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