Run Plugins off Command Line

AFNI Message Board
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Hi everyone
I’m new to the whole AFNI thing. Let me know if I’ve created a duplicate post, I’ve looked everywhere to see if there was an answer to this, but I couldn’t find anything.

So my overall aim is to be able to try and automate AFNI using the command line/via a python script with as minimal user interaction with the AFNI GUI as possible. So I was wondering if it’s possible to execute plugins via the command line/python script. Specifically I want to be able to use the 3ddump98 plugin to dump and close to a specific file. Is this possible?

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Howdy-

Sundry related points:
1) General note on running AFNI from command line:
A lot of this whole AFNI thing can be “driven” from the command line
https://afni.nimh.nih.gov/pub/dist/doc/program_help/README.driver.html

2) Specific note on using ‘3ddump98’ capability in AFNI:
On another note re. 3ddump98, it is one of the not-so-used plugins that you have to set an environment for to be able to enable in the GUI now. See the description of “AFNI_ALLOW_somename_PLUGIN” here:
https://afni.nimh.nih.gov/pub/dist/doc/program_help/README.environment.html

3) Stepping back a moment
I’ve never heard of the 3ddump98 plugin before, actually. Looking at the help for it, it seems like the command line program 3dmaskdump would do what you want?
https://afni.nimh.nih.gov/pub/dist/doc/htmldoc/programs/___auto_help/_3dmaskdump.help.html
It is possible there is an easier way to do what you want. For example, if you want to do full FMRI processing, check out the help of the program “afni_proc.py”-- Rick’s function makes it a joy to construct a processing stream in a straightforward manner.

4) A not-so-brief introduction to AFNI:
A searchable set of (growing) documentation is here:
https://afni.nimh.nih.gov/pub/dist/doc/htmldoc/index.html
The help of each program is online here:
https://afni.nimh.nih.gov/pub/dist/doc/htmldoc/programs/main_toc.html

-pt

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Thanks very much pt!