FreeSurfer Work Flows
FreeSurferWorkFlows describes processing workflows for FreeSurfer. FreeSurferWorkFlows includes:
BasicReconstruction (fully automated)
TroubleshootingReconstruction (if the automated programs fail, manual intervention required)
HistoricalReconstruction (semi-automated, with routine use of manual edits to segmented white matter volume)
SubcorticalSegmentation (already included in Basic workflow, but must be done separately if using Historical workflow)
Use the Basic workflow if you are starting to process data. Use the Historic 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 to use, you will need to process all your data with that same workflow.