
"(and the fade-out feature will be disabled).\n" ,
"\n" ,
"--------------------------------\n" ,
"Variable: AFNI_FIM_PERCENT_LIMIT (editable)\n" ,
"--------------------------------\n" ,
"This sets an upper limit on the % Change that the FIM+ computation\n" ,
"will compute. For example\n" ,
"\n" ,
" setenv AFNI_FIM_PERCENT_LIMIT 50\n" ,
"\n" ,
"means that computed values over 50% will be set to 50%, and values\n" ,
"below -50% will be set to -50%. This can be useful to avoid scaling\n" ,
"problems that arise when some spurious voxels with tiny baselines have\n" ,
"huge percent changes. This limit applies to all 3 possible percentages\n" ,
"that FIM and FIM+ can compute: % from baseline, % from average, and\n" ,
"% from top.\n" ,
"\n" ,
"---------------------------\n" ,
"Variable: AFNI_NOTES_DLINES\n" ,
"---------------------------\n" ,
"This sets the upper limit on the number of lines displayed in the\n" ,
"Notes plugin, for each note. If not present, the limit is 9 lines\n" ,
"shown per note at once. To see a note longer than this limit, you'll\n" ,
"have to use the vertical scrollbar.\n" ,
"\n" ,
"-----------------------\n" ,
"Variable: AFNI_FIM_MASK\n" ,
"-----------------------\n" ,
"This chooses the default subset of values computed with the FIM+\n" ,
"button in a graph window. The mask should be the sum of the desired\n" ,
"values from this list:\n" ,
"\n" ,
" 1 = Fit Coef\n" ,
" 2 = Best Index\n" ,
" 4 = % Change\n" ,
" 8 = Baseline\n" ,
" 16 = Correlation\n" ,
" 32 = % From Ave\n" ,
" 64 = Average\n" ,
" 128 = % From Top\n" ,
" 256 = Topline\n" ,
" 512 = Sigma Resid\n" ,
"\n" ,
"If you don't set this variable, the default mask is 23 = 1+2+4+16.\n" ,
"\n" ,
"-----------------------------------\n" ,
"Variable: AFNI_NO_BYTEORDER_WARNING\n" ,
"-----------------------------------\n" ,
"If this YES/NO variable is set to YES, then AFNI program will not\n" ,
"warn you when reading in a dataset that does not contain a byte\n" ,
"order flag. The default is to issue such a warning. Only older\n" ,
"versions of AFNI create datasets that don't have the byte order\n" ,
"flag. (See also the variable AFNI_BYTEORDER, described far above.)\n" ,
"The purpose of this warning is to alert you to possible problems\n" ,
"when you move datasets between computers with different CPU types.\n" ,
"\n" ,
"--------------------------\n" ,
"Variable: AFNI_PCOR_DENEPS\n" ,
"--------------------------\n" ,
"The correlation coefficient calculated in FIM is calculated as the\n" ,
"ratio of two quantities. If the denominator is negative or zero,\n" ,
"then this value is meaningless and may even cause the program to\n" ,
"crash. Mathematically, the denominator cannot be zero or negative,\n" ,
"but this could arise due to finite precision arithmetic on the computer\n" ,
"(i.e., roundoff error accumulation). To avoid this problem, the routine\n" ,
"that computes the correlation coefficient compares the denominator to a\n" ,
"value (called DENEPS) - if the denominator is less than DENEPS, then\n" ,
"the correlation coefficient for that voxel is set to zero.\n" ,
"\n" ,
"The denominator that is being computed is proportional to the variance\n" ,
"of the time series. If the voxel time series data is very small, then\n" ,
"the variance will be really small - so much so that the DENEPS test\n" ,
"will be failed, even though it shouldn't be. This problem has arisen\n" ,
"when people input time series whose typical value is 0.001 or smaller.\n" ,
"It never occurred to me that people would input data this small to the\n" ,
"AFNI FIM routines. To get around this difficulty, set this environment\n" ,
"variable to a value for DENEPS; for example\n" ,
" setenv AFNI_PCOR_DENEPS 0.0\n" ,
"will turn off the checking entirely. Or you could do\n" ,
" setenv AFNI_PCOR_DENEPS 1.e-10\n" ,
"\n" ,
"-----------------------------\n" ,
"Variable: AFNI_ENFORCE_ASPECT (editable)\n" ,
"-----------------------------\n" ,
"Some Linux window managers do no enforce the aspect ratio (width to height\n" ,
"proportion) request that the image display module makes. This means that\n" ,
"image windows can become undesirably distorted when manually resized.\n" ,
"Setting this YES/NO variable to YES will make AFNI itself enforce the\n" ,
"aspect ratio whenever an image window is resized.\n" ,
"\n" ,
"----------------------------------------\n" ,
"Variables: AFNI_<plug_filename>_butcolor\n" ,
"----------------------------------------\n" ,
"These variables (one for each AFNI plugin) let you set the menu button colors\n" ,
"for the Plugins menu item. For example\n" ,
" setenv AFNI_plug_power_butcolor red3\n" ,
"will make the \"Power Spectrum\" button appear in a dark red color. The format\n" ,
"of the variable is exemplified above: the <plug_filename> is replaced by the\n" ,
"filename of the plugin (after removing the suffix). Note that it is possible\n" ,
"for the plugin author to hardcode the menu button for his/her plugin, in\n" ,
"which case the corresponding environment variable will have no effect.\n" ,
"\n" ,
"Colors are specified as described in file README.setup. If you are using\n" ,
"an X11 PseudoColor visual, then you should be economical with color usage!\n" ,
"\n" ,
"The purpose of this feature is to let you highlight the plugins that you\n" ,
"use most frequently. The size of the of plugin menu is growing, and it\n" ,
"is easy to misplace what you most use in the list.\n" ,
"\n" ,
"-----------------------------\n" ,
"Variable: AFNI_MARKERS_NOQUAL (editable)\n" ,
"-----------------------------\n" ,
"If this YES/NO variable is set to YES, then the interactive AFNI program\n" ,
"behaves as if the \"-noqual\" command line option had been included. This\n" ,
"feature was added at the request of Dr. Michael S. Beauchamp, who has a\n" ,
"very rare neurological disorder called \"noqaulagnosia\".\n" ,
"\n" ,
"----------------------\n" ,
"Variable: AFNI_OPTIONS\n" ,
"----------------------\n" ,
"In the spirit of the previous variable, this variable can be used to set\n" ,
"up command line options that will always be passed to the interactive\n" ,
"AFNI program. If more than one option is needed, then they should be\n" ,
"separated by spaces, and the whole value of the variable will need to be\n" ,
"placed in quotes. For example\n" ,
"\n" ,
" setenv AFNI_OPTIONS \"-noqual -ncolors 60\"\n" ,
"\n" ,
"Note that the AFNI command line option \"-nomall\" cannot be specified this\n" ,
"way (cf. the discussion under variable AFNI_NO_MCW_MALLOC).\n" ,
"\n" ,
"------------------------------\n" ,
"Variable: AFNI_NO_SIDES_LABELS (editable)\n" ,
"------------------------------\n" ,
"As of 01 Dec 1999, the interactive AFNI program now displays a label\n" ,
"beneath each image window showing which side of the image is on the left\n" ,
"edge of the window. This label is based on the anatomical directions\n" ,
"encoded in the anatomical dataset .HEAD file, usually when to3d was used\n" ,
"to create the file. If you do NOT want these labels displayed (why not?),\n" ,
"set this YES/NO environment variable to YES.\n" ,
"\n" ,
"----------------------------------\n" ,
"Variable: AFNI_NO_ADOPTION_WARNING\n" ,
"----------------------------------\n" ,
"AFNI now can print a warning when it forces a dataset to have an anatomy\n" ,
"parent dataset (the \"forced adoption\" function). This happens when\n" ,
"there a dataset does not have an anatomy parent encoded into its .HEAD\n" ,
"file (either via to3d or 3drefit), and there is more than one anatomical\n" ,
"dataset in the directory that has Talairach transformation markers\n" ,
"attached. If you wish to enable this warning, set this YES/NO variable\n" ,
"to NO. For more information on this subject, please see\n" ,
" http://afni.nimh.nih.gov/afni/afni_faq.shtml#AnatParent .\n" ,
"\n" ,
"-----------------------------------\n" ,
"Variable: AFNI_NO_NEGATIVES_WARNING\n" ,
"-----------------------------------\n" ,
"If this YES/NO variable is set to YES, then to3d will skip the usual\n" ,
"warning that it pops up in a message window when it discovers negative\n" ,
"values in the input short images. (The warning will still be printed\n" ,
"to stdout.)\n" ,
"\n" ,
"----------------------\n" ,
"Variable: AFNI_NO_XDBE\n" ,
"----------------------\n" ,
"If this YES/NO variable is set to YES, then the X11 Double Buffer\n" ,
"Extension (XDBE) will not be used, even if the X11 server supports it.\n" ,
"This is needed when the X11 server says that it supports it, but actually\n" ,
"does not implement it correctly - this is a problem on the Xsgi server\n" ,
"running under IRIX 6.5.3 on R4400 machines.\n" ,
"\n" ,
"------------------------------\n" ,
"Variable: AFNI_VIEW_ANAT_BRICK (editable)\n" ,
" AFNI_VIEW_FUNC_BRICK (editable)\n" ,
"------------------------------\n" ,
"One of the (very few) confusing parts of AFNI is the \"warp-on-demand\"\n" ,
"viewing of transformed datasets (e.g., in the +tlrc coordinate system).\n" ,
"This allows you to look at slices taken from transformed volumes without\n" ,
"actually computing and storing the entire transformed dataset. This\n" ,
"viewing mode is controlled by from the \"Define Datamode\" control panel.\n" ,
"When an anatomical dataset has a +tlrc.BRIK file, then you can choose\n" ,
"between \"View Anat Data Brick\" and \"Warp Anat on Demand\"; when there\n" ,
"is no +tlrc.BRIK file for the dataset, then only \"Warp Anat on Demand\"\n" ,
"is possible.\n" ,
"\n" ,
"If you switch the Talairach view when the current anat dataset does\n" ,
"not have a +tlrc.BRIK file, then the \"Warp Anat on Demand\" mode will\n" ,
"be turned on. If you then switch to a dataset that does have a\n" ,
"+tlrc.BRIK file, \"Warp Anat on Demand\" will still be turned on,\n" ,
"although the \"View Anat Data Brick\" option will be enabled.\n" ,
"\n" ,
"If you set the YES/NO variable AFNI_VIEW_ANAT_BRICK to YES,\n" ,
"then \"View Anat Data Brick\" will be turned on whenever possible after\n" ,
"switching datasets. Similarly, setting AFNI_VIEW_FUNC_BRICK to YES\n" ,
"will engage \"View Func Data Brick\" whenever possible (when the BRIK\n" ,
"file exists and its grid spacing matches the anatomical grid spacing).\n" ,
"Note that switching any dataset (func or anat) triggers the same\n" ,
"routine, and will set either or both \"View Brick\" modes on. When\n" ,
"these environment variables are present, the only way to switch to\n" ,
"\"Warp\" mode when \"View Brick\" mode is possible is to do it manually\n" ,
"(by clicking on the toggle button) when you want this.\n" ,
"\n" ,
"When you use one of the drawing plugins (\"Draw Dataset\" or \"Gyrus Finder\"),\n" ,
"you must operate directly on the dataset BRIK. For this reason, it is\n" ,
"important to be in \"View Data Brick\" mode on these occasions. Setting\n" ,
"these variables is one way to ensure that this will happen whenever\n" ,
"possible.\n" ,
"\n" ,
"When AFNI is in \"Warp Anat on Demand\" mode, the word \"{warp}\" will\n" ,
"appear in the windows' titlebars. This provides a reminder of the\n" ,
"viewing mode you are using (warped from a brick, or data directly\n" ,
"extracted from a brick), since the \"Define Datamode\" control panel\n" ,
"will not always be open.\n" ,
"\n" ,
"08 Aug 2003: I have modified the way these variables are treated in\n" ,
"AFNI so that they now default to the \"YES\" behavior. If you don't\n" ,
"want this, you have to explicitly set them to \"NO\" from this day forth.\n" ,
"\n" ,
"----------------\n" ,
"Variable: TMPDIR\n" ,
"----------------\n" ,
"This variable specifies the directory where temporary files are to be\n" ,
"written. It is not unique to AFNI, but is used by many Unix programs.\n" ,
"You must have permission to write into this directory. If you want to\n" ,
"use the current directory, setting TMPDIR to \".\" would work. If TMPDIR\n" ,
"is not defined, directory /tmp will be used. On some systems, this\n" ,
"directory may not have enough space for the creation of large temporary\n" ,
"datasets. On most Unix systems, you can tell the size of various disk\n" ,
"partitions using a command like \"df -k\" (on HPUX, \"bdf\" works).\n" ,
"\n" ,
"----------------------------\n" ,
"Variable: AFNI_GRAYSCALE_BOT\n" ,
"----------------------------\n" ,
"This variable sets the darkest level shown in a grayscale image window.\n" ,
"The default value is 55 (a leftover from Andrzej Jesmanowicz). You can\n" ,
"set this value to anything from 0 to 254.\n" ,
"\n" ,
"----------------------------\n" ,
"Variable: AFNI_SYSTEM_AFNIRC\n" ,
"----------------------------\n" ,
"If this variable is set, it is the name of a file to be read like the\n" ,
"user's .afnirc file (see README.setup). The purpose is to allow a\n" ,
"system-wide setup file to be used. To do this, you would create such\n" ,
"a file in a useful place - perhaps where you store the AFNI binaries.\n" ,
"Then each user account should have the equivalent of\n" ,
"\n" ,
" setenv AFNI_SYSTEM_AFNIRC /place/where/setup/is/stored/.afnirc\n" ,
"\n" ,
"defined in its .cshrc (.bashrc, etc.) file. Note that it doesn't make\n" ,
"sense to define this variable in the user's .afnirc file, since that\n" ,
"file won't be read until AFTER this file is read. Also note that use\n" ,
"of the -skip_afnirc option will cause both the system and user setup\n" ,
