Why Apptainer?

On the HPC, you will use Apptainer instead of Docker for security reasons (i.e., Docker processes have elevated privileges, allowing bad actors to run commands on the HPC that they shouldn't. For that reason, Docker has never been allowed on the HPC).
Apptainer is a fork of the Singularity project. You can still use the singularity command to call Apptainer and it is quite compatible with singularity.

apptainer or singularity

In the scripts I'll have you run, I've switched to using the apptainer command, just in case the difference matters someday.

I will reference either Singularity or Apptainer in the descriptions that follow (the videos are a little older, so they reference singularity)
An Apptainer (or Singularity) image can be generated from a recipe file (you'll see one in the video below) or created from a Docker image (pulled from Dockerhub).
I maintain and share several common BIDS apps (e.g. MRIQC, fMRIPrep, and QSIprep) and some other Apptainer images (e.g., MRtrix3, surfice) on the HPC for you. These are stored in a designated directory /contrib/singularity/shared/neuroimaging that you can only visit if you are in interactive mode.
You can save Apptainer images yourself in your home or groups area, if you want the extra control or want to install something I don't provide.
I also provide working batch scripts that estimate the resources necessary for running each of these containerized applications on typical data. These should be a good starting point.

Apptainer (5 pts)