Sure, let's say I have a script which preprocesses user data with afni_proc.py and then does this:
afni -com "SWITCH_UNDERLAY TT_N27" -com "SWITCH_OVERLAY my_overlay"
3dcalc -a Clust_mask+orig -expr "within(a,2,2)" -prefix roi
I would want to preprocess my data, open AFNI, threshold/clusterize it, save the mask, and have it immediately run my 3dcalc command (this is just an example).
What happens is that once AFNI is closed, by either closing the window or hitting 'done' twice, in my shell I see:
** AFNI wraps up: Better to visit hell in your lifetime than afterwards!
and nothing after it (I have to hit control-c to bring back up my shell prompt 'username@server~>). Not sure how to have it continue running my shell script.
Edited 1 time(s). Last edit at 06/25/2015 04:57PM by dk.