"files to be skipped.\n" ,
"\n" ,
"------------------------\n" ,
"Variable: AFNI_PBAR_IMXY (editable)\n" ,
"------------------------\n" ,
"This variable determines the size of the image saved when the\n" ,
"\"Save to PPM\" button is selected for a color pbar. It should be\n" ,
"in the format\n" ,
" setenv AFNI_PBAR_IMXY 20x256\n" ,
"which means to set the x-size (horizontal) to 20 pixels and the\n" ,
"y-size (vertical) to 256 pixels. These values are the default,\n" ,
"by the way.\n" ,
"\n" ,
"--------------------------\n" ,
"Variable: AFNI_LAYOUT_FILE\n" ,
"--------------------------\n" ,
"If defined, this variable is the name of a file to read at startup\n" ,
"to define the \"layout\" of AFNI windows at the program start. If\n" ,
"this name starts with a '/' character, then it is an absolute path;\n" ,
"otherwise, it is taken to be a path relative to the user's home\n" ,
"directory ($HOME). If the AFNI command line switch \"-layout\" is\n" ,
"used, it will override this specification.\n" ,
"\n" ,
"The simplest way to produce a layout file is to use the \"Save Layout\"\n" ,
"button on the Datamode->Misc menu. You can then edit this file;\n" ,
"the format should be fairly self-explanatory. The structure of the\n" ,
"file is similar to the .afnirc file (cf. README.setup). In fact,\n" ,
"the layout file can be included into .afnirc (since it is just another\n" ,
"*** section) and then setting AFNI_LAYOUT_FILE = .afnirc in the\n" ,
"***ENVIRONMENT section should work.\n" ,
"\n" ,
"A sample layout file:\n" ,
"\n" ,
"***LAYOUT\n" ,
" A geom=+73+1106 // start controller A\n" ,
" A.sagittalimage geom=320x320+59+159 ifrac=0.8 // and Sagittal image\n" ,
" A.sagittalgraph geom=570x440+490+147 matrix=9 // and Sagittal graph\n" ,
" B // start controller B\n" ,
" B.plugin.ROI_Average // start a plugin\n" ,
"\n" ,
"Each window to be opened has a separate command line in this file.\n" ,
"The \"geom=\" qualifiers specify the size and position of the windows.\n" ,
"For images, \"ifrac=\" can be used to specify the fraction of the window\n" ,
"occupied by the image (if \"ifrac=1.0\", then no control widgets will be\n" ,
"visible). For graphs, \"matrix=\" can be used to control the initial\n" ,
"number of sub-graphs displayed. For plugins, the label on the button\n" ,
"that starts the plugin is used after the \".plugin.\" string (blanks\n" ,
"should be filled with underscores \"_\"). In the example above, the last\n" ,
"two windows to be opened do not have a \"geom=\" qualifier, so their\n" ,
"placement will be chosen by the window manager.\n" ,
"\n" ,
"If you add \"slow\" after the \"***LAYOUT\", then each window operation\n" ,
"will be paused for 1 second to let you watch the layout operations\n" ,
"proceed gradually. Otherwise, they will be executed as fast as\n" ,
"possible (which still may not be all that fast).\n" ,
"\n" ,
"Using layouts with a window manager that requires user placement\n" ,
"of new windows (e.g., twm) is a futile and frustrating exercise.\n" ,
"\n" ,
"-------------------------\n" ,
"Variable: AFNI_tsplotgeom\n" ,
"-------------------------\n" ,
"Related to the above, if you set this environment variable (in the\n" ,
"***ENVIRONMENT section, not in the ***LAYOUT section), it is used\n" ,
"to set the geometry of the plotting windows used for time series\n" ,
"plots, histograms, etc. -- all the graphs except the dataset plots.\n" ,
"Its format should be something like \"550x350\"; this example sets\n" ,
"the width to 550 pixels and the height to 350 pixels. If you don't\n" ,
"set this, the default is \"200x200\", which is quite small on a high\n" ,
"resolution display.\n" ,
"\n" ,
"--------------------------\n" ,
"Variables: AFNI_REALTIME_*\n" ,
"--------------------------\n" ,
"This set of variables allows you to control the initial setup of the\n" ,
"realtime data acquisition plugin (menu item \"RT Options\"). Normally,\n" ,
"this plugin is active only if AFNI is started with the \"-rt\" command\n" ,
"line option. (It will consume CPU time continually as it polls for\n" ,
"an incoming data connection, which is why you don't want it running\n" ,
"by default.) The following variables can be used to initialize the\n" ,
"plugin's options:\n" ,
"\n" ,
"AFNI_REALTIME_Activate = This is a YES/NO variable, and allows you\n" ,
" to have the realtime plugin active without\n" ,
" using the \"-rt\" command line option. If\n" ,
" this variable is set to YES, then you can\n" ,
" disable the realtime plugin with \"-nort\".\n" ,
"\n" ,
"The variables below are used to set the initial status of the widgets\n" ,
"in the realtime plugin's control window. Each one has the same name as\n" ,
"the labels in the control window, with blanks replaced by underscores.\n" ,
"The values to set for these variables are exact copies of the inputs\n" ,
"you would specify interactively (again, with blanks replaced by\n" ,
"underscores). For details as to the meaning of these options, see\n" ,
"the plugin's Help window.\n" ,
"\n" ,
"AFNI_REALTIME_Images_Only = \"No\" or \"Yes\"\n" ,
"AFNI_REALTIME_Root = name for datasets to be created\n" ,
"AFNI_REALTIME_Update = an integer from 0 to 19\n" ,
"AFNI_REALTIME_Function = \"None\" or \"FIM\" (cf. AFNI_FIM_IDEAL below)\n" ,
"AFNI_REALTIME_Verbose = \"No\", \"Yes\", or \"Very\"\n" ,
"AFNI_REALTIME_Registration = \"None\", \"2D:_realtime\", \"2D:_at_end\",\n" ,
" \"3D:_realtime\", \"3D:_at_end\",\n" ,
" or \"3D:_estimate\"\n" ,
"AFNI_REALTIME_Base_Image = an integer from 0 to 59\n" ,
"AFNI_REALTIME_Resampling = \"Cubic\", \"Quintic\", \"Heptic\", \"Fourier\",\n" ,
" or \"Hept+Four\"\n" ,
"AFNI_REALTIME_Graph = \"No\", \"Yes\", or \"Realtime\"\n" ,
"AFNI_REALTIME_NR = an integer from 5 to 9999\n" ,
"AFNI_REALTIME_YR = a floating point number from 0.1 to 10.0\n" ,
"\n" ,
"The following internal controls can only be set using these environment\n" ,
"variables (there is no GUI to set these values):\n" ,
"\n" ,
"AFNI_REALTIME_volreg_maxite = an integer >= 1 [default = 9]\n" ,
"AFNI_REALTIME_volreg_maxite_est = an integer >= 1 [default = 1]\n" ,
"AFNI_REALTIME_volreg_graphgeom = something like 320x320+59+159\n" ,
"\n" ,
"AFNI_REALTIME_CHILDWAIT = max wait time (in sec) for child info\n" ,
" process [default = 66.6]; not needed if\n" ,
" child info process is not used\n" ,
"\n" ,
"AFNI_REALTIME_WRITEWAIT = if the image data pauses for this number\n" ,
" of seconds, then the datasets being constructed\n" ,
" will be written to disk [default=37.954];\n" ,
" since this output may take several seconds,\n" ,
" you may need to adjust this if you are in\n" ,
" fact doing imaging with a very long TR.\n" ,
" Note that after this wait, the plugin can\n" ,
" still receive image data -- even if the image\n" ,
" source program is silent for a very long time,\n" ,
" AFNI will still be waiting patiently for data.\n" ,
"\n" ,
"AFNI_GRAPH_AUTOGRID = By default, if the number of time points in an\n" ,
" AFNI graph viewer changes, the density of\n" ,
" vertical grid lines changes. If you don't\n" ,
" want this to happen, set this variable to NO.\n" ,
"\n" ,
"For more information about how the realtime plugin works, read the file\n" ,
"README.realtime.\n" ,
"\n" ,
"------------------------\n" ,
"Variable: AFNI_FIM_IDEAL\n" ,
"------------------------\n" ,
"This variable specifies the filename of the initial FIM ideal timeseries.\n" ,
"The main use of this would be to be able to initialize the Realtime\n" ,
"plugin without direct user intervention.\n" ,
"\n" ,
"----------------------------------\n" ,
"Variable: AFNI_PLUGINS_ALPHABETIZE\n" ,
"----------------------------------\n" ,
"If this YES/NO variable is set to NO, then the plugin buttons will\n" ,
"not be alphabetized on the menu, and they will appear in the\n" ,
"order which AFNI chooses. Otherwise, the plugin menu buttons will\n" ,
"be alphabetized by default. Alphabetizing is done without regard to\n" ,
"case (using the C library routine strcasecmp).\n" ,
"\n" ,
"----------------------------\n" ,
"Variable: AFNI_VOLREG_EDGING\n" ,
"----------------------------\n" ,
"This variable affects the operation of 3dvolreg, the volume registration\n" ,
"plugin, and the 3D registration code in the realtime acquisition plugin.\n" ,
"It determines the size of the region around the edges of the base volume\n" ,
"where the default weight will be set to zero. Call the value of this\n" ,
"variable 'ee'. If 'ee' is a plain number (e.g., 5), then it is a voxel\n" ,
"count, giving the thickness along each face of the 3D brick. If 'ee' is\n" ,
"of the form '5%', then it is a fraction of of each brick size. For\n" ,
"example, '5%' of a 256x256x124 volume means that 13 voxels on each side\n" ,
"of the xy-axes will get zero weight, and 6 along the z-axis. '5%' is\n" ,
"the default value used by the 3D registration routines (in mri_3dalign.c)\n" ,
"if no other value is specified.\n" ,
"\n" ,
"--------------------\n" ,
"Variable: AFNI_TRACE\n" ,
"--------------------\n" ,
"This variable controls the initial setting of the tracing (debugging)\n" ,
"code when AFNI programs startup. If it is set to 'y', then tracing\n" ,
"is turned on and set to the LOW mode (like -trace in AFNI). If it is\n" ,
"set to 'Y', then tracing is turned on and set to the HIGH mode (like\n" ,
"-TRACE in AFNI). Anything else, and tracing is turned off.\n" ,
"\n" ,
"N.B.: You can't set this variable in .afnirc and expect it to have\n" ,
" any effect (and why would you want to?), since it is read from\n" ,
" the environment BEFORE the .afnirc file is read in.\n" ,
"\n" ,
"N.B.: At this moment (26 Jan 2001), only the AFNI program itself is\n" ,
" configured for tracing. As time goes on, the entire AFNI\n" ,
" programming library and suite of programs will be revamped for\n" ,
" this purpose. The goal is to make it easier to find bugs, and\n" ,
" localize crashes.\n" ,
"\n" ,
"-------------------------\n" ,
"Variable: AFNI_TRACE_FILE\n" ,
"-------------------------\n" ,
"If this variable is set, then the output from the AFNI function tracing\n" ,
"macros will be written to a file with that name, rather than to stdout.\n" ,
"This variable cannot be set in .afnirc; the intention is to provide a\n" ,
"way to get 'clean' tracing output (not mixed up with other program junk)\n" ,
"that can be fed to Ziad Saad's AnalyzeTrace function.\n" ,
"\n" ,
"------------------------\n" ,
"Variable: AFNI_ROTA_ZPAD\n" ,
"------------------------\n" ,
"This variable controls the amount of zero-padding used during 3D rotations\n" ,
"in 3drotate, 3dvolreg, etc. It provides a default value for the \"-zpad\"\n" ,
"options of these programs. If zero-padding is used, then this many voxels\n" ,
"are padded out on each edge (all 6 faces) of a 3D brick before rotation.\n" ,
"After the rotation, these perimeter values (whatever they might be) will\n" ,
"be stripped off. If \"-zpad\" is used on the command line, it overrides\n" ,
"this value. Zero padding during rotation is useful to avoid edge effects,\n" ,
"the worst of which is the loss of data off the edge of the volume during\n" ,
"the 4 shearing stages.\n" ,
"\n" ,
"------------------------\n" ,
"Variable: AFNI_TO3D_ZPAD\n" ,
"------------------------\n" ,
"This variable sets the number of slices added on each z-face in datasets\n" ,
"created by program to3d. It provides a default value for the \"-zpad\" option\n" ,
"of that program. It can be set to an integer, meaning a slice count, or\n" ,
"a number of millimeters, meaning a minimum distance to pad:\n" ,
" setenv AFNI_TO3D_ZPAD 2\n" ,
" setenv AFNI_TO3D_ZPAD 16mm\n" ,
"If \"-zpad\" is used on the to3d command line, it overrides this value.\n" ,
"If neither is present, no zero padding is used. Note well that this\n" ,
"padding is only in the z-direction, unlike that of AFNI_ROTA_ZPAD.\n" ,
"\n" ,
"----------------------------\n" ,
"Variable: AFNI_IMAGE_MINFRAC (editable)\n" ,
"----------------------------\n" ,
"This variable sets the minimum size of an image window when it is first\n" ,
"opened, in terms of a fraction of the overall screen area. By default,\n" ,
"this value is set to 0.02; you can override this by (for example)\n" ,
" setenv AFNI_IMAGE_MINFRAC 0.05\n" ,
"If you set this value to 0.0, then there will be no minimum. This is\n" ,
"the old behavior, where the initial window size is always 1 screen pixel\n" ,
"per data pixel, and can lead to image windows that are hard to resize or\n" ,
"otherwise use (when the dataset is small). The largest value I recommend\n" ,
"for AFNI_IMAGE_MINFRAC is 0.1; however, you can set it to as large as 0.9\n" ,
"if you are completely crazy, but I'm not responsible for the results --\n" ,
"don't even think of complaining or commenting to me about problems that\n" ,
"arise if you try this!\n" ,
"\n" ,
"----------------------------\n" ,
"Variable: AFNI_IMAGE_MAXFRAC\n" ,
"----------------------------\n" ,
"This variable sets the maximum size of an image window, as a fraction of\n" ,
"the width and height of the screen. The default value is 0.9. This lets\n" ,
"you prevent image windows from auto-resizing to be too big when you\n" ,
"change datasets. Note that if you have turned on AFNI_ENFORCE_ASPECT, then\n" ,
"this feature will prevent you from resizing a window to be larger than\n" ,
