Workshop 6 - Scripts, containers and running analyses on the academic computing cluster¶
Welcome to the sixth workshop of the MRICN course!
Prior workshops introduced you to running MRI analysis with various FSL tools by either using the FSL GUI or typing a simple command in the terminal. In this workshop we will look at how to automate FSL analyses by creating scripts. Subsequently, we will explore how to run FSL scripts more efficiently by submitting jobs to the cluster. The final part of this workshop will introduce how to use FSL containers rather than pre-installed versions of FSL using different modules available on BEAR apps.
Overview of Workshop 6
Topics for this workshop include:
- Knowing how to automate neuroimaging analyses by
bashscripting - Understanding how to submit and managing analysis jobs on the BlueBEAR cluster using Slurm
- Working with FSL software containers using Apptainer as an alternative to pre-installed versions
More information
The BEAR Technical Docs provides guidance on submitting jobs to the cluster.
The copy of this workshop notes can be found on Canvas 39058 - LM Magnetic Resonance Imaging in Cognitive Neuroscience in Week 06 workshop materials.