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:

Recommended:

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 Basic 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 -autorecon-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:

-Deletions are marked like this.
+Additions are marked like this.
 Line 13:
- * BasicReconstruction (fully automated, but without routine user checks for possible failures during processing)
-Line 19:
+Line 18:
-The BasicReconstruction workflow is recommended if you are just starting to process data, since it requires less manual time.
+The RecommendedReconstruction workflow is run step-wise, you can save time by running all the steps at once or using the '''-autorecon-all''' flag and checking all of your output at the end.
-Line 21:
+Line 20:
-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.
+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.