We are running freesurfer as part of a bigger pipelines with other steps that can be performed in parallel to freesurfer reconstruction. So far we have set the openmp flag to the number of all available cores. However, our experience with ANTs and AFNI which also capitalize on the OpenMP parallelization is that there is little benefit of using more than 8-10 cores (even if more are available). Does this also apply to FreeSurfer? Does anyone have done some benchmarking of this?

Thanks in advance for your help.

Best,

Chris