Summary: Anatomy of Apptainer & Docker BIDS runs

Docker -i = interactive--provide feedback in terminal, do not just run in the background.
Docker --rm means clean up after running.
Apptainer --cleanenv means run in a clean environment (i.e., isolate the code in the container).
Apptainer --bind is equivalent to Docker -v: both are flags that precede bind statements.
Docker requires the bind statements to use absolute paths (PWD counts).
- Apptainer can use absolute paths, but also understands relative paths.
Locations: Docker containers are organized by the Docker Engine and do not appear as normal files on your system. If you provide the container name, then Docker will find it in its secret stash. By comparison, Apptainer containers are *.sif files sitting on your disk at some path you decide.
Naming: You need to indicate the path to the named Apptainer container file when you run it. Note that, by default the Docker container is named exactly as it is specified on Dockerhub. Because we always choose the name of the Apptainer container, we can provide a better name.
BIDS requires you to list the input and output directories. For Docker this must be the mount inside the container. For Apptainer, you can use the mounts inside the container or the host directories (relative or absolute) -Both Docker and Apptainer use the same BIDS syntax:
- BIDS may require you to list the level of analysis, usually participant or group.
- BIDS: If you list participant as the level of analysis, then you can optionally list which participants.

A more detailed comparison is available in the Docker-Singularity Rosetta Stone.

Apptainer (5)