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 manually (which allows you to check and correct any errors), and automatically (which could encounter problems with segmentations and cortical tracing).
If you are interested in running longitudinal analysis, you will also need to pre-process the data using the longitudinal pre-processing pipeline.
...
Pre-processing with manual corrections
...
| Code Block |
|---|
recon-all -i /scratch/project/FTD#### -subjid subject_1 -all |
...