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

FreeSurferWorkFlows include:

Recommended:

BasicReconstruction (fully automated)
TroubleshootingReconstruction (where manual intervention is required when the automated programs fail)
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)

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 study's data using the same workflow.

User Contributed:

-  ⇤ ← Revision 11 as of 2005-08-12 14:46:17 → 
  Size: 652
  Editor: EvelinaBusa
  Comment:
+   ← Revision 32 as of 2005-08-17 12:42:07 → ⇥
  Size: 1446
  Editor: EvelinaBusa
  Comment:
-Deletions are marked like this.
+Additions are marked like this.
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-FreeSurferWorkFlows describes processing workflows for FreeSurfer. FreeSurferWorkFlows includes:
+FreeSurferWorkFlows describes processing workflows for FreeSurfer. An overview of the major processing steps taking place in a standard FreeSurfer workflow are described in this document: [http://surfer.nmr.mgh.harvard.edu/docs/ftp/pub/docs/FSL_anatomical_stream.pdf Building Anatomical Models with Freesurfer].
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-Recommended:
 * BasicReconstruction (with no manual edits to the segmented wm volume)
 * IntermediateReconstruction
 * HistoricalReconstruction (with routine manual edits to the segmented wm volume)
 * SubcorticalSegmentation
+FreeSurferWorkFlows include:
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-User Contributed:
 * FreeSurferAnatomicalReconstruction
+'''Recommended:'''
 * BasicReconstruction (fully automated)
 * TroubleshootingReconstruction (where manual intervention is required when the automated programs fail)
 * 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)

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 study's data using the same workflow.     

'''User Contributed:'''
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+Line 23:
- * FreeSurferRemoteAccess