"the AFNI_IMAGE_MAXFRAC fraction of the screen dimensions.\n" ,
"\n" ,
"-----------------------\n" ,
"Variable: AFNI_AUTOGZIP (cf. AFNI_COMPRESSOR) (editable)\n" ,
"-----------------------\n" ,
"If this YES/NO variable is set to YES, then when AFNI programs write a\n" ,
"dataset .BRIK file to disk, they will test to see if the data is easily\n" ,
"compressible (at least 80%). If so, then the GZIP compression will be\n" ,
"used. (For this to work, the gzip program must be in your path.) This\n" ,
"can be useful if you are dealing with mask datasets, which are usually\n" ,
"highly compressible, but don't want the overhead of trying to compress\n" ,
"and decompress arbitrary MRI datasets.\n" ,
"\n" ,
"A command line method to carry out compression of datasets that will\n" ,
"compress well is to use a csh script like the following:\n" ,
"\n" ,
" #!/bin/csh\n" ,
" foreach fred ( `find . -name \\*.BRIK -print` )\n" ,
" ent16 -%50 < $fred\n" ,
" if( $status == 1 ) gzip -1v $fred\n" ,
" end\n" ,
"\n" ,
"This will only gzip .BRIK files that the program ent16 estimates will\n" ,
"compress by at least 50%. Note that ent16's estimate of compression\n" ,
"may be high or low relative to what gzip actually does.\n" ,
"\n" ,
"------------------------------\n" ,
"Variable: AFNI_DONT_MOVE_MENUS (editable)\n" ,
"------------------------------\n" ,
"If this YES/NO variable is set to YES, then the functions that try\n" ,
"to move popup menus to \"good\" locations on screens will be skipped.\n" ,
"This seems to be necessary on some Solaris systems, where the menus\n" ,
"can end up being moved to bizarre locations.\n" ,
"\n" ,
"----------------------------\n" ,
"Variable: AFNI_MINC_DATASETS\n" ,
"----------------------------\n" ,
"If this YES/NO variable is not set to NO, then MINC-format files\n" ,
"with name suffix .mnc will be read into the interactive AFNI\n" ,
"program at startup, along with standard .HEAD/.BRIK datasets.\n" ,
"That is, you have to set this variable explicitly to NO if you\n" ,
"don't want MINC-format files to be automatically recognized by\n" ,
"the interactive AFNI program. This variable does not affect\n" ,
"the ability of command line programs (3dSomething) to read\n" ,
".mnc input files.\n" ,
"\n" ,
"----------------------------\n" ,
"Variable: AFNI_MINC_FLOATIZE\n" ,
"----------------------------\n" ,
"If this YES/NO variable is set to YES, then when MINC-format files\n" ,
"are read in as datasets, their values will be scaled to floats.\n" ,
"Otherwise, their values will be scaled to the same data type as\n" ,
"stored in the file. In some cases, the latter behavior is not\n" ,
"good; for example, if a byte-valued file (intrinsic range 0..255)\n" ,
"is scaled to the range 0..0.5 in the MINC header, then after\n" ,
"conversion back to bytes, the resulting AFNI dataset values will\n" ,
"all be zero. Setting AFNI_MINC_FLOATIZE to YES will cause the\n" ,
"scaled values to be stored as floats.\n" ,
"\n" ,
"------------------------------\n" ,
"Variable: AFNI_MINC_SLICESCALE\n" ,
"------------------------------\n" ,
"If this YES/NO variable is set to NO, then AFNI will not use the\n" ,
"image-min and image-max scaling when reading data from MINC files.\n" ,
"Normally, you want this scaling, since MINC files are scaled separately\n" ,
"in each slice. However, if the image-min and image-max values in the\n" ,
"MINC file are damaged, then you can turn off the scaling this way.\n" ,
"\n" ,
"----------------------------\n" ,
"Variable: AFNI_ANALYZE_SCALE\n" ,
"----------------------------\n" ,
"If this YES/NO variable is set to NO, then the \"funused1\" entry\n" ,
"in the Mayo Analyze .hdr file will not be used as a scale factor\n" ,
"for the images contained in the corresponding .img file. Otherwise,\n" ,
"if funused1 is positive and not equal to 1.0, all the image data\n" ,
"in the .img file will be scaled by this value.\n" ,
"\n" ,
"-------------------------------\n" ,
"Variable: AFNI_ANALYZE_FLOATIZE\n" ,
"-------------------------------\n" ,
"If this YES/NO variable is set to YES, then Mayo Analyze files\n" ,
"will be scaled to floats on input. Otherwise, they will be read\n" ,
"in the format in which they are stored in the .img file. Conversion\n" ,
"to floats can be useful if the scaling factor is such that the image\n" ,
"native format can't hold the scaled values; for example, if short\n" ,
"values in the image range from -1000..1000 and the scale factor\n" ,
"is 0.0001, then the scaled values range from -0.1..0.1, which would\n" ,
"be truncated to 0 in the scaled image if it is not \"floatized\".\n" ,
"(Conversion to floats will only be done to byte, short, and int\n" ,
"image types.)\n" ,
"\n" ,
"---------------------------------\n" ,
"Variable: AFNI_ANALYZE_ORIGINATOR\n" ,
"---------------------------------\n" ,
"If this YES/NO variable is set to YES, then AFNI will attempt\n" ,
"to read and use the ORIGINATOR field in a Mayo Analyze file\n" ,
"to set the origin of the pixel space in AFNI. This origin\n" ,
"can be used directly by several programs--the main AFNI viewer,\n" ,
"and all of the 3dxxxx programs, including especially 3dcopy,\n" ,
"which is the preferred way to convert an Analyze format file\n" ,
"to an AFNI native file.\n" ,
"This variable will also force 3dAFNItoANALYZE to write the\n" ,
"ORIGINATOR field into the output Analyze file based on the\n" ,
"input AFNI file's origin information.\n" ,
"The ORIGINATOR field should be compatible with SPM in most\n" ,
"cases, but please verify this.\n" ,
"\n" ,
"--------------------------\n" ,
"Variable: AFNI_START_SMALL\n" ,
"--------------------------\n" ,
"If this YES/NO variable is set to YES, then when AFNI starts, it will\n" ,
"look for the smallest datasets in the first session, and choose these\n" ,
"as its starting point. This can be useful if you also use the layout\n" ,
"feature to pop open an image window on startup; in that case, if the\n" ,
"default starting dataset (the first alphabetical) is huge, you won't\n" ,
"see anything while the program reads all of into memory before displaying\n" ,
"the first image.\n" ,
"\n" ,
"---------------------------\n" ,
"Variable: AFNI_MENU_COLSIZE\n" ,
"---------------------------\n" ,
"This numerical variable sets the maximum number of entries in a popup\n" ,
"menu column (e.g., like the sub-brick menus for bucket datasets). The\n" ,
"default value is 20, but you may want to make this larger (say 40). When\n" ,
"you have a menu with a huge number of entries, the menu can become so\n" ,
"wide that it doesn't fit on the screen. Letting the columns be longer\n" ,
"will make the menus be narrower across the screen.\n" ,
"\n" ,
"Another way to get a handle on such huge menus is to Button-3 (right)\n" ,
"click on the label to the left of the menu. This will popup a one-\n" ,
"column scrollable list chooser that is equivalent to the menu. In this\n" ,
"way, it is still possible to use menus that have hundreds of entries.\n" ,
"The maximum number of entries shown at one time in a scrollable list\n" ,
"chooser is given by variable AFNI_chooser_listmax if it exists, otherwise\n" ,
"by AFNI_MENU_COLSIZE.\n" ,
"\n" ,
"-----------------------------\n" ,
"Variable: AFNI_GLOBAL_SESSION\n" ,
"-----------------------------\n" ,
"This variable, if it exists, is the name of a directory that contains\n" ,
"\"global\" datasets - ones that you want to be visible in each \"Switch Underlay\"\n" ,
"or \"Switch Overlay\" menu. Pointers to the datasets read from this directory\n" ,
"will be appended to the dataset list for each directory read from the\n" ,
"command line. In the \"Switch\" choosers, these datasets are marked with\n" ,
"the character 'G' at the right, and they appear last in the list.\n" ,
"\n" ,
"It really only makes sense to put +tlrc datasets in the global session\n" ,
"directory, since only they can be presumed to be aligned with other datasets.\n" ,
"Also, it is probably best if you make sure each global anatomical dataset\n" ,
"has itself as the anatomy parent; this can be enforced by issuing the command\n" ,
" 3drefit -apar SELF *.HEAD\n" ,
"in the global session directory.\n" ,
"\n" ,
"When you Switch Sessions and are viewing a global dataset, it is likely that\n" ,
"you will NOT be viewing the same dataset after the Switch Session. You will\n" ,
"have to then Switch Underlay and/or Switch Overlay to get back to the same\n" ,
"global dataset(s).\n" ,
"\n" ,
"If you start AFNI and there are no datasets in the sessions given on the\n" ,
"command line, then the directory specified by this variable becomes the\n" ,
"default session. If there are no datasets there, either, then AFNI makes\n" ,
"up a dummy dataset (AFNI cannot operate without at least one dataset).\n" ,
"\n" ,
"------------------------------\n" ,
"Variable: AFNI_DISP_SCROLLBARS (editable)\n" ,
"------------------------------\n" ,
"If this YES/NO variable is set to YES, then the 'Disp' control window\n" ,
"(on the image viewers) will have scrollbars attached. This window has\n" ,
"grown larger over the years, and for some people with pitifully small\n" ,
"displays (e.g., laptops), it is now taller than their screens. If\n" ,
"activated, this option will prevent the Disp window from being so tall\n" ,
"and will attach scrollbars so you can access all of its contents.\n" ,
"\n" ,
"Note: If you change this value interactively, via Edit Environment, the\n" ,
"change will only affect Disp windows opened after you 'Set' the variable.\n" ,
"That is, already opened Disp windows won't suddenly get scrollbars if\n" ,
"you change this to YES.\n" ,
"\n" ,
"------------------------------\n" ,
"Variable: AFNI_GRAPH_TEXTLIMIT (editable)\n" ,
"------------------------------\n" ,
"This numerical variable sets the upper limit on the number of rows shown\n" ,
"in the Button-3 popup in a sub-graph. If the number of rows in the popup\n" ,
"would be more than this value, a text window with scrollbars is used\n" ,
"instead of a \"spring-loaded\" menu pane. If you set this value to 1, then\n" ,
"the text window will always be used. Note that a text window does not\n" ,
"automatically popdown, but must be explicitly dismissed by the user\n" ,
"pressing the \"Quit\" button.\n" ,
"\n" ,
"-----------------------------\n" ,
"Variable: AFNI_GRAPH_BASELINE\n" ,
"-----------------------------\n" ,
"This variable should be set to one of the strings \"Individual\", \"Common\",\n" ,
"or \"Global\", corresponding to the choices on the Opt->Baseline menu in\n" ,
"a graph window. (Actually, only the first letter of the string will be\n" ,
"used.) This variable will determine the initial setting of the Baseline\n" ,
"menu when a graph window opens.\n" ,
"\n" ,
"-------------------------------\n" ,
"Variable: AFNI_GRAPH_GLOBALBASE\n" ,
"-------------------------------\n" ,
"Normally, the global baseline for a graph window is set to the smallest\n" ,
"value found in the entire 3D+time dataset. This variable lets you specify\n" ,
"a numerical value to be used for this purpose instead. Probably the most\n" ,
"common setting (for those who want to use this feature at all, which means\n" ,
"Mike Beauchamp) would be\n" ,
" setenv AFNI_GRAPH_GLOBALBASE 0\n" ,
"Of course, you can always change the global baseline from the Opt->Baseline\n" ,
"menu.\n" ,
"\n" ,
"--------------------------\n" ,
"Variable: AFNI_VALUE_LABEL (editable)\n" ,
"--------------------------\n" ,
"If this YES/NO variable is set to YES, then the data value label on the\n" ,
"Define Overlay control panel will be turned on when only 1 or 2 image\n" ,
"viewer windows are open. This will consume more CPU time and redrawing\n" ,
"time than the default, which is that this label is only turned on when\n" ,
"all 3 image viewer windows are open. If you are operating X11 remotely\n" ,
"over a slow connection, this option should not be turned on.\n" ,
"\n" ,
"----------------------------\n" ,
"Variable: AFNI_SUMA_BOXCOLOR (editable)\n" ,
"----------------------------\n" ,
"This string defines the color used for overlaying surface nodes transmitted\n" ,
"from SUMA to AFNI. The default is an orangish-yellow. If you like yellow,\n" ,
"then do\n" ,
" setenv AFNI_SUMA_COLOR yellow\n" ,
"If this is set to \"none\", then these lines won't be plotted.\n" ,
"\n" ,
"-----------------------------\n" ,
"Variable: AFNI_SUMA_LINECOLOR (editable)\n" ,
"-----------------------------\n" ,
"This string defines the color used for overlaying the intersection of SUMA\n" ,
"surface triangles with image slice planes. The default is white. If this\n" ,
"is set to \"none\", then these lines won't be plotted.\n" ,
"\n" ,
"---------------------------\n" ,
"Variable: AFNI_SUMA_BOXSIZE (editable)\n" ,
"---------------------------\n" ,
"This variable defines the size of the boxes drawn at each surface node\n" ,
"transmitted from SUMA. The default is 0.25, which means that each box is\n" ,
"plus and minus 1/4 of a voxel size about the node location. If you want a\n" ,
"larger box, you could try\n" ,
" setenv AFNI_SUMA_BOXSIZE 0.5\n" ,
"\n" ,
"----------------------------\n" ,
"Variable: AFNI_SUMA_LINESIZE (editable)\n" ,
"----------------------------\n" ,
"This variable sets the thickness of the lines used when drawing a surface\n" ,
"intersection overlay. The units are the width of the entire image;\n" ,
