Hello afni experts,
I am not sure if somebody here can help me with the type of problem I have.
Our lab switched recently to a new grid-system where we have to now use singularity and an afni container.
In this new set up I have the issue that although my shell script for generating the proc.py script includes directory paths starting with /mnt/… (referencing to our mounted storage disk) the generated proc.py script includes directory paths starting with /tmp/… (this was the reference we used in the old system) As a consequence the proc script does not run because it can not find the data (as the data is in /mnt/… and not /tmp…).
(When I execute the shell script with the afni container I bind the storage disk)
SAFNI=“singularity exec -B /mnt/yassamri/BEACoN/ProcessedData/rsfMRI/RSFA /mnt/home/stark/mycontainers/ccafni2.sif”
$SAFNI tcsh generate_afni_proc_CVR_TEST.sh $1
I don t understand why the shell script would make a proc_py script with referencing /tmp/… when it includes /mnt/… references.
What am I missing?
Thank you very much for any help!