FreeSurfer Work Flows
FreeSurferWorkFlows describes processing workflows for FreeSurfer. An overview of the major processing steps taking place in a standard FreeSurfer workflow are described in this document: [http://surfer.nmr.mgh.harvard.edu/docs/ftp/pub/docs/FSL_anatomical_stream.pdf Building Anatomical Models with Freesurfer].
For more detail you can view the Morphometry and Reconstruction section of the FsTutorial.
BasicReconstruction (fully automated)
TroubleshootingReconstruction (where manual intervention is required when the automated programs fail)
HistoricalReconstruction (semi-automated, with routine manual edits of the segmented white matter volume)
SubcorticalSegmentation (already included in Basic workflow, but must be done separately if using Historical workflow)
The BasicReconstruction workflow is recommended if you are just starting to process data, since it requires less manual time. The HistoricalReconstruction workflow is recommended if you have already processed large amounts of data using previous versions of FreeSurfer that required routine manual edits, and you do not wish to reprocess them with the Basic workflow. Any additional subjects you add, however, will need to be processed using the HistoricalReconstruction workflow.
IMPORTANT: Whichever workflow you choose, be sure to process all your study's data using the same workflow!