"reasonable values are in the range 0..0.01; 0 means to draw the thinnest\n" ,
"line possible. Since this is editable, you can experiment with it to\n" ,
"see what looks good.\n" ,
"\n" ,
"-------------------------\n" ,
"Variable: AFNI_NIML_START\n" ,
"-------------------------\n" ,
"If this YES/NO variable is set to YES, then NIML listening will be engaged\n" ,
"from when AFNI starts. You can also enable NIML from the command line with\n" ,
"the option \"-niml\", and from the Datamode->Misc menu item \"Start NIML\".\n" ,
"\n" ,
"NIML is the mechanism by which AFNI talks to other programs - it is the\n" ,
"successor to plugouts. At this moment (Mar 2002), the only external NIML\n" ,
"program is SUMA - the surface mapper.\n" ,
"\n" ,
"---------------------------\n" ,
"Variable: AFNI_KEEP_PANNING (editable)\n" ,
"---------------------------\n" ,
"If this YES/NO variable is set to YES, then when the Zoom pan gets turned\n" ,
"on in the AFNI image viewer, it will stay on until it is explicitly turned\n" ,
"off. (The default behavior is to turn panning off after the user releases\n" ,
"the mouse button.)\n" ,
"\n" ,
"-------------------------------\n" ,
"Variable: AFNI_IMAGE_LABEL_MODE\n" ,
"-------------------------------\n" ,
"This integer determines the placement of the image coordinate labels drawn\n" ,
"in the AFNI image viewer windows. The possible values are\n" ,
" 0 = Labels are off\n" ,
" 1 = Labels in upper left\n" ,
" 2 = Labels in upper right\n" ,
" 3 = Labels in lower left\n" ,
" 4 = Labels in lower right\n" ,
" 5 = Labels in upper middle\n" ,
" 6 = Labels in lower middle\n" ,
"You can also control the placement and size of the labels from the Button-3\n" ,
"(right-click) popup menu attached to the intensity bar to the right of the\n" ,
"image sub-window.\n" ,
"\n" ,
"-------------------------------\n" ,
"Variable: AFNI_IMAGE_LABEL_SIZE\n" ,
"-------------------------------\n" ,
"This integer determines the size of the image coordinate labels:\n" ,
" 0 = Small\n" ,
" 1 = Medium\n" ,
" 2 = Large\n" ,
" 3 = Huge\n" ,
" 4 = Enormous\n" ,
"\n" ,
"--------------------------------\n" ,
"Variable: AFNI_IMAGE_LABEL_COLOR (editable)\n" ,
"--------------------------------\n" ,
"This variable controls the color of the image coordinate labels.\n" ,
"\n" ,
"----------------------------------\n" ,
"Variable: AFNI_IMAGE_LABEL_SETBACK (editable)\n" ,
"----------------------------------\n" ,
"This variable, a floating point value between 0 and 0.1, determines how\n" ,
"far from the edge an image coordinate label will be drawn. The units are\n" ,
"fractions of the image width/height.\n" ,
"\n" ,
"------------------------------\n" ,
"Variable: AFNI_CROSSHAIR_LINES (editable)\n" ,
"------------------------------\n" ,
"If this YES/NO variable is set to YES, then the image crosshairs will be\n" ,
"drawn using lines rather than pixels. By default (this is the original\n" ,
"AFNI way), crosshair lines are drawn the same way as functional overlays:\n" ,
"by putting color pixels on top of the image. The new way draws lines on\n" ,
"top of the image instead. The difference is quite visible when the image\n" ,
"is zoomed; overlay by pixels shows the crosshair lines as fat blobs, but\n" ,
"the lines are drawn as thin as possible, no matter what the image window\n" ,
"size and zoom factor.\n" ,
"\n" ,
"Good points about crosshairs drawn with lines:\n" ,
" - They are less obtrusive than pixel overlay, especially if you zoom\n" ,
" or enlarge the image a lot\n" ,
" - When doing a montage with Spacing=1, they'll look better in the\n" ,
" orthogonal slices.\n" ,
"Good points about crosshairs drawn with pixel overlay:\n" ,
" - Pixel overlays can be rendered as translucent (on X11 TrueColor displays);\n" ,
" geometrical overlays are always solid color.\n" ,
"So you have to decide what you need most. You can change this item using\n" ,
"the \"Edit Environment\" pseudo-plugin on the Datamode->Misc menu, so you\n" ,
"can play with it interactively to get the features you want.\n" ,
"\n" ,
"----------------------------\n" ,
"Variable: AFNI_CROP_ZOOMSAVE (editable)\n" ,
"----------------------------\n" ,
"When saving a zoomed image, the default is to save the entire zoomed image,\n" ,
"not just the part you see. If this YES/NO variable is set to YES, then only\n" ,
"the visible part will be saved.\n" ,
"\n" ,
"---------------------------\n" ,
"Variables: AFNI_TLRC_BBOX_*\n" ,
"---------------------------\n" ,
"These variables let you choose the size of the \"Talairach Box\", into which\n" ,
"+tlrc datasets are transformed. If defined, they should be positive values,\n" ,
"in mm. The 5 variables (any or all of which may be used) are:\n" ,
"\n" ,
" AFNI_TLRC_BBOX_LAT = distance from midline to maximum left/right position\n" ,
" [default=80]\n" ,
" AFNI_TLRC_BBOX_ANT = distance from AC to most anterior point in box\n" ,
" [default=80]\n" ,
" AFNI_TLRC_BBOX_POS = distance from AC to most posterior point in box\n" ,
" [default=110]\n" ,
" AFNI_TLRC_BBOX_INF = distance from AC-PC line to most inferior point in box\n" ,
" [default=55 for small box, 65 for big box]\n" ,
" AFNI_TLRC_BBOX_SUP = distance from AC-PC line to most superior point in box\n" ,
" [default=85]\n" ,
"\n" ,
"For example, \"setenv AFNI_TLRC_BBOX_INF 100\" lets you define the +tlrc box\n" ,
"to extend 100 mm below the AC-PC line. Please note that virtually all the\n" ,
"3d* analysis programs (3dANOVA, etc.) do voxel-by-voxel analyses. This fact\n" ,
"means that you will be unable to compare datasets created in +tlrc coordinates\n" ,
"with different box sizes. Also, you will be unable to overlay regions from\n" ,
"the Talairach Daemon database onto odd-sized +tlrc datasets. Therefore, I\n" ,
"recommend that these variables be used only when strictly needed, and with\n" ,
"caution.\n" ,
"\n" ,
"Lastly, try hard not to mix TLRC datasets created with various box sizes in\n" ,
"the same session. Strange things may happen.\n" ,
"\n" ,
"---------------------------\n" ,
"Variables: AFNI_ACPC_BBOX_*\n" ,
"---------------------------\n" ,
"The variables let you choose the size of the \"ACPC Box\", into which \n" ,
"+acpc datasets are transformed. If defined, they should be positive values,\n" ,
"in mm. The 6 variables (any or all of which may be used) are:\n" ,
"\n" ,
" AFNI_ACPC_BBOX_LAT = distance from midline to maximum left/right position\n" ,
" [default=95]\n" ,
" AFNI_ACPC_BBOX_ANT = distance from AC to most anterior point in box\n" ,
" [default=95]\n" ,
" AFNI_ACPC_BBOX_POS = distance from AC to most posterior point in box\n" ,
" [default=140]\n" ,
" AFNI_ACPC_BBOX_INF = distance from AC-PC line to most inferior point in box\n" ,
" [default=70]\n" ,
" AFNI_ACPC_BBOX_SUP = distance from AC-PC line to most superior point in box\n" ,
" [default=100]\n" ,
"\n" ,
"Check example and heed ALL warnings for variables AFNI_TLRC_BBOX_* above.\n" ,
"\n" ,
"-------------------------\n" ,
"Variable: AFNI_TTRR_SETUP\n" ,
"-------------------------\n" ,
"Name of a file to be loaded to define Talairach Atlas Colors, when the Atlas\n" ,
"Colors control panel is first created. Format is the same as a file created\n" ,
"from this control panel's \"Save\" button. This filename should be an absolute\n" ,
"path (e.g., /home/yourname/.afni_ttcolors), since otherwise it will be read\n" ,
"relative to the directory in which you start AFNI.\n" ,
"\n" ,
"-----------------------------\n" ,
"Variable: AFNI_LOAD_PRINTSIZE\n" ,
"-----------------------------\n" ,
"AFNI will print (to stderr) a warning that it is loading a large dataset from\n" ,
"disk. This value determines the meaning of \"large\". For example, setting\n" ,
"this variable to \"40M\" means that loading a dataset larger than 40 Megabytes\n" ,
"will trigger the warning. If not given, the default value is 100 Megabytes.\n" ,
"The purpose of the warning is just to let the user know that it may be several\n" ,
"seconds before the dataset is loaded (e.g., before the images appear). If you\n" ,
"don't want this warning at all, set this variable to the string \"0\".\n" ,
"\n" ,
"-------------------------------\n" ,
"Variable: AFNI_ANALYZE_DATASETS\n" ,
"-------------------------------\n" ,
"If this YES/NO variable is not set to NO, then ANALYZE-format files with name\n" ,
"suffix .hdr will be read into the interactive AFNI program at startup, along\n" ,
"with standard .HEAD/.BRIK datasets. That is, you have to set this variable\n" ,
"explicitly to NO if you don't want ANALYZE-format files to be automatically\n" ,
"recognized by the interactive AFNI program. This variable does not affect\n" ,
"the ability of command line programs (3dSomething) to read .hdr input files.\n" ,
"\n" ,
"-----------------------------\n" ,
"Variable: AFNI_ANALYZE_ORIENT\n" ,
"-----------------------------\n" ,
"ANALYZE .hdr files do not contain reliable information about the orientation\n" ,
"of the data volumes. By default, AFNI assumes that these datasets are\n" ,
"oriented in LPI order. You can set this variable to a different default\n" ,
"order. See AFNI_ORIENT for details on the 3 letter format for this.\n" ,
"\n" ,
"---------------------------------\n" ,
"Variable: AFNI_ANALYZE_AUTOCENTER\n" ,
"---------------------------------\n" ,
"ANALYZE .hdr files do not contain information about the origin of coordinates.\n" ,
"The default AFNI approach mirrors that of FSL - the outermost corner of the\n" ,
"first voxel in the dataset is set to (0,0,0). If you set this variable\n" ,
"(AFNI_ANALYZE_AUTOCENTER) to YES, then instead (0,0,0) will be set to the\n" ,
"center of the 3D ANALYZE array. This is the default that would be applied\n" ,
"if you read the ANALYZE array into program to3d.\n" ,
"\n" ,
"----------------------------\n" ,
"Variable: AFNI_VERSION_CHECK\n" ,
"----------------------------\n" ,
"If this YES/NO variable is set to NO, then AFNI will not try to check if its\n" ,
"version is up-to-date when it starts. Otherwise, it will try to check the\n" ,
"program version with the AFNI web server.\n" ,
"\n" ,
"-------------------------\n" ,
"Variable: AFNI_MOTD_CHECK\n" ,
"-------------------------\n" ,
"Similarly, if this YES/NO variable is set to NO, then AFNI will not display\n" ,
"and fetch the AFNI \"Message of the Day\" at startup. You can always check\n" ,
"the MOTD by using the Datamode->Misc menu.\n" ,
"\n" ,
"-----------------------------------\n" ,
"Variable: AFNI_SLICE_SPACING_IS_GAP\n" ,
"-----------------------------------\n" ,
"This YES/NO variable is designed to patch a flaw in some DICOM files, where\n" ,
"the \"Spacing Between Slices\" attribute is erroneously set to the gap between\n" ,
"the slices, rather than the center-to-center slice distance specified in\n" ,
"the DICOM standard. If this variable is set to YES, then the \"Slice Thickness\"\n" ,
"attribute will always be added to \"Spacing Between Slices\" to get the z voxel\n" ,
"size (assuming both attributes are present in the DICOM file).\n" ,
"\n" ,
"To check if a DICOM file has this problem, you can read it into to3d with\n" ,
"the command \"to3d suspect_file_name\". A warning will be printed to the\n" ,
"terminal window if attribute \"Spacing Between Slices\" is less than\n" ,
"attribute \"Slice Thickness\". Another way to check is with a command like so\n" ,
"\n" ,
" dicom_hdr suspect_file_name | grep \"Slice\"\n" ,
"\n" ,
"then check if the \"Spacing Between Slices\" and \"Slice Thickness\" values are\n" ,
"correct for the given acquisition. We have only seen this problem in GE\n" ,
"generated DICOM files, but that doesn't mean it won't occur elsewhere.\n" ,
"\n" ,
"If this variable is set to NO, then this patchup will never be made.\n" ,
"The z voxel size will be set to \"Spacing Between Slices\" if present,\n" ,
"otherwise to \"Slice Thickness\". This may be needed for some Phillips pulse\n" ,
"sequences, which can report \"Spacing Between Slices\" < \"Slice Thickness\".\n" ,
"In such a case, if this variable is not set, the wrong z voxel size will\n" ,
"be assigned!\n" ,
"\n" ,
"If this variable is not set at all, AND if \"Spacing Between Slices\" is less\n" ,
"less than 0.99 times \"Slice Thickness\", it will be treated as a gap;\n" ,
"that is, the z voxel size will again be set to \"Spacing Between Slices\" +\n" ,
"\"Slice Thickness\" if \"Spacing Between Slices\" < 0.99*\"Slice Thickness\".\n" ,
"Otherwise, the z voxel size will be set to the larger of\n" ,
"\"Spacing Between Slices\" and \"Slice Thickness\".\n" ,
"\n" ,
"N.B.: \"YES\", \"NO\", and \"not set\" have 3 different sets of behavior!\n" ,
" In the summary below, if a variable isn't set, treat it as zero:\n" ,
"\n" ,
" YES => dz = Thickness + Spacing\n" ,
" NO => dz = Spacing if present, otherwise Thickness\n" ,
" not set => if( Spacing > 0 && Spacing < 0.99*Thickness )\n" ,
" dz = Thickness + Spacing\n" ,
" else\n" ,
" dz = MAX( Thickness , Spacing )\n" ,
"\n" ,
"If neither variable is set, then dz=1 mm, which is probably wrong.\n" ,
"\n" ,
"Sorry about this complexity, but the situation with various manufacturers\n" ,
"is complicated, murky, and confusingly maddening.\n" ,
"\n" ,
"---------------------------------------------------\n" ,
"Variables: AFNI_DICOM_RESCALE and AFNI_DICOM_WINDOW\n" ,
"---------------------------------------------------\n" ,
