FreeSurfer Work Flows
FreeSurferWorkFlows describes processing workflows for FreeSurfer. An overview of the major processing steps taking place in a common FreeSurfer work flow are described in this document: [http://surfer.nmr.mgh.harvard.edu/docs/ftp/pub/docs/FSL_anatomical_stream.pdf Building Anatomical Models with Freesurfer].
BasicReconstruction (fully automated)
HistoricalReconstruction (semi-automated, with routine use of manual edits to segmented white matter volume)
TroubleshootingReconstruction (where manual intervention is required when the automated programs fail)
SubcorticalSegmentation (already included in Basic workflow, but must be done separately if using Historical workflow)
Use the BasicReconstruction workflow if you are just starting to process data. Use the HistoricalReconstruction workflow if you have already processed large amounts of data using previous versions of FreeSurfer which required manual edits, and you do not wish to reprocess them with the Basic workflow.
IMPORTANT: Whichever workflow you choose, be sure to process all your data using the same workflow.