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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 PDF slide presentation: Building Anatomical Models with Freesurfer, and also FreeSurferAnalysisPipelineOverview.
RecommendedReconstruction (with routine checks for automated program failures, and subsequent manual intervention)
HistoricalReconstruction (semi-automated, with routine manual edits of the segmented white matter volume)
SubcorticalSegmentation (already included in Recommended workflow, but must be done separately if using Historical workflow)
The RecommendedReconstruction workflow is run step-wise; you can save time by running all the steps at once or using the -all flag and checking all of your output at the end.
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 Recommended workflow. Any additional subjects you add, however, will also 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!