For any lost souls who are wondering what the solution is -- I had the same problem and just debugged it.

For me, at least, the problem was running the script from within the 'bin' directory as "./fmriqa_generate.pl" which causes the script not to know which directory it is being run from, and thus not to be able to find the files it needs.

It worked when I either invoked the script using its full pathname (starting with a slash), or added the 'bin' directory to my path and ran the script as simply "fmriqa_generate.pl"

(I'm on a Mac but from a quick pass through the Perl, I expect the experience to be the same with any *nix operating system.)

Now on to my next challenge -- getting ImageMagick working correctly with the same script...

Cheers,
MJ

PS Hi Shashwath!