Hi Nicole,

Actually, just your script calling afni_proc.py is enough. You
just have a few scripting problems in there. The errors have
nothing to do with afni_proc.py.

1. The -copy_anat line has a comment at the end of it.
That is not legal because you are trying to use the '\' line
continuation character. The result of this should be a
'-do_block: Command not found' error.

2. If you want to embed comments in the middle of a single
command with line extenders, then the comments must also
have line continuations at the end. So this will give you a
few more "Command not found' errors.

3. There is a blank line between the last -gltsym and -jobs.
Either delete the blank line or put a line continuation there.
This should result in a '-jobs: Command not found' error.

If any of this is not clear, please let me know.

One thing I suggest when scripting like this, is to test your
script by putting 'echo' before the main command. Then
just see if it looks like you expect it to. So here, the command
would be:

echo afni_proc.py -subj_id ...

Once it looks good, remove the 'echo'.

- rick