FreeSurfer is a software suite for processing, analyzing, and visualizing human brain structural MRI images. It generates processed volumetric and surface data in subject native space.

The main workhorse of Freesurfer is recon-all, which is discussed in Andy's Brain Book. There are modifications on recon-all for high-field (7T) MRI, high-resolution (submillimeter) MRI, and longitudinal data.

Freesurfer commands (recon-all and many, many more) can be run via the command line if you install the software and be sure to set up your terminal correctly with:

export FREESURFER_HOME=/path/to/fs/software
source $FREESURFER_HOME/SetUpFreesurfer.sh
export SUBJECTS_DIR=/path/to/fs/output

However for ease + reproducibility, you can also use the freesurfer BIDS app: https://github.com/bids-apps/freesurfer. Here is an example

For Brain Mechanisms R01 (7T) freesurfer has been run many times with different versions and different inputs. See Freesurfer for BrainMechR01 (7T).