Great question!
Within FreeSurfer, ‘recon-all’ is the command and oft-mentioned workflow for structural reconstruction of brain MRI. This processing stream is limited to only processing a single brain at-one-time. Therefore using traditional parallelization on a cluster is a perfect fit, that is, submitting 10’s to 100’s of ‘recon-all’ jobs at once.
A typical ‘recon-all’ job with 1-core will take 5-6 hours. This probably doesn’t matter to the researcher who needs to process 10’s to 100’s of brains. However, in cases where they may need to process a single brain (or have seemingly unlimited resources…) they can speed-up the individual runtimes with these flags.
Briefly, because ‘recon-all’ splits the brain into 2 hemispheres for reconstruction, it is forced to sequentially process the left-hemisphere and then the right-hemisphere. The developers recognized this bottleneck and added support for Open-MP framework. By simply adding the above flags and allocating across 4 cores (2-cores per hemisphere), the ‘recon-all’ job will now take 3-4 hours.
Hope this adds more context!
-Mitch