Hi-
The instructions, with some examples, for driving AFNI are here:
[
afni.nimh.nih.gov]
and the plugout instructions are:
[
afni.nimh.nih.gov]
Looking at the first example in the first file, I think you would want your AFNI commands in the file to look something like:
afni -com 'OPEN_WINDOW A.axialimage' \
-com 'SWITCH_UNDERLAY anat'
If you wanted to, you could use the scripts to enter file names on the command line and to pass the file names to the commands, that way having a flexible tool. But if you have consistent names, then you could put static names after the SWITCH_UNDERLAY option.
--pt