I have a general question. When I run ‘brew update’ and update Homebrew, does that in any way affect how the AFNI binaries work. I understand that I can’t update the AFNI binaries throughout the processing of data on the off chance that it changes how the data are processed and alters the results of the final analyses; however, does updating Homebrew result in the same problem? Or is it ok to keep updating that regularly?
It should be okay to update homebrew. If anything
happened, the result would not be a change in AFNI
results, say, but that some AFNI programs would
cease to work.
For example, if you update gcc, then that might
in turn update libgomp.1.dylib, but that might break
any link you made at install time.
The fix would be to re-do the link, no big deal. And
“afni_system_check.py -check_all” should suggest
how to do that.
Regarding updating AFNI itself, it does make sense
to leave the AFNI version static for the duration of
an analysis. On the other hand, it might make even
more sense to update AFNI regularly, and then re-do
the full analysis after collecting all subject data.
At the end of a 2 or 3 year study, would you rather
be working with current software, or 2-3 year old
software? I usually suggest staying current.