FreeSurfer Work Flows

FreeSurferWorkFlows describes processing workflows for FreeSurfer. FreeSurferWorkFlows includes:

Recommended:

BasicReconstruction (fully automated)
HistoricalReconstruction (semi-automated, with routine use of manual edits to segmented white matter volume)
TroubleshootingReconstruction (where manual intervention is required when the automated programs fail)
SubcorticalSegmentation (already included in Basic workflow, but must be done separately if using Historical workflow)

Use the BasicReconstruction workflow if you are just starting to process data. Use the HistoricalReconstruction 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, be sure to process all your data using the same workflow.

User Contributed:

-  ⇤ ← Revision 1 as of 2004-07-23 11:37:59 → 
  Size: 317
  Editor: aqua
  Comment:
+   ← Revision 27 as of 2005-08-15 15:17:54 → ⇥
  Size: 1229
  Editor: EvelinaBusa
  Comment:
-Deletions are marked like this.
+Additions are marked like this.
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+[wiki:Self:FreeSurferWiki top] | [wiki:Self:WorkFlows previous] | [wiki:Self:BasicReconstruction next]

= FreeSurfer Work Flows =
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+Line 7:
-  * [wiki:/FreeSurferWorkFlows/StructuralAnalysis StructuralAnalysis]
  * [wiki:/FreeSurferWorkFlows/FunctionalAnalysis FunctionalAnalysis]
  * [wiki:/FreeSurferWorkFlows/DiffusionAnalysis DiffusionAnalysis]
+'''Recommended:'''
 * BasicReconstruction (fully automated)
 * HistoricalReconstruction (semi-automated, with routine use of manual edits to segmented white matter volume)
 * TroubleshootingReconstruction (where manual intervention is required when the automated programs fail)
 * SubcorticalSegmentation (already included in Basic workflow, but must be done separately if using Historical workflow)
-Line 7:
+Line 13:
+Use the BasicReconstruction workflow if you are just starting to process data.
Use the HistoricalReconstruction 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, be sure to process ''all'' your data using the same workflow.     

'''User Contributed:'''
 * FreeSurferAnatomicalReconstruction
 * FreeSurferOccipitalFlattenedPatch
 * FreeSurferIndividualAnalysis
 * FreeSurferGroupAnalysis