Hi, Carissa-
Re. the processing you uploaded: yes, I looked at the script, and have scripting-based comments to start, and still need to look more at the processing details; I will write back separately about that.
About putting a local copy of AFNI binaries on your system, some things I note from information provided so far (mainly in the afni_system_check.py output):
+ your HPC is set to use the "linux_openmp_64" binaries (so that is what we'll use for the local version).
+ your command line login shell is "bash" (though we will setup both bash and tcsh environments).
I will nominate putting the AFNI binaries in a directory called "abin" in your home directory (this mirrors what the general setup instructions have for users on their individual systems).
So, you can copy+paste the following commands (what each does is just noted each code block). If anything fails at a block, I would pause the process and ask a question here.
+ go to home directory; download the AFNI script for installing stuff; run it with some particular choices of package and unpacking location:
cd
curl -O [afni.nimh.nih.gov]
tcsh @update.afni.binaries -package linux_openmp_64.tgz -bindir abin -no_recur
+ set up bash shell to have this local AFNI version, which lives in "~/abin", first in your path:
echo "" >> ~/.bashrc
echo "export PATH=$HOME/abin:$PATH" >> ~/.bashrc
echo "" >> ~/.bashrc
+ set up tcsh shell to have this local AFNI version, which lives in "~/abin", first in your path:
echo "" >> ~/.cshrc
echo "set path = ( $HOME/abin $path )" >> ~/.cshrc
echo "" >> ~/.cshrc
Then, if you log out and log back in, things *should* be set. You can verify this by typing:
afni -ver
and
which afni
The first should show you a modern version of AFNI from April, 2021 (not the system one from 2019), and the latter should be something like "YOUR_HOME_DIR/abin/afni" (not the likely long path to where your system has its version of AFNI).
If that all looks good, I would also run:
apsearch -update_all_afni_help
... which will update all your autocompletions of AFNI program options as you type anything on the commmand line.
--pt
