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 using recon-all 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.
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