AFNI Message Board

Dear AFNI users-

We are very pleased to announce that the new AFNI Message Board framework is up! Please join us at:

https://discuss.afni.nimh.nih.gov

Existing user accounts have been migrated, so returning users can login by requesting a password reset. New users can create accounts, as well, through a standard account creation process. Please note that these setup emails might initially go to spam folders (esp. for NIH users!), so please check those locations in the beginning.

The current Message Board discussion threads have been migrated to the new framework. The current Message Board will remain visible, but read-only, for a little while.

Sincerely, AFNI HQ

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dk
June 25, 2015 04:56PM
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.
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Subject Author Posted

Integrating AFNI into shell script?

dk June 25, 2015 01:58PM

Re: Integrating AFNI into shell script?

rick reynolds June 25, 2015 04:30PM

Re: Integrating AFNI into shell script?

dk June 25, 2015 04:56PM

Re: Integrating AFNI into shell script?

rick reynolds June 25, 2015 09:20PM

Re: Integrating AFNI into shell script?

dk June 26, 2015 08:59AM