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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: [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:MorphAndRecon Morphometry and Reconstruction section] of the FsTutorial.

FreeSurferWorkFlows include:


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 also need to be processed using the HistoricalReconstruction workflow.

User Contributed: