I was reading the documentation for running fMRIPrep via a Singularity container, and am a little confused regarding when it’s necessary to mount certain items to the container. For example, I normally run fMRIPrep like this:
export FS_LICENSE=$FREESURFER_HOME/license.txt unset PYTHONPATH; singularity run /containers/fmriprep-20.0.7.simg \ $bids_root_dir $bids_root_dir/derivatives \ ...
This works perfectly fine for me. Prior to version 20.0.7, I would bind my templateflow directory to the container, but no longer need to, and do not mount my bids root directory or specific subject folders to the container. However, in the slurm example in the linked documentation, the data is explicitly mounted. I was therefore wondering when it’s necessary to mount the data? Is it only required when using
--cleanenv or are there other reasons?
Thanks for the help!