Oops. There was a typo, present only inside the CYGWIN code. Since I've purged Windows from my life (mostly), I haven't tried a Cygwin compile in quite some time. The source code on this site should now be fixed (at least for this bug). Let me know how the compile proceeds.

I'm not sure what you mean by point (i). For point (ii), you need to set up the macro INSTALLDIR in Makefile.cygwin (or Makefile, after you do cp Makefile.cygwin Makefile) to be the name of a directory in which to install the AFNI binaries. What I usually do is change INSTALLDIR to $(HOME)/abin, which will put the binaries into a directory named "abin" under your Cygwin home directory.

In Unix/Linux/Cygwin, there is the concept of the "path" (which DOS also had, in case you are old enough to remember DOS). The path is the list of directories on the system that are searched for programs when you type a program name at the command line. If you type "afni" at the command line, but there is no program named "afni" in any of the path directories, then you'll get a message like "afni: Command not found". You can get around this problem by putting the abin/ directory into your path, or by running AFNI by typing the full path to its program file, as in "~/abin/afni" (the "~" is Unix shorthand for the name of your home directory).

Setting the path is preferable. How you do that depends on the Unix shell that you use. By default, I think Cygwin uses the "ash" shell. In that case, I think you set the path by a command like
export PATH=${PATH}:${HOME}/abin
You can put this in a startup file, so that it will always be executed when you start a Cygwin shell. Probably such a file would be named ".ashrc" (and go in your home directory), but I'm not sure. I never actually used ash, and I don't have a Cygwin available any more. At this point, we are now getting into Unix/Cygwin support issues, drifting away from AFNI itself. If you know someone who has some Unix/Linux experience, getting her/his help would be a lot faster than asking questions here, where the turnaround is slow.

bob cox