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| = FreeSurfer Tutorial = | [[FreeSurferWiki|top]] |
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| [wiki:Self:FsTutorial/Overview 1. Tutorial Overview] [[BR]] [wiki:Self:FsTutorial/InstallAndSetup 2. Installation and Setup] [[BR]] [wiki:Self:FsTutorial/MorphAndRecon 3. Morphometry and Reconstruction] [[BR]] [wiki:Self:FsTutorial/GroupAnalysis 4. Group Analysis] [[BR]] [wiki:Self:FsTutorial/Visualization 5. Visualization and Inspection of Group Analysis Results] [[BR]] [wiki:Self:FsTutorial/FSLFeatFreeSurfer 6. Applying FreeSurfer Tools to FSL fMRI Analysis (FEAT)] [[BR]] |
##= FreeSurfer Slides = ## 1. [[http://surfer.nmr.mgh.harvard.edu/pub/docs/freesurfer.intro.ppt|Introduction to Freesurfer - Bruce Fischl]] ## 1. [[http://surfer.nmr.mgh.harvard.edu/pub/docs/freesurfer.recon.ppt|Anatomical Analysis with Freesurfer - Doug Greve]] ## 1. [[http://surfer.nmr.mgh.harvard.edu/pub/docs/freesurfer.groupanalysis.ppt|Surface-based Group Analysis - Doug Greve]] ## 1. [[http://surfer.nmr.mgh.harvard.edu/pub/docs/freesurfer.feat.ppt|Applying FreeSurfer Tools to FSL fMRI Analysis - Doug Greve]] |
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| [wiki:Self:FsTutorial/Exercises Exercise Overview] | ## 1. [[attachment:freesurfer.intro.2008.ppt|Introduction to Freesurfer - Bruce Fischl]] ## 1. [[attachment:freesurfer.recon.ppt|Anatomical Analysis with Freesurfer - Doug Greve]] ## 1. [[attachment:freesurfer.groupanalysis.ppt|Surface-based Group Analysis - Doug Greve]] ## 1. [[attachment:freesurfer.feat.ppt|Applying FreeSurfer Tools to FSL fMRI Analysis - Doug Greve]] |
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| [wiki:Self:FsTutorial/FileFormats File Formats] | = FreeSurfer Tutorial and Workshop = == Overview == The !FreeSurfer tools deal with two main types of data: volumetric data (volumes of voxels) and surface data (polygons that tile a surface). The talks and tutorials should familiarize you with !FreeSurfer's volume and surface processing streams, the recommended workflow to execute these, and many of their component tools. The tutorials also describes some of !FreeSurfer's tools for registering volumetric datasets, performing group analysis on morphology data, and integrating multi-modal output with !FreeSurfer (overlaying color coded parametric maps onto the cortical surface and visualizing plotted results). After completing the tutorials, you should be able to: |
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| [wiki:Self:FsTutorial/Tools FreeSurfer Tools] | * perform surface reconstructions; * generate subcortical segmentations; * fix errors encountered during the volume or surface processing; * overlay functional data onto surfaces; * perform group analysis of structural (e.g. thickness) and functional data. |
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| [wiki:Self:FsTutorial/Glossary Glossary] | == Course Outline == During the tutorial sessions, you will be shown a variety of command strings on the tutorial wiki pages. Only those that appear between lines should be copy-and-pasted into the terminal for this tutorial. Those commands appear like this: ---- {{{ command arg1 arg2 }}} ---- <<Include(CourseSchedule)>> ## * '''Session 1''' ## * [[FsTutorial/OutputData|Session 1a]] - Use the volume and surface viewing tools to observe correctly processed output data. ## * [[FsTutorial/TroubleshootingData|Session 1b]] - See examples of problematic output data, and learn how to fix the problems. ## * [[FsTutorial/MorphAndRecon|Extra]] - Long-form tutorial covering Freesurfer's morphometry and reconstruction tool [[recon-all]]. ## * [[ReconAllDevTable|Extra]] - recon-all process-flow reference table. ## * '''Session 2''' ## * [[FsTutorial/QdecGroupAnalysis|Session 2a]] - Learn how to conduct a group analysis using Qdec, and to visualize and inspect the results. ## * [[FsTutorial/FslFeatFreeSurfer|Session 2b]] - Applying !FreeSurfer tools to FSL fMRI Analysis (FEAT) ## * [[FsTutorial/GroupAnalysis|Extra]] - Group Analysis tutorial using mri_glmfit from the command line, prior to the release of Qdec. ## * [[FsTutorial/Visualization|Extra]] - Visualization and inspection of group analysis results using tksurfer, prior to release of Qdec. == Additional == * Home page: http://surfer.nmr.mgh.harvard.edu * Mailing list: send mail to majordomo@surfer.nmr.mgh.harvard.edu with the following command in the body of your email message: subscribe freesurfer * [[FsTutorial/Data|Getting the tutorial data]] (necessary only if you are not taking a formal course where data is provided) ## * [[FsTutorial/Exercises|Listing of all exercises]] * [[FsTutorial/Tools|FreeSurfer tools]] * [[FsTutorial/Glossary|Glossary]] * [[Articles|References]] ## * [[FsTutorial/SnapShot|PDF and HTML snapshot]] ## * 4pp PDFs: [[attachment:intro4pp.pdf]], [[attachment:recon4pp.pdf]], [[attachment:group4pp.pdf]] [[attachment:feat4pp.pdf]] * [[FsTutorial/Acknowledgements|Acknowledgements]] |
FreeSurfer Tutorial and Workshop
Overview
The FreeSurfer tools deal with two main types of data: volumetric data (volumes of voxels) and surface data (polygons that tile a surface). The talks and tutorials should familiarize you with FreeSurfer's volume and surface processing streams, the recommended workflow to execute these, and many of their component tools. The tutorials also describes some of FreeSurfer's tools for registering volumetric datasets, performing group analysis on morphology data, and integrating multi-modal output with FreeSurfer (overlaying color coded parametric maps onto the cortical surface and visualizing plotted results). After completing the tutorials, you should be able to:
- perform surface reconstructions;
- generate subcortical segmentations;
- fix errors encountered during the volume or surface processing;
- overlay functional data onto surfaces;
- perform group analysis of structural (e.g. thickness) and functional data.
Course Outline
During the tutorial sessions, you will be shown a variety of command strings on the tutorial wiki pages. Only those that appear between lines should be copy-and-pasted into the terminal for this tutorial. Those commands appear like this:
command arg1 arg2
Additional
Home page: http://surfer.nmr.mgh.harvard.edu
Mailing list: send mail to majordomo@surfer.nmr.mgh.harvard.edu with the following command in the body of your email message: subscribe freesurfer
Getting the tutorial data (necessary only if you are not taking a formal course where data is provided)