I face a problem using singularity running fmriprep (see pics & below) in HPC Centos. I ran below in the command line:
singularity shell -B /storage/users/ /usr/local/bin/fmriprep-20.2.6.simg \ /storage/users/jguesten/PHD/data/MEMTRAIN2 /storage/users/iliopoul/PHD/data/MEMTRAIN2/derivatives \ participant \ --participant-label ah88
I get the error:
Path does not exist: < /storage/users/jguesten/PHD/data/MEMTRAIN2>. (i.e. the input folder).
However, when I run the above code with “shell” instead of “run” to get into the virtual environm of the container, I can /cd to /storage/users etc. which shows me that these folders are mounted.
Does not make sense to me.
- When I tree the same idea in a shell script ("bash <script_name> see screenshot), I get an error that the “/storage/users/jguesten/PHD/data/MEMTRAIN2 is a directory”.
Any idea ? I struggle a lot to make it work. Thank you very much in advance