When singularity begins a container, no data from your machine goes inside of it by default (except for your home drive). So if you want fMRIPrep to be able to read from / write to a drive, you need to mount it with the -B argument. All relevant drives should be mounted (some people may have their bids root and scratch directory on different file system). You can mount multiple drives with -B /drive1,/drive2 etc.
Best,
Steven