Once again, sorry I've only been able to work on my end sporadically.

With make tricked into not trying to build the docs, everything compiles and installs fine (at least for 64-bit, I haven't tried 32 yet), and the segfaults are gone.

However, there's a bit of weirdness with fmriqa_qenerate.pl ; when I call it on the .bxh I've created for my test data (with analyze2bxh), the script tries to call bxh_brainmask with the option
  --method=localmin
and bxh_brainmask fails with
> Unsupported mask method 'localmin'

Was there a recent change to bxh_brainmask that didn't propagate up to fmriqa_generate.pl (bxh_brainmask --help only mentions 'threshold' and 'rank' as methods), or should I be thinking user error?

Thanks yet again.