"DICOM image files can contain rescaling and windowing \"tags\". If present,\n" ,
"these values indicate to affinely modify the values stored in the file.\n" ,
"As far as I can tell, \"rescale\" means that the values should always be\n" ,
"modified, whereas \"window\" means the values should be modified for display\n" ,
"purposes. If both are present, the rescale comes before window. These\n" ,
"two YES/NO environment variables control whether the AFNI image input\n" ,
"functions (used in to3d) should apply the rescale and window tags.\n" ,
"\n" ,
"It is my impression from the laconic, terse, and opaque DICOM manual that\n" ,
"window tags are intended for display purposes only, and that they aren't\n" ,
"needed for signal processing. But you'll have to examine your own data to\n" ,
"decide whether to use these options -- manufacturers seem to differ.\n" ,
"Plus, I don't have that much experience with DICOM data from many different\n" ,
"sources.\n" ,
"\n" ,
"-----------------------\n" ,
"Variable: IDCODE_PREFIX\n" ,
"-----------------------\n" ,
"AFNI stores with each dataset a unique string, called an \"idcode\". An example\n" ,
"is \"XYZ_MoNLqdNOwMNEYmKSBytfJg\". You can alter the first three characters of\n" ,
"the idcode with this variable. For example,\n" ,
" setenv IDCODE_PREFIX RWC\n" ,
"sets the first 3 characters of newly generated idcodes to be the initials of\n" ,
"AFNI's author. I find this a handy way to \"brand\" my datasets. Of course,\n" ,
"there are only 17576 possible 3 letter combinations (140608 if you allow for\n" ,
"case), so you should claim your prefix soon!!!\n" ,
"\n" ,
"Idcodes are used to store links between datasets. For example, when SUMA\n" ,
"sends a surface to AFNI, it identifies the dataset to which the surface is\n" ,
"to be associated with the dataset's idcode. Similarly, when AFNI sends a\n" ,
"color overlay to SUMA, it uses the surface idcode to indicate which surface\n" ,
"family the overlay is to be mapped onto.\n" ,
"\n" ,
"-------------------------\n" ,
"Variable: AFNI_AGIF_DELAY\n" ,
"-------------------------\n" ,
"This is the time delay between frames when writing an animated GIF file from\n" ,
"an image viewer window. The units are 100ths of seconds; the default value\n" ,
"is 20 (= 5 frames per second).\n" ,
"\n" ,
"-----------------------------\n" ,
"Variable: AFNI_MPEG_FRAMERATE\n" ,
"-----------------------------\n" ,
"This value sets the frame rate (per second) of the MPEG-1 output animation\n" ,
"from the image viewer window. The legal values allowed by MPEG-1 are\n" ,
"24, 25, 30, 50, and 60; 24 is the default.\n" ,
"\n" ,
"-----------------------------\n" ,
"Variable: AFNI_STARTUP_SCRIPT\n" ,
"-----------------------------\n" ,
"If this is set, this is the name of an AFNI Script to run when AFNI first\n" ,
"starts. (See the file README.driver for information about AFNI Scripts.)\n" ,
"If this is not set, it defaults to \".afni.startup_script\". The program first\n" ,
"tries to read this filename from the current working directory; if that fails,\n" ,
"then it tries to read from your home directory. No error message is given\n" ,
"if neither file can be read.\n" ,
"\n" ,
"You can save a file \".afni.startup_script\" that will recreate the window\n" ,
"layout you currently have. Use the \"Datamode->Misc->Save Layout\" button\n" ,
"and press \"Set\" on the popup control without entering any filename. Instead\n" ,
"of a Layout file (cf. AFNI_LAYOUT_FILE above), you'll get a Script file.\n" ,
"\n" ,
"The capabilities of Script files are being expanded. Not all features of\n" ,
"the AFNI window setup are currently save-able this way.\n" ,
"\n" ,
"You can load a Script file interactively during an AFNI run by using the\n" ,
"button \"Datamode->Misc->Run Script\". As a 'secret' option, if you enter\n" ,
"a line containing a blank in the the filename dialog, that line will be\n" ,
"executed as a single command, rather than be used as a script filename.\n" ,
"\n" ,
"------------------------------\n" ,
"Variable: AFNI_DEFAULT_OPACITY\n" ,
"------------------------------\n" ,
"This should be set to an integer from 1..9, and controls the default opacity\n" ,
"setting for the color overlay in image viewer windows.\n" ,
"\n" ,
"-----------------------------\n" ,
"Variable: AFNI_DEFAULT_IMSAVE\n" ,
"-----------------------------\n" ,
"This should be set to the suffix of the image format to which you want to save\n" ,
"from an image viewer. The suffixes AFNI knows about (as of 23 Jan 2003) are\n" ,
" ppm = Portable PixMap format = cat\n" ,
" jpg = Joint Photographics Experts Group (JPEG) format = cjpeg\n" ,
" gif = Compuserve Graphics Interchange File (GIF) format = ppmtogif\n" ,
" tif = Tagged Image File Format (TIFF) = ppm2tiff or pnmtotiff\n" ,
" bmp = Windows Bitmap (BMP) format = ppmtobmp\n" ,
" eps = Encapsulated PostScript format = pnmtops\n" ,
" pdf = Portable Document Format = epstopdf\n" ,
" png = Portable Network Graphics format = pnmtopng\n" ,
"The third column is the name of the external filter program that AFNI uses to\n" ,
"write the format. If a filter is not present on your system, then that option\n" ,
"is not available. Most of these filters are part of the netpbm package.\n" ,
"\n" ,
"-----------------------------\n" ,
"Variables: AFNI_COLORSCALE_xx for xx=01, 02, ..., 99\n" ,
"-----------------------------\n" ,
"These variables let you name files to be read it at AFNI startup to define\n" ,
"\"continuous\" colorscales for the \"**\" mode of the color pbar. These files\n" ,
"will be looked for in the current directory when you start AFNI, or in your\n" ,
"home directory (if they aren't in the current directory). A sample file:\n" ,
"\n" ,
" Yellow-Red-Blue\n" ,
" 1.0 #ffff00\n" ,
" 0.7 #ffaa00\n" ,
" 0.5 #ff0000\n" ,
" 0.3 #aa00aa\n" ,
" 0.0 #0000ff\n" ,
"\n" ,
"The first line is the name of this colorscale, to go in the colorscale popup\n" ,
"chooser. The succeeding lines each have a number and a color definition.\n" ,
"The numbers should be decreasing, and indicate the location on the colorscale.\n" ,
"The largest number corresponds to the top of the colorscale and the smallest\n" ,
"to the bottom - intermediate numbers denote intermediate locations. The colors\n" ,
"at each location are specified using X11 notation (cf. \"man XParseColor\").\n" ,
"In this example, I'm using hexadecimal colors, in the form #rrggbb, where each\n" ,
"hex pair ranges from 00 to ff. Another color format is \"rgbi:rf/gf/bf\",\n" ,
"where each value rf,gf,bf is a number between 0.0 and 1.0 (inclusive); for\n" ,
"example, yellow would be \"rgbi:1.0/1.0/0.0\".\n" ,
"\n" ,
"Colors are interpolated (linearly in RGB space) between the break locations\n" ,
"given in the file. There are actually 128 color locations on a colorscale.\n" ,
"\n" ,
"An alternative format for the file is to omit the numbers indicating the\n" ,
"break locations. In this case, the break locations will be taken to be\n" ,
"equally spaced. For example:\n" ,
"\n" ,
" Yellow-Red-Blue\n" ,
" #ffff00\n" ,
" #ffaa00\n" ,
" #ff0000\n" ,
" #aa00aa\n" ,
" #0000ff\n" ,
"\n" ,
"This example is not exactly the same as the other one, since the breakpoints\n" ,
"are evenly spaced now (as if they had been given as 1.0, 0.75, 0.5, 0.25,\n" ,
"and 0.0). With this format, if you want to manually specify all 128 colors,\n" ,
"you can do so, 1 color per line, remembering that the first line of the file\n" ,
"is taken to be the colorscale title (no blanks allowed in the title!).\n" ,
"\n" ,
"---------------------------------\n" ,
"Variable: AFNI_COLORSCALE_DEFAULT\n" ,
"---------------------------------\n" ,
"If set, this is the name of the default colorscale to use in setup. As a\n" ,
"special case, if you DO NOT want a colorscale to be setup by default at all,\n" ,
"then set this variable to the string \"NO\".\n" ,
"N.B.: This variable only applies if you are using AFNI with a TrueColor X11\n" ,
"visual. If you are using a PseudoColor visual, then this variable is ignored!\n" ,
"\n" ,
"----------------------------\n" ,
"Variable: AFNI_RESCAN_METHOD\n" ,
"----------------------------\n" ,
"On 28 Dec 2002, I modified the way that the \"Rescan\" operation in AFNI works\n" ,
"when re-reading datasets from sessions. The old way would purge and replace\n" ,
"all datasets; the new way just adds datasets that didn't exist before.\n" ,
"There are some differences between these methods:\n" ,
" \"Replace\" will detect changes to a dataset, so if you add a brick using\n" ,
" 3dTcat -glueto (for example), this will be reflected in AFNI.\n" ,
" \"Replace\" will cause troubles if you are using a dataset in a plugin;\n" ,
" the two main examples are volume rendering and the drawing plugin.\n" ,
" This problem will occur even if you didn't do anything to the dataset\n" ,
" on disk, since the internal pointer to the dataset will have been\n" ,
" changed by the rescan, but the plugins won't know that.\n" ,
" \"Add\" will not detect changes to a dataset on disk, but it also won't\n" ,
" affect the pointers to the existing datasets.\n" ,
"You can choose to use the \"Replace\" method (the old style) by setting\n" ,
"this environment variable to the string \"REPLACE\".\n" ,
"\n" ,
"---------------------------\n" ,
"Variable: AFNI_OLD_PPMTOBMP\n" ,
"---------------------------\n" ,
"The old (before 21 Feb 2003) usage of netpbm program \"ppmtobmp\" was to\n" ,
"write a color image quantized to 255 colors. The new usage is to write\n" ,
"a 24-bit image, which is thus not color-quantized. If you want the old\n" ,
"behavior, set this environment variable to YES. This setting (YES) will\n" ,
"be necessary if you have an older version of ppmtobmp in your path, which\n" ,
"doesn't support the \"-bpp\" option.\n" ,
"\n" ,
"------------------------------\n" ,
"Variable: AFNI_1DPLOT_COLOR_xx\n" ,
"------------------------------\n" ,
"This variable lets you set the colors used in the 1dplot program (and other\n" ,
"similar graphs). Here, \"xx\" is a number from \"01\" to \"19\". The value of\n" ,
"the environment variable must be in the form \"rgbi:rf/gf/bf\", where each\n" ,
"color intensity (rf, gf, bf) is a number between 0.0 and 1.0. For example,\n" ,
"\"rgbi:1.0/1.0/0.0\" is yellow. By default, the first 4 colors are defined\n" ,
"as the equivalents of\n" ,
" setenv AFNI_1DPLOT_COLOR_01 rgbi:0.0/0.0/0.0\n" ,
" setenv AFNI_1DPLOT_COLOR_02 rgbi:0.9/0.0/0.0\n" ,
" setenv AFNI_1DPLOT_COLOR_03 rgbi:0.0/0.7/0.0\n" ,
" setenv AFNI_1DPLOT_COLOR_04 rgbi:0.0/0.0/0.9\n" ,
"which are black, red, green, and blue, respectively. You can alter these\n" ,
"colors, or leave them unchanged and start defining colors at 05. The largest\n" ,
"color number you define will be the last color index used; if more line colors\n" ,
"are needed, they will cycle back to color 01. If you leave a gap in the\n" ,
"numbering (e.g., you define color 07 but not 05 or 06), then the undefined\n" ,
"colors will be black.\n" ,
"\n" ,
"---------------------------------\n" ,
"Variable: AFNI_SIEMENS_INTERLEAVE\n" ,
"---------------------------------\n" ,
"The old (pre-DICOM) Siemens .ima image mosaic format sometimes stores the\n" ,
"multi-slice EPI data in correct spatial order and sometimes in correct\n" ,
"time acquisition order. In the latter case, the images are stored in\n" ,
"a spatially-interleaved fashion. As far as I know, there is no way to\n" ,
"tell this from the .ima file header itself. Therefore, if you have a\n" ,
"problem with such files, set this variable to YES to un-interleave the\n" ,
"images when to3d reads them. One way to tell if the images need to be\n" ,
"un-interleaved is to do\n" ,
" afni -im fred.ima\n" ,
"then look at the images in an Axial image viewer. If the slices make up\n" ,
"a single coherent volume, then they are NOT interleaved. If the slices\n" ,
"look like they make up 2 separate brain volumes, then they need to be\n" ,
"un-interleaved, and you need to set this variable to YES.\n" ,
"\n" ,
"-----------------------------\n" ,
"Variable: AFNI_TRY_DICOM_LAST\n" ,
"-----------------------------\n" ,
"When to3d tries to read an image file, it guesses the format from the\n" ,
"filename. However, this doesn't always work. In particular, DICOM files\n" ,
"don't have any fixed filename suffix or prefix. If all else fails, to3d\n" ,
"normally tries to read a file as a DICOM file, and as a last resort, as\n" ,
"a flat binary file. However, if a file is NOT a DICOM file, the DICOM\n" ,
"reading function will print out a lot of error messages, since there is\n" ,
"also no standard internal marker in all DICOM files that identify them.\n" ,
"Most people don't like all these messages (perhaps hundreds per file),\n" ,
"even if the program then successfully reads their flat binary files.\n" ,
"\n" ,
"If this YES/NO variable is set to YES, then the normal last-resort order\n" ,
"of reading described above is reversed. If to3d can't read the file any\n" ,
"other way, it will try it as a flat binary file. If that fails, then\n" ,
"DICOM will be the ultimate resort, instead of being the penultimate\n" ,
"resort that it is by default. This may help elide some error messages.\n" ,
"However, if you have a DICOM file that is exactly 131072 bytes long\n" ,
