using with afni container

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 script includes directory paths starting with /mnt/… (referencing to our mounted storage disk) the generated 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 $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!


At the bottom of the created processing script should be a repetition of the command used to make it, without any variables. Can you please copy+paste that here?

Also, you have an “echo $top_dir” in the script with the command. What does that display when you run the singularity command?


It seems likely that part of the process is using a link to /mnt which actually resolves to /tmp.
Running “ls -l /” from the container might clarify that.

  • rick