After a system update, “afni_proc.py” would not run after the “-execute” flag. It would immediately end after generating the TCSH script. After troubleshooting, I found the problem was in setting the zero-padded list of runs .For example, if I have a subject with one run, the line in the TCSH script would be:
set runs = (`count -digits 2 1 1`)
Running “count -digits 2 1 1” yields:
usage: count <expected line count>
Performing “afni_system_check.py -check_all” suggests that everything is set up fine. And, everything works fine after adjusting the TCSH script or “afni_proc.py” (lines 2236 and 2237) so that the number of runs is hard-coded by writing
set runs = ( 01 )
in the TCSH script, instead of referencing the count function.
It seems that the “count” program is not working my system, as it did previously, after recent system updates. Options listed at http://bit.ly/2wefZ5I, outside of zero-padding with “-digits”, also all fail to work.
EDIT: The function works perfectly fine when I call "~/abin/count" (i.e. reference the path where the function count is stored). So the issue is not with the function, but rather that the updated system is not referencing the AFNI function count, but another function with the same name. So, I will figure that out. Thank you.