FreeSurfer performs the whole cortical reconstruction process and generates it their unique FreeSurfer file format using the command recon-all. Outlined below are instructions on how to pre-process structural T1 data automatically (which could encounter problems with segmentations and cortical tracing), and manually (which allows you to check and correct any errors).
AFTER conducting recon-all:
If you are interested in running longitudinal analysis, you will also need to pre-process the data using the longitudinal pre-processing pipeline.
If you are interested in running analysis segmenting hippocampal subfields or amygdala, you should run further processing and analysis as outlined here.
...
Running whole pre-processing pipeline automatically
...