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 * SubcorticalSegmentation (already included in Basic workflow, but must be done separately if using Historical workflow)  * SubcorticalSegmentation (already included in Recommended workflow, but must be done separately if using Historical workflow)

[wiki:FreeSurferWiki top] | [wiki:WorkFlows previous] | [wiki:BasicReconstruction next]

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: [http://surfer.nmr.mgh.harvard.edu/docs/ftp/pub/docs/FSL_anatomical_stream.pdf Building Anatomical Models with Freesurfer], and also FreeSurferAnalysisPipelineOverview.

For more detail you can view the [wiki:FsTutorial/MorphAndRecon Morphometry and Reconstruction section] of the FsTutorial.

FreeSurferWorkFlows include:


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!

User Contributed:

FreeSurferWorkFlows (last edited 2011-07-05 13:39:53 by AllisonStevens)