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| [wiki:Self:FreeSurferWiki top] | [wiki:Self:WorkFlows previous] | [wiki:Self:BasicReconstruction next] | [[FreeSurferWiki|top]] | [[WorkFlows|previous]] | [[BasicReconstruction|next]] |
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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 PDF slide presentation: [[http://surfer.nmr.mgh.harvard.edu/docs/ftp/pub/docs/freesurfer.intro.pdf|Building Anatomical Models with Freesurfer]], and also FreeSurferAnalysisPipelineOverview. |
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| '''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) |
For more detail you can view the [[FsTutorial/MorphAndRecon|Morphometry and Reconstruction section]] of the FsTutorial. |
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| 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. |
FreeSurferWorkFlows include: |
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| '''User Contributed:''' * FreeSurferAnatomicalReconstruction |
* FsFastUnpackData * RecommendedReconstruction (with routine checks for automated program failures, and subsequent manual intervention) * LongitudinalProcessing * FreeSurferGroupAnalysis |
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| * FreeSurferIndividualAnalysis * FreeSurferGroupAnalysis |
* VolumeRoiCorticalThickness * PairedAnalysis |
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: Building Anatomical Models with Freesurfer, and also FreeSurferAnalysisPipelineOverview.
For more detail you can view the Morphometry and Reconstruction section of the FsTutorial.
FreeSurferWorkFlows include:
RecommendedReconstruction (with routine checks for automated program failures, and subsequent manual intervention)