"(for example), then it will be interpreted as a headerless 256x256 image\n" ,
"of shorts, instead of whatever it really is. So only set this variable\n" ,
"to YES if necessary!\n" ,
"\n" ,
"-----------------------------\n" ,
"Variable: AFNI_THRESH_BIGSTEP\n" ,
"-----------------------------\n" ,
"The AFNI threshold sliders (in the Define Overlay control panels and the\n" ,
"Render Dataset plugins) are divided into 10000 steps from bottom to top.\n" ,
"If you click in the trough or use the PageUp/PageDown keys, the default\n" ,
"action is to move the slider 10 of the steps at once. (The up and down\n" ,
"arrow keys move 1 step at a time.) You can change this big step from the\n" ,
"default of 10 to any value between 1 and 1000 by setting this environment\n" ,
"variable; for example\n" ,
" setenv AFNI_THRESH_BIGSTEP 100\n" ,
"will move the slider 1% of its height per PageUp/PageDown key or mouse click.\n" ,
"\n" ,
"--------------------------\n" ,
"Variable: AFNI_THRESH_AUTO (editable)\n" ,
"--------------------------\n" ,
"If this YES/NO variable is set to YES, then whenever you switch overlay datasets,\n" ,
"the function threshold slider will automatically change to some value that may\n" ,
"be appropriate for the values in the new dataset. [This is for Ziad!]\n" ,
"\n" ,
"------------------------------\n" ,
"Variable: AFNI_SNAPFILE_PREFIX\n" ,
"------------------------------\n" ,
"Image files saved with the \"snapfile\" (or \"record to file\") by default have\n" ,
"filenames of the form \"S_000001.ppm\". The prefix \"S\" can be altered by\n" ,
"setting this environment variable; for example,\n" ,
" setenv AFNI_SNAPFILE_PREFIX Elvis\n" ,
"will save snapfiles with names like \"Elvis_000666.ppm\". You can view snapfiles\n" ,
"with the \"aiv\" (\"AFNI Image Viewer\") utility, the \"xv\" program, or many other\n" ,
"Unix utilities.\n" ,
"\n" ,
"-------------------------------\n" ,
"Variable: AFNI_STARTUP_WARNINGS\n" ,
"-------------------------------\n" ,
"When the interactive AFNI program starts, it may pop up warnings about the\n" ,
"programming environment for which it was compiled. At this time, there are\n" ,
"two such warning messages possible:\n" ,
" LessTiff: AFNI will work with LessTif, but works better with Motif.\n" ,
" Button-3: On Solaris 2.8, Button-3 popup menus don't work quite properly.\n" ,
"If you are tired of seeing these messages, set AFNI_STARTUP_WARNINGS to NO.\n" ,
"\n" ,
"----------------------\n" ,
"Variable: AFNI_1D_TIME\n" ,
"----------------------\n" ,
"If this YES/NO variable is set to YES, then when a multicolumn .1D file is\n" ,
"read in as an AFNI dataset, the column variable is taken to be time, and\n" ,
"a time-dependent dataset is created. The default is to create a bucket\n" ,
"dataset.\n" ,
"\n" ,
"-------------------------\n" ,
"Variable: AFNI_1D_TIME_TR\n" ,
"-------------------------\n" ,
"If this is set, and AFNI_1D_TIME is YES, then this determines the TR (in\n" ,
"seconds) of a .1D file read in as an AFNI dataset.\n" ,
"\n" ,
"------------------------\n" ,
"Variable: AFNI_3D_BINARY\n" ,
"------------------------\n" ,
"If this is set to YES, then .3D files are written by AFNI programs in\n" ,
"binary, rather than the default text mode. Binary files will be more\n" ,
"compact (usually) and faster to read in.\n" ,
"\n" ,
"--------------------------\n" ,
"Variable: AFNI_MAX_OPTMENU (editable)\n" ,
"--------------------------\n" ,
"This variable (default=255) sets the maximum number of entries allowed\n" ,
"in an AFNI \"option menu\" -- these are the buttons that popup a menu\n" ,
"of values from which to choose, and which also let you popup a text\n" ,
"list chooser by right-clicking in the menu's label. (Example: the\n" ,
"sub-brick option menus \"Anat\", \"Func\", \"Thr\" on the \"Define Overlay\"\n" ,
"control panel.)\n" ,
"\n" ,
"Some computer systems may crash when an option menu gets too big.\n" ,
"That's why there is a default limit in AFNI of 255 entries. However,\n" ,
"if you have a bucket dataset with more than 255 sub-bricks, this makes\n" ,
"it impossible to view the later data volumes. If this problem arises,\n" ,
"you can try setting this environment variable to a larger limit (e.g.,\n" ,
"99999 would take care of all currently imaginable cases).\n" ,
"\n" ,
"---------------------------------\n" ,
"Variable: AFNI_VALUE_LABEL_DTABLE\n" ,
"---------------------------------\n" ,
"This variable sets a filename that holds a default value-label table\n" ,
"for the Draw Dataset plugin. A sample file is shown below:\n" ,
"\n" ,
" <VALUE_LABEL_DTABLE\n" ,
" ni_type=\"2*String\"\n" ,
" ni_dimen=\"3\" >\n" ,
" \"1\" \"elvis\"\n" ,
" \"2\" \"presley\"\n" ,
" \"3\" \"memphis\"\n" ,
" </VALUE_LABEL_DTABLE>\n" ,
"\n" ,
"The 'ni_dimen' attribute is the number of value-label pairs; in the\n" ,
" above example it is 3.\n" ,
"Each value-label pair is shown on a separate line. The values and\n" ,
" labels are strings, enclosed in quote characters. There should be\n" ,
" exactly as many value-label pairs as specified in 'ni_dimen'.\n" ,
"If you really want to put a double quote character \" in a label,\n" ,
" you can enclose the label in single forward quotes ' instead.\n" ,
"When you 'Save' a drawn dataset from the Draw Dataset plugin, the\n" ,
" .HEAD file attribute VALUE_LABEL_DTABLE will contain a table in\n" ,
" exactly this XML-based format.\n" ,
"\n" ,
"-------------------------------\n" ,
"Variable: AFNI_STROKE_THRESHOLD (editable)\n" ,
"-------------------------------\n" ,
"If you press Button-1 in an image window, and then move it left or\n" ,
"right (\"stroke it\") before releasing the button, the grayscale mapping\n" ,
"changes in the same way as if you pressed the 'c' button up and the 'b'\n" ,
"button down. This variable sets the threshold for the stroking movement\n" ,
"size in pixels; a movement of this number of pixels rightwards corresponds\n" ,
"to one press of 'c' up and 'b' down, while a leftwards movement is like\n" ,
"one press of 'c' down and 'b' up. Larger movements make larger adjustments.\n" ,
"\n" ,
"A larger threshold makes the stroking less sensitive; a smaller threshold\n" ,
"makes it more sensitive. The value you choose will depend on your personal\n" ,
"taste. The default is 32 pixels, which is the flavor I prefer. If you set\n" ,
"this variable to 0, then the stroking function is disabled.\n" ,
"\n" ,
"-------------------------------\n" ,
"Variable: AFNI_STROKE_AUTOPLOT (editable)\n" ,
"-------------------------------\n" ,
"If this variable is set to YES, then the graymap-versus-data value plot\n" ,
"(manually controlled by \"Display Graymap Plot\") is automatically popped\n" ,
"up when the grayscale mapping is altered by using the stroking feature\n" ,
"described above. When the stroke is finished, the plot will pop down.\n" ,
"N.B.: when the 'Draw Dataset' plugin is active, this option is disabled\n" ,
"temporarily.\n" ,
"\n" ,
"-----------------------------\n" ,
"Variable: AFNI_IMAGE_MINTOMAX (editable)\n" ,
"-----------------------------\n" ,
"If this variable is set to YES, then image viewer windows will be set\n" ,
"to the \"Min-to-Max\" state rather than the default \"2%-to-98%\" state\n" ,
"when they are opened. If you set this in the \"Edit Environment\"\n" ,
"control, it only affects image viewer windows opened after that point.\n" ,
"\n" ,
"--------------------------------\n" ,
"Variable: AFNI_IMAGE_GLOBALRANGE (editable)\n" ,
"--------------------------------\n" ,
"If this variable is set to YES, then the image viewer windows will be\n" ,
"set to scale the bottom gray level to the minimum value in the 3D\n" ,
"volume and the top gray level to the maximum value in the 3D volume.\n" ,
"This setting overrides the \"Min-to-Max\" and \"2%-to-98%\" settings in\n" ,
"the \"Disp\" control panel. This setting also applies to all image\n" ,
"viewers. If you set this in the \"Edit Environment\" control, it will\n" ,
"apply to all open image viewers immediately, as well as to any image\n" ,
"viewers opened later.\n" ,
" It is important to realize that if you use the 'Display Range'\n" ,
"popup to set the bot-top range for the grayscale, these settings\n" ,
"will override the global range UNTIL you switch datasets or switch\n" ,
"sub-bricks within a dataset. At that point, the global range for\n" ,
"the new volume will be enforced. This change can be confusing.\n" ,
"Therefore, the info label beneath the slider shows the source of\n" ,
"the bot-top grayscale values:\n" ,
" [2%-98%] = from the 2% to 98% points on the slice histogram\n" ,
" [Min2Max] = from the 0% to 100% points on the slice histogram\n" ,
" [Glob] = set from the entire volume min and max values\n" ,
" [User] = set by the user from 'Display Range'\n" ,
" absent = not applicable (e.g., underlay image is RGB)\n" ,
"The popup 'hint' for the grayscale bar shows the current values\n" ,
"of the bot-top range, if you want to know what numbers correspond\n" ,
"to the image at which you are gazing so fondly.\n" ,
" Finally, note that when a montage is built, the number-to-grayscale\n" ,
"algorithm is applied to each slice separately, and then the montage\n" ,
"is assembled. For [2%-98%] and [Min2Max], this fact means that each\n" ,
"slice will (probably) have a separate grayscale conversion range.\n" ,
"\n" ,
"----------------------------\n" ,
"Variable: AFNI_DRAW_UNDOSIZE (editable)\n" ,
"----------------------------\n" ,
"This variable sets the size (in units of Megabytes) of the Undo/Redo\n" ,
"buffer in the Draw Dataset plugin. The default value is 6. If you\n" ,
"are short on memory, you could set this to 1. If you are running out\n" ,
"of undo levels, you could set this to a larger value; however, this\n" ,
"would only be needed if you are drawing huge 3D swaths of data at a\n" ,
"time (e.g., using the 3D sphere option with a large radius).\n" ,
"\n" ,
"---------------------\n" ,
"Variable: AFNI_SPEECH (editable)\n" ,
"---------------------\n" ,
"If this YES/NO variable is set to NO, then the AFNI speech synthesis\n" ,
"is disabled. At the current time (Nov 2003), only the Mac OS X 10.3\n" ,
"version of AFNI uses speech synthesis in any way. And that's just\n" ,
"for fun.\n" ,
"\n" ,
"------------------------------\n" ,
"Variable: AFNI_IMAGE_ZEROCOLOR\n" ,
"------------------------------\n" ,
"This variable, if set to the string name of one of the colors in the\n" ,
"color chooser menus (e.g., \"Black\"), will result in voxels whose value\n" ,
"is 0 being set to this color in the slice viewing windows (except when\n" ,
"viewing RGB images). The main function is to avoid having to use the\n" ,
"\"Choose Zero Color\" menu all the time, especially when you use the \"Swap\"\n" ,
"feature to invert the grayscale map (e.g., to make a T2 weighted image\n" ,
"look sort of like a T1 weighted image).\n" ,
"\n" ,
"----------------------------\n" ,
"Variable: AFNI_MPEG_DATASETS\n" ,
"----------------------------\n" ,
"This variable can be used to allow MPEG files to be read in as AFNI datasets.\n" ,
"Such datasets are inherently 3 dimensional. How they will be organized inside\n" ,
"AFNI depends on the setting of this variable. The options are:\n" ,
" SPACE = the frame sequence number will be the z-axis\n" ,
" TIME = the frame sequence number will be the time axis\n" ,
" NO = MPEG files won't be read as AFNI datasets\n" ,
" (they can still be read as images into to3d, aiv, etc.)\n" ,
"If this variable is NOT set to anything, then it is the same as SPACE.\n" ,
"\n" ,
"MPEG filenames input to AFNI programs (as sources of images or as datasets)\n" ,
"must end in \".mpg\", \".MPG\", \".mpeg\", or \".MPEG\". MPEG datasets will be read\n" ,
"so that the individal images are displayed in an Axial image window.\n" ,
"\n" ,
"---------------------------\n" ,
"Variable: AFNI_MPEG_GRAYIZE\n" ,
"---------------------------\n" ,
"If this YES/NO variable is set to YES, then MPEG files read into AFNI,\n" ,
"to3d, or aiv will be converted to grayscale, even if the images in\n" ,
"the movie are in color.\n" ,
"\n" ,
"--------------------------\n" ,
"Variable: AFNI_VIDEO_DELAY (editable)\n" ,
"--------------------------\n" ,
"This is the number of milliseconds the AFNI waits between drawing new\n" ,
"images when the 'V' or 'v' keys are pressed in an image (or graph)\n" ,
"window. The default value is 1, which is faster than video can be\n" ,
"displayed anyway. Set this to a larger value (e.g, 100) to slow down\n" ,
"the image redraw rate.\n" ,
"\n" ,
"----------------------------\n" ,
"Variable: AFNI_IMAGE_ENTROPY (editable)\n" ,
"----------------------------\n" ,
"If this numeric variable is set, this is the entropy of an image below\n" ,
"which the 2%-98% image scaling will be disabled, and min-to-max will\n" ,
"be used instead. The units are bits/byte; a useful threshold seems to\n" ,
"be in the range (0.2,0.5). For images that only have a few values\n" ,
"different from 0, the 2%-98% scaling can produce weird artifacts. Such\n" ,
"images will also have a very low entropy. Since this variable can be\n" ,
"changed interactively from the Edit Environment controls, you can play\n" ,
"with it to see how it affects your images.\n" ,
"\n" ,
"----------------------------\n" ,
"Variable: AFNI_LOGO16 (etc.)\n" ,
"----------------------------\n" ,
"If this variable is set to YES, then the 'AFNI' background logo used in\n" ,
"the controller and image windows will be enabled. By default, it is off.\n" ,
"You can control the colors of this logo by the following variables:\n" ,
" AFNI_LOGO16_FOREGROUND_x\n" ,
" AFNI_LOGO16_BACKGROUND_x\n" ,
"where 'x' is 'A', 'B', 'C', etc., for the various controller labels.\n" ,
"If AFNI_LOGO16_BACKGROUND_x isn't set, then AFNI_LOGO16_BACKGROUND\n" ,
"(with no suffix) is checked as an alternate. The values of these\n" ,
"variables should be the names of one of the labels on the color chooser\n" ,
"menus (e.g., the \"Xhairs Color\" menu). You can use these variables to\n" ,
"make the windows for the various controllers somewhat distinct in\n" ,
"appearance. If these color variables are not set at all, then AFNI\n" ,
"uses some colors of my choosing for this purpose.\n" ,
"\n" ,
"--------------------------\n" ,
"Variable: AFNI_THRESH_LOCK (editable)\n" ,
"--------------------------\n" ,
"This variable can be used to lock the Define Overlay threshold sliders\n" ,
"together. There are three possibilities:\n" ,
" NO (the default) => each controller's slider is independent\n" ,
" VALUE => the numerical value on each slider will be the same\n" ,
" P-VALUE => the p-value for each slider will be the same\n" ,
"This locking only applies to AFNI controllers that are Lock-ed together\n" ,
"(cf. AFNI_ALWAYS_LOCK and the Define Datamode->Lock menu). If p-values\n" ,
"are locked, this lock will also only apply to controllers whose current\n" ,
"Threshold sub-brick has a known statistical distribution.\n" ,
"\n" ,
"When you drag a locked threshold slider, the other one will only change\n" ,
"when you release the mouse button -- they won't slide in tandem, but will\n" ,
"just jump to the final value.\n" ,
"\n" ,
"------------------------\n" ,
"Variable: AFNI_PBAR_LOCK (editable)\n" ,
"------------------------\n" ,
"If this variable is set to YES, then the Define Overlay color bars\n" ,
"(the \"pbars\") of AFNI controllers that are Lock-ed together will be\n" ,
"coordinated. Changes to one locked pbar will be reflected in the\n" ,
"others immediately.\n" ,
"\n" ,
"----------------------------\n" ,
"Variable: AFNI_IMAGE_ZOOM_NN (editable)\n" ,
"----------------------------\n" ,
"If this variable is set to YES, then image viewer windows will use\n" ,
"nearest neighbor interpolation for zooming. The default is linear\n" ,
"interpolation, which produces smoother-looking images. However, some\n" ,
"people want to see the actual data values represented in the window,\n" ,
"not some fancy-schmancy interpolated values designed to look good but\n" ,
"in fact making a mockery of a sham of a mockery of a travesty of two\n" ,
"mockeries of a sham of reality.\n" ,
"\n" ,
"------------------------------\n" ,
"Variable: AFNI_DISABLE_CURSORS\n" ,
"------------------------------\n" ,
"If this variable is set to YES, then AFNI will not try to change the X11\n" ,
"cursor shape. This feature is available because it seems that sometimes\n" ,
"particular X11 installations choices of cursor and AFNI's choices don't\n" ,
"work together well. If you have unpleasant cursors in AFNI (e.g., an X),\n" ,
"try setting this variable to YES.\n" ,
"\n" ,
"-----------------------------\n" ,
"Variable: AFNI_SLAVE_FUNCTIME (editable)\n" ,
"-----------------------------\n" ,
"When the underlay and overlay datasets both are time-dependent, switching\n" ,
"the time index will change both the underlay and overlay sub-bricks. If\n" ,
"you want the time index control to change ONLY the underlay sub-brick,\n" ,
"then set this variable to NO.\n" ,
"\n" ,
"----------------------------\n" ,
"Variable: AFNI_SLAVE_THRTIME (editable)\n" ,
"----------------------------\n" ,
"When the underlay and overlay datasets both are time-dependent, switching\n" ,
"the time index will change both the underlay and overlay sub-bricks, but\n" ,
"NOT the threshold sub-brick. If you want the time index control to change\n" ,
"the threshold sub-brick, then set this variable to YES.\n" ,
"\n" ,
"----------------------------\n" ,
"Variable: AFNI_CLICK_MESSAGE\n" ,
"----------------------------\n" ,
"If this veriable is set to NO, then the string\n" ,
" [---------------]\n" ,
" [ Click in Text ]\n" ,
" [ to Pop Down!! ]\n" ,
"will NOT be appended to the very first popup message window that AFNI\n" ,
"creates. This message was added because some people do not realize\n" ,
"that the way to get rid of these popups (before they vanish on their\n" ,
"own after 30 seconds) is to click in them. You know who you are.\n" ,
"However, if you are advanced enough to read this file, then you probably\n" ,
"aren't one of THEM.\n" ,
"\n" ,
"------------------------------------\n" ,
"Variable: AFNI_REALTIME_MP_HOST_PORT (editable)\n" ,
"------------------------------------\n" ,
"When this variable is set, the realtime plugin will attempt to open a tcp\n" ,
"socket to the corresponding host and port, and will send the six registration\n" ,
"correction parameters for each 3D volume received by the plugin. This applies\n" ,
"only to the case of graphing 3D registration. The socket will be opened at\n" ,
"the start of each run, and will be closed at the end. A simple example of\n" ,
"what to set this variable to is localhost:53214. See 'serial_helper -help'\n" ,
"for more details.\n" ,
"\n" ,
"-----------------------------\n" ,
"Variable: AFNI_X11_REDECORATE (editable)\n" ,
"-----------------------------\n" ,
"By default, AFNI tries to change some of the \"decorations\" (control buttons)\n" ,
"on some of the windows it creates (e.g., removing resize handles). If you\n" ,
"don't want this to happen, set this variable to NO. This variable only\n" ,
"has an effect on windows created AFTER it is set, so if you change this\n" ,
"interactively in the Edit Environment plugin, it will not affect existing\n" ,
"windows. Normally, you would want to set this in your .afnirc file.\n" ,
"\n" ,
"-------------------------------\n" ,
"Variable: AFNI_IMAGE_SAVESQUARE\n" ,
"-------------------------------\n" ,
"YES/NO: Forces images (from the image view \"Save\" button) to be saved with\n" ,
"square pixels, even if they are stored with nonsquare pixels.\n" ,
"\n" ,
"-------------------------------\n" ,
"Variable: AFNI_BUCKET_LABELSIZE\n" ,
"-------------------------------\n" ,
"THIS VARIABLE HAS BEEN REMOVED FROM AFNI.\n" ,
"\n" ,
"Formerly, it was used to set the width of the \"ULay\", \"OLay\", and \"Thr\" menu\n" ,
"choosers on the \"Define Overlay\" control panel. As of 03 May 2005, AFNI now\n" ,
"calculates the default width based on the longest sub-brick label input\n" ,
"for each dataset.\n" ,
"\n" ,
"-------------------------\n" ,
"Variable: AFNI_MAX_1DSIZE\n" ,
"-------------------------\n" ,
"Sets the maximum size (in bytes) of each 1D file that will be automatically\n" ,
"loaded when AFNI starts. The default is 123 Kbytes. The intention is to\n" ,
"prevent loading of very large files that are not intended to be used for\n" ,
"graphing/FIMming purposes.\n" ,
"\n" ,
"---------------------------\n" ,
"Variable: AFNI_TITLE_LABEL2 (editable)\n" ,
"---------------------------\n" ,
"If this YES/NO variable is YES, then the AFNI window titlebars will show\n" ,
"the 'label2' field from the AFNI dataset .HEAD file, rather than the\n" ,
"dataset filename. If the label2 field is set to a nontrivial value,\n" ,
"that is. You can set the label2 field with the 3drefit command.\n" ,
"\n" ,
"-------------------------------\n" ,
"Variable: AFNI_SHOW_SURF_POPUPS\n" ,
"-------------------------------\n" ,
"If this YES/NO variable is set to YES, then when AFNI receives surface\n" ,
"nodes, triangles or normals from suma, a popup message will be displayed.\n" ,
"Otherwise, the message will be send to stderr (on the terminal window).\n" ,
"\n" ,
"-------------------------------\n" ,
"Variable: AFNI_KILL_SURF_POPUPS\n" ,
"-------------------------------\n" ,
"If this YES/NO variable is set to YES, then when AFNI receives surface\n" ,
"nodes, triangles or normals from suma, no messages will be displayed,\n" ,
"either in a popup or stderr. Note that if errors occur, popups will\n" ,
"still be shown; this just turns off the normal information messages.\n" ,
"N.B.: If AFNI_SHOW_SURF_POPUPS is YES, then it wins over\n" ,
" AFNI_KILL_SURF_POPUPS being YES. If neither is set, then\n" ,
" messages are displayed to stderr.\n" ,
"\n" ,
"-----------------------------\n" ,
"Variable: AFNI_EDGIZE_OVERLAY (editable)\n" ,
"-----------------------------\n" ,
"If set to YES, then the color overlays in the image windows will only\n" ,
"have their edge pixels displayed. That is, each 'blob' will be hollowed\n" ,
"out, leaving only its edges. If you do this, you probably want to make\n" ,
"the color overlay opaque, so that the results are easily seen.\n" ,
"\n" ,
"--------------------------\n" ,
"Variable: AFNI_NIFTI_DEBUG (editable)\n" ,
"--------------------------\n" ,
"This integral variable determines the debug level used by the nifti_io\n" ,
"library functions. If set to 0, only errors are reported by the library.\n" ,
"The maximum debug level used is currently 4. Note that if this is changed\n" ,
"from within AFNI, a 'Rescan: This' operation should probably be performed,\n" ,
"which will force a re-reading of the datasets and so force an elicitation\n" ,
"of the NIfTI debug messages (for .nii files, that is).\n" ,
"\n" ,
"--------------------------\n" ,
"Variable: AFNI_NIFTI_NOEXT\n" ,
"--------------------------\n" ,
"When writing a '.nii' (or '.nii.gz') file from an AFNI program, normally\n" ,
"a NIfTI-1.1 extension field with some extra AFNI header information is\n" ,
"written into the output file. If you set this variable to YES, then\n" ,
"this extension is not written, which will make the output be a 'pure'\n" ,
"NIfTI-1.1 file. Only use this if absolutely necessary. You can also\n" ,
"use the 'nifti_tool' program to strip extension data from a NIfTI-1.1\n" ,
"dataset file.\n" ,
"\n" ,
"---------------------------\n" ,
"Variable: AFNI_OVERLAY_ZERO (editable)\n" ,
"---------------------------\n" ,
"If set to YES, this variable indicates that voxels in the overlay dataset\n" ,
"that have the numerical value of 0 will get colored when the Inten color\n" ,
"scale on the Define Datamode panel indicates that 0 has a color that isn't\n" ,
"\"none\". The default way that AFNI works is NOT to colorize voxels that\n" ,
"are 0, even if they should otherwise get a color.\n" ,
"\n" ,
"---------------------------\n" ,
"Variable: NIML_TRUSTHOST_xx\n" ,
"---------------------------\n" ,
"These environment variables ('xx' = '01', '02', ..., '99') set the names\n" ,
"and/or addresses of external computer hosts to trust with NIML TCP/IP\n" ,
"connections, which are how AFNI and SUMA communicate. Should only be\n" ,
"necessary to use these if you are using AFNI and SUMA on different\n" ,
"machines. Connections from machines not on the trusted list will be\n" ,
"rejected, for the sake of security. The 'localhost' or 127.0.0.1 address\n" ,
"and local class B network 192.168.0.* addresses are always trusted.\n" ,
"\n" ,
"---------------------------\n" ,
"Variable: AFNI_DONT_LOGFILE\n" ,
"---------------------------\n" ,
"Most AFNI programs write a copy of their command line to a file in your\n" ,
"home directory named \".afni.log\". If you do NOT want the log to be\n" ,
"kept, set this environment variable to YES. The purpose of the log\n" ,
"is for you to be able to look back and see what AFNI commands you used\n" ,
"in the past. However, if you are doing a vast number of commands inside\n" ,
"a script, the log file might eventually become gigantic (the Kevin Murphy\n" ,
"effect).\n" ,
"\n" ,
"-------------------------\n" ,
"Variable: AFNI_WRITE_NIML\n" ,
"-------------------------\n" ,
"If this variable is set to YES, then AFNI .HEAD files will be written in\n" ,
"the new NIML (XML subset) format, rather than the 'classic' format. The\n" ,
"volumetric image data is still in the pure binary .BRIK file, not XML-ified\n" ,
"in any way. At present (Jun 2005) this format is experimental, but will\n" ,
"someday soon become the default.\n" ,
"\n" ,
"---------------------------------\n" ,
"Variable: AFNI_ALLOW_MILLISECONDS\n" ,
"---------------------------------\n" ,
"The TR value (time step) in 3D+time datasets created with to3d can be flagged\n" ,
"as being in units of milliseconds (ms) or seconds (s). This situation is\n" ,
"unfortunate, as some AFNI programs assume that the units are always s, which\n" ,
"doesn't work well when the TR is actually in ms. On 15 Aug 2005, AFNI dataset\n" ,
"I/O was modified to only write out TR in s units, and to convert ms units\n" ,
"to s units on input. If you absolutely need to store TR in ms, then you\n" ,
"must set this environment variable to YES. I strongly recommend against\n" ,
"such a setting, but recall the AFNI philosophy: \"provide mechanism, not\n" ,
"policy\" -- in other words, if you want to shoot yourself in the foot, go\n" ,
"right ahead. This variable is just the safety on the revolver.\n" ,
"\n" ,
"------------------------------\n" ,
"Variable: AFNI_TTATLAS_CAUTION (editable)\n" ,
"------------------------------\n" ,
"If this YES/NO variable is set to NO, then the warning about the potential\n" ,
