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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/FSL_anatomical_stream.pdf Building Anatomical Models with Freesurfer]. and also FreeSurferAnalysisPipelineOverview. |
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| Recommended: * BasicReconstruction (fully automated) * TroubleshootingReconstruction (if the automated programs fail, manual intervention required) * HistoricalReconstruction (semi-automated, with routine use of manual edits to segmented white matter volume) |
For more detail you can view the [wiki:Self: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) |
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| Use the Basic workflow if you are starting to process data. Use the Historic 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 to use, you will need to process all your data with that same 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. |
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| User Contributed: * FreeSurferAnatomicalReconstruction |
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:''' |
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| * FreeSurferIndividualAnalysis | |
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| * FreeSurferRemoteAccess |
[wiki:FreeSurferWiki top] | [wiki:WorkFlows previous] | [wiki:BasicReconstruction next]
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: