I have edited both of the setup scripts, I can run the reun_pestica.sh script and afni and matlab do their thing but it always errors out on that it can not find or open ./card_mean...or ./resp_mean files. I noticed that they were symbolic links to files housed within the pestica_volumes folder. The link to that folder is good. In an effort to get past this error, I moved the referenced files from the volumes folder up to the level of the links (which I removed) and renamed them to match what the script was asking for. It still says that it cannot open the files when run. Any thoughts?

Hi Chris,

Sorry for the delay. I think the environment variable setting PESTICA_DIR may not be set or may not be being passed through to the run_pestica.sh script. Can you setup PESTICA, then in your shell type:

env | grep PESTICA

and post the output? There should be 3 or 4 variables set, depending on your version, mine shows:

PESTICA_SLICE_TIMING=siemens-alt-asc
PESTICA_MATLAB_POOLSIZE=3
PESTICA_DIR=/mnt/netScratch/ebeall/pestica_afni_v2
PESTICA_VOL=16mm3

If these variables are not set, then you need to source the setup_pestica.sh script if you use bash or the other script if you use tcsh (to find out your shell, type echo $SHELL).

If these variables are already set, then it may be an issue with your shell. The first thing I would try is edit run_pestica.sh to include "env| grep PESTICA; return; exit"  near the top (but below #! /bin/bash) and post the output. Hope this helps.

Erik