"errors in the \"Where am I?\" popup will not appear. This is purely for\n" ,
"cosmetic purposes, Ziad.\n" ,
"\n" ,
"--------------------------\n" ,
"Variable: AFNI_AUTO_RESCAN\n" ,
"--------------------------\n" ,
"If this YES/NO variable is set to YES, then the interactive AFNI program\n" ,
"will rescan all session directories every 15 seconds for new datasets.\n" ,
"Basically, this is just a way for you to avoid pressing the 'Rescan'\n" ,
"buttons. Note that if AFNI_AUTO_RESCAN is enabled, then the rescan\n" ,
"method will be 'Add', not 'Replace', no matter what you set variable\n" ,
"AFNI_RESCAN_METHOD to.\n" ,
"\n" ,
"-------------------------------\n" ,
"Variable: AFNI_RESCAN_AT_SWITCH\n" ,
"-------------------------------\n" ,
"If this YES/NO variable is set to YES, then the interactive AFNI program\n" ,
"will rescan all session directories everytime you click on either of the\n" ,
"'Overlay' or 'Underlay' buttons. Basically, this is just another way for\n" ,
"you to avoid pressing the 'Rescan' buttons. (Unlike with AFNI_AUTO_RESCAN,\n" ,
"the AFNI_RESCAN_METHOD settings are respected.)\n" ,
"\n" ,
"--------------------------\n" ,
"Variable: AFNI_WEB_BROWSER\n" ,
"--------------------------\n" ,
"This variable should be set to the full executable path to a Web browser,\n" ,
"as in\n" ,
" setenv AFNI_WEB_BROWSER /usr/bin/mozilla\n" ,
"If it is not set, AFNI will scan your path to see if it can find a browser,\n" ,
"looking for \"firefox\", \"mozilla\", \"netscape\", and \"opera\" (in that order).\n" ,
"If a browser is found, or set, then the 'hidden' popup menu (in the blank\n" ,
"square to the right of the 'done' button) will have a menu item to open it.\n" ,
"\n" ,
"----------------------------\n" ,
"Variable: AFNI_JPEG_COMPRESS\n" ,
"----------------------------\n" ,
"This variable determines the compression quality of JPEG files saved in\n" ,
"the AFNI GUI and 3dDeconvolve. Its value can be set to an integer from\n" ,
"1 to 100. If not set, the default value is 95%.\n" ,
"\n" ,
"---------------------------\n" ,
"Variable: AFNI_NLFIM_METHOD\n" ,
"---------------------------\n" ,
"Can be used to set the optimization method using in the NLfit plugin\n" ,
"(not in 3dNLfim). The methods available are\n" ,
" SIMPLEX (the default)\n" ,
" POWELL (the NEWUOA method)\n" ,
" BOTH (use both methods, choose the 'best' result)\n" ,
"\n" ,
"----------------------------\n" ,
"Variable: AFNI_OVERLAY_ONTOP\n" ,
"----------------------------\n" ,
"If this variable is set to YES, then the 'Overlay' button will be above\n" ,
"the 'Underlay' button on the AFNI control panel. The default, from the\n" ,
"olden days, is to have the 'Underlay' button above the 'Overlay' button,\n" ,
"which some people find confusing.\n" ,
"\n" ,
"-----------------------------\n" ,
"Variable: AFNI_DATASET_BROWSE (editable)\n" ,
"-----------------------------\n" ,
"If this variable is set to YES, then when you 'browse' through a dataset\n" ,
"chooser ('Overlay' or 'Underlay' list) with the mouse or arrow keys, then\n" ,
"as a dataset is selected in the list, AFNI will immediately switch to\n" ,
"viewing that dataset. This can be convenient for scrolling through datasets,\n" ,
"but can also consume memory and CPU time very quickly.\n" ,
"\n" ,
"------------------------------\n" ,
"Variable: AFNI_DISABLE_TEAROFF\n" ,
"------------------------------\n" ,
"If this variable is set to YES, then the AFNI GUI will not allow popup or\n" ,
"popdown menus to be 'torn off'. The default is to enable tear off for most\n" ,
"menus, but this may cause bad things on some platforms (like program death).\n" ,
"\n" ,
"-------------------------------\n" ,
"Variable: AFNI_PLUGOUT_TCP_BASE\n" ,
"-------------------------------\n" ,
"This integer will override the base TCP port used by afni to listen for\n" ,
"plugouts. This allows multiple instances of afni on one machine, where\n" ,
"each can listen for plugouts. Valid port numbers are 1024..65535.\n" ,
"\n" ,
"-----------------------------------\n" ,
"Variable: AFNI_IMAGE_TICK_DIV_IN_MM\n" ,
"-----------------------------------\n" ,
"If this YES/NO variable is set to YES, then the Tick Div. value in an\n" ,
"image window will be interpreted as a separation distance, in mm, as\n" ,
"opposed to the number of tick divisions along each edge. In that case,\n" ,
"a larger value would produce fewer ticks, as they would be farther apart.\n" ,
"\n" ,
"----------------------------\n" ,
"Variable: AFNI_IMAGRA_CLOSER\n" ,
"----------------------------\n" ,
"If this YES/NO variable is set to YES, then when you click in an 'Image'\n" ,
"or 'Graph' button for a viewer window that is already open (so the button\n" ,
"is displayed in inverted colors), then the corresponding viewer window\n" ,
"will close. The default action is to try to raise the viewer window to\n" ,
"the front, but some window managers (I'm looking at you, FC5) don't allow\n" ,
"this action. So this provides a way to kill the window, at least, if you've\n" ,
"lost it in desktop hell somewhere.\n" ,
"\n" ,
"------------------------------\n" ,
"Variable: AFNI_DONT_DECONFLICT\n" ,
"------------------------------\n" ,
"As of 06 Jun 2007, when AFNI programs write datasets to disk, they will check if\n" ,
"the filename already exists; if so, then the filename will be 'deconflicted' --\n" ,
"changed to a filename that does not conflict with an existing file. For example,\n" ,
"\"fred+orig\" could be changed to \"fred_AA1+orig\". If you do NOT want this\n" ,
"automatic deconflicting, then set this variable to YES -- in that case, dataset\n" ,
"files will be overwritten if a conflict occurs. If you want the program to\n" ,
"stop when it finds an output conflict and NOT write anything, then set this\n" ,
"variable to DEATH (or anything starting with a 'D').\n" ,
"\n" ,
"----------------------------------------------------------------------\n" ,
"--- variables specific to NIML I/O\n" ,
"----------------------------------------------------------------------\n" ,
"\n" ,
"-----------------------------------\n" ,
"Variable: AFNI_NIML_DEBUG\n" ,
"-----------------------------------\n" ,
"This integer sets the debugging level in some niml I/O routines, particularly\n" ,
"those in thd_niml.c. Currently used values range from 0 to 3.\n" ,
"\n" ,
"-----------------------------------\n" ,
"Variable: AFNI_NSD_ADD_NODES\n" ,
"-----------------------------------\n" ,
"If this YES/NO variable is set to YES, then when a NI_SURF_DSET dataset\n" ,
"is written to disk, if it has no node list attribute, a default list will\n" ,
"be created.\n" ,
"\n" ,
"-----------------------------------\n" ,
"Variable: AFNI_NSD_TO_FLOAT\n" ,
"-----------------------------------\n" ,
"If this YES/NO variable is set to NO, then any necessary conversion of\n" ,
"NI_SURF_DSET datasets to type float will be blocked. Otherwise, all such\n" ,
"datasets will be written as float.\n" ,
"\n" ,
"-----------------------------------\n" ,
"Variable: AFNI_NIML_TEXT_DATA\n" ,
"-----------------------------------\n" ,
"If this YES/NO variable is set to YES, then NI_SURF_DSET datasets will be\n" ,
"written with data in text format. Otherwise, data will be in binary.\n" ,
"\n" ,
"-----------------------------\n" ,
"Variable: AFNI_SIMPLE_HISTORY\n" ,
"-----------------------------\n" ,
"A few programs (particularly 3dcalc) create a complicated history note\n" ,
"in the output dataset header, by including the history of all inputs.\n" ,
"This history can become inordinately long and pointless when 3calc is\n" ,
"run in a long chain of calculations. Setting this variable to YES will\n" ,
"turn off this cumulation of all histories, and may make your dataset\n" ,
"headers more manageable.\n" ,
"\n" ,
"----------------------------------------------------------------------\n" ,
"--- END: variables specific to NIML I/O\n" ,
"----------------------------------------------------------------------\n" ,
"\n" ,
"=============================================\n" ,
"| Robert W Cox, PhD |\n" ,
"| Scientific and Statistical Computing Core |\n" ,
"| National Institute of Mental Health |\n" ,
"| National Institutes of Health |\n" ,
"| Department of Health & Human Services |\n" ,
"| United States of America |\n" ,
"| Earth, United Federation of Planets |\n" ,
"=============================================\n" ,
"\n" ,
"############################################################################\n" ,
"##### Variables that Specifically Affect the Operation of 3dDeconvolve #####\n" ,
"############################################################################\n" ,
"\n" ,
"-----------------------------------\n" ,
"Variable: AFNI_3dDeconvolve_GOFORIT\n" ,
"-----------------------------------\n" ,
"If this variable is set to YES, then 3dDeconvolve behaves as if you used the\n" ,
"'-GOFORIT' option on the command line -- that is, it will continue to run\n" ,
"even if it detects serious non-fatal problems with the problem setup.\n" ,
"\n" ,
"--------------------------------\n" ,
"Variable: AFNI_3dDeconvolve_NIML\n" ,
"--------------------------------\n" ,
"3dDeconvolve outputs the regression matrix 'X' into a file formatted in\n" ,
"the 'NIML' .1D format -- with an XML-style header in '#' comments at the\n" ,
"start of the file. If you DON'T want this format, just plain numbers,\n" ,
"set this variable to NO.\n" ,
"\n" ,
"----------------------------------\n" ,
"Variable: AFNI_3dDeconvolve_extend\n" ,
"----------------------------------\n" ,
"If you input a stimulus time series (via the -stim_file option) to\n" ,
"3dDeconvolve that is shorter than needed for the regression analysis, the\n" ,
"program will normally print a warning message and extend the time series\n" ,
"with zero values to the needed length. If you would rather have the program\n" ,
"stop if it detects this problem (the behavior before 22 Oct 2003), then set\n" ,
"this environment variable to NO.\n" ,
"\n" ,
"---------------------------------\n" ,
"Variable: AFNI_3dDeconvolve_nodup\n" ,
"---------------------------------\n" ,
"If this variable is set to YES, then if the 3dDeconvolve program detects\n" ,
"duplicate input stimulus filenames or duplicate regressors, the program\n" ,
"will fail (with an error message) rather than attempt to continue.\n" ,
"\n" ,
"-----------------------------------------\n" ,
"Variable: AFNI_3dDeconvolve_nodata_extras\n" ,
"-----------------------------------------\n" ,
"When using the -nodata option in 3dDeconvolve, the default printout gives\n" ,
"the 'normalized standard deviation' for each stimulus parameter. If you\n" ,
"set this variable to YES, then the printout will include the -polort\n" ,
"baseline parameters as well, and also the L2 norm of each column in\n" ,
"the regression matrix.\n" ,
"\n" ,
"--------------------------\n" ,
"Variable: AFNI_XJPEG_COLOR\n" ,
"--------------------------\n" ,
"Determines the color of the lines drawn between the column boxes in the\n" ,
"output from the -xjpeg option to 3dDeconvolve. The color format is\n" ,
"\"rgbi:rf/gf/bf\", where each value rf,gf,bf is a number between 0.0 and 1.0\n" ,
"(inclusive); for example, yellow would be \"rgbi:1.0/1.0/0.0\". As a\n" ,
"special case, if this value is the string \"none\" or \"NONE\", then these\n" ,
"lines will not be drawn.\n" ,
"\n" ,
"-------------------------\n" ,
"Variable: AFNI_XJPEG_IMXY\n" ,
"-------------------------\n" ,
"This variable determines the size of the image saved when via the -xjpeg\n" ,
"option to 3dDeconvolve. It should be in the format AxB, where 'A' is the\n" ,
"number of pixels the image is to be wide (across the matrix rows) and 'B'\n" ,
"is the number of pixels high (down the columns); for example:\n" ,
" setenv AFNI_XJPEG_IMXY 768x1024\n" ,
"which means to set the x-size (horizontal) to 768 pixels and the y-size\n" ,
"(vertical) to 1024 pixels. These values are the default, by the way.\n" ,
"\n" ,
"If the first value 'A' is negative and less than -1, its absolute value\n" ,
"is the number of pixels across PER ROW. If the second value 'B' is\n" ,
"negative, its absolute value is the number of pixels down PER ROW.\n" ,
"(Usually there are many fewer columns than rows.)\n" ,
"\n" ,
"-------------------------\n" ,
"Variable: AFNI_XSAVE_TEXT\n" ,
"-------------------------\n" ,
"If this YES/NO variable is set to YES, then the .xsave file created by\n" ,
"the \"-xsave\" option to 3dDeconvolve will be saved in text format. The\n" ,
"default is a binary format, which preserves the full accuracy of the\n" ,
"matrices stored therein. However, if you want to look at the .xsave\n" ,
"file yourself, the binary format is hard to grok. Note that the two\n" ,
"forms are not quite equivalent, since the binary format stores the\n" ,
"exact matrices used internally in the program, whereas the ASCII format\n" ,
"stores only a decimal approximation of these matrices.\n" ,
"\n" ,
"---------------------------\n" ,
"Variable: AFNI_GLTSYM_PRINT\n" ,
"---------------------------\n" ,
"If this YES/NO variable is set to YES, then the GLT matrices generated\n" ,
"in 3dDeconvolve by the \"-gltsym\" option will be printed to the screen\n" ,
"when the program starts up.\n" ,
NULL } ;
#define NUM_readme_env 2512
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