• LessTif isn't a perfect implementation of Motif. Some user interface widgets are mangled, and display in rather funky ways.
• Apparently you can't set a Toggle button on a popup menu in LessTif. This means that the "Rec" function on image viewers doesn't work, among many other things. I don't know any way around this problem.
• When I choose from an option menu that is itself part of a popup menu (e.g., in a graph viewer FIM->Ignore menu), sometimes AFNI freezes up and won't return control of the mouse or keyboard to the X11 server.
  • The only way out that I know is to kill the afni process, which you must do from the text mode Cygwin window (since you can't access an X11 terminal window when AFNI is so frozen):
    • In the Microsoft taskbar, bring the original Cygwin text mode shell window to the front.
    • Type "ps -elaf" to get a list of Cygwin processes.
    • Type "kill xxxx", where "xxxx" is the PID (process identifier) of the afni process.
    • You can now go back to the X11 window.
  • A workaround for this problem is to click the right mouse button in the label at the left of the option menu, which will popup a string chooser equivalent to the option menu.
  • I suspect this is a LessTif bug, but don't know what else to say about it.
    • Unfortunately, OpenMotif cannot legally be redistributed for use with Cygwin, so I can't compile AFNI with this tool for you.
• Plugins are hard-compiled into afni.exe, which means that you cannot add your own plugins without recompiling. If you want to add plugins, you have to edit Makefile.INCLUDE and fixed_plugins.h as well (look for the string "fixed" in Makefile.INCLUDE; the format of fixed_plugins.h should be self-explanatory).
• 3dNLfim and its associated plugin have not been adapted to Cygwin yet. Neither has 3dTSgen. (This will require modifying the model-loading code in a fashion similar to the way the plugin startup had to be changed.)
• I haven't used AFNI much on Cygwin, so don't know how well it performs or if it is prone to crashing.
  • The AFNI creed: all users are beta-testers for life (and beyond).
  • Report AFNI problems on the Message Board, please, not by e-mail.

Problems with Cygwin itself:

• Filenames can't contain a colon ":", since that is interpreted by Microsoft Windows as a indicating a disk drive name. This factoid means that some of the AFNI sample datasets can't be directly loaded onto Microsoft Windows systems, since their names include colons.
• The tcsh shell behaves peculiarly sometimes, so I stopped using it entirely. This is unfortunate, since I don't really like bash.
• On my Win2000 laptop the X11 server takes a few seconds to start up, but otherwise works pretty well.
• On my 2 Win98 home machines, the X11 server seems quite slow (it takes over a minute to start up). After that, it seems to work OK.
  • On my home Win98 systems, Cygwin/X11 also seem to consume all the memory after a while, forcing a reboot. I haven't seen this problem on Win2000.
  • Of course, since I only boot Win98 about once a quarter, this doesn't actually bother me much, but it may bother you.
  • Based on this extremely limited experience, I'd say that if you want to use AFNI on Microsoft Windows+Cygwin, then you probably want a WinNT derived platform (NT, 2000, XP?), and not a Win95 derived platform.
• The X11 server sometimes "forgets" to shift down after you press the Shift key and type several uppercase letters at once (this happened several times when I was editing with vi - the editor for real men). The only way to fix this that I know of is to kill the X11 server and restart it. Better use Caps-Lock if you have to type a bunch of uppercase letters together.
  • Another fix seems to be to press the Shift key several times in a row quickly. This brings up a Microsoft Windows usability interface dialog. You can then "Cancel" that dialog, and the Shift mode of the server will be fixed.
  • Pressing and releasing either the Left or Right shift key quickly sometimes makes the problem go away, also. And sometimes not.
  • This is a known bug on the Cygwin/XFree86 discussion lists, but apparently a hard one to fix, since X11 and Microsoft have very different underlying keyboard handling concepts.
• The "mwm" window manager that comes with LessTif is nicer looking than the default "twm" manager, but for some reason it sucks up all the CPU time it can get. This makes the X11 server seem very slow.
  • You probably won't like twm - most young folks today have trouble using such an archaic window manager (from the 1980's, I think).
    • For one thing, it requires the user to place manually new windows on the screen (that's what the outline that appears is for).
    • To resize a twm window, you click-and-hold in the box in the window's upper-right corner, and drag the cursor outside the window; then you can drag the window outline to a new size (larger or smaller). This is quite non-intuitive and takes some practice.
  • Other window managers are available at the Cygwin XFree86 download mirrors (in the contrib/ directory), but I haven't tried any of them.
    • I have made a version of the FVWM window manager (similar to mwm) available in file fvwm.tgz. This suffers from the same "100% CPU" usage as mwm, but I modified the source code to run FVWM in "nice" mode, so it doesn't strongly interfere with other programs ("nice" means it runs at a lower priority). Instructions for downloading/installing FVWM from here are in the /pub/dist/cygwin/README file.
  • I read somewhere that KDE has been ported to Cygwin as well, but since I dislike KDE (it looks too much like Microsoft Windows for my taste), haven't investigated the matter.
• Please don't ask us for help with Cygwin/XFree86 itself. We aren't experts, or even regular users. The FAQ, documentation, mailing lists, and archives at http://www.cygwin.com are the place to look for guidance in these matters.