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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 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 describe 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/Exercises Exercise Overview] | * 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/FileFormats File Formats] | Note: 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 }}} ---- == Note: Please DO NOT try to download the tutorial data during the course! == We have copies of this data stored on servers located in the course room. Attempting to download this data from the public link ([[FsTutorial/Data|this link]]) during the course presents excessive and unnecessary load on our network, and likely will fail due to this load. '''Please contact a staff member for help in getting this data.''' |
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| [wiki:Self:FsTutorial/Tools FreeSurfer Tools] | '''Laptop damage policy: If liquid is spilled on a provided laptop, then you are liable for payment of the repair costs!''' |
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| [wiki:Self:FsTutorial/Glossary Glossary] | == Question / Suggestion Box == During the course, if you have questions or suggestions, [[http://surfer.nmr.mgh.harvard.edu/cgi-bin/fsurfer/questions.cgi|please follow this link]] to submit them (anonymously, or not). We will process them during the course and give feedback at the end. ##== Course Evaluation == ##Please fill out our course evaluation [[https://spreadsheets.google.com/viewform?hl=en&formkey=dGNqMkJaeE52Z0o0b0tvWmJGN3dWckE6MA|here]]. You can fill it in throughout the remainder of the course but you can't save your answers and finish it later so be sure to submit it before you leave. == Course Schedule == ## select one of the course schedules, comment-out the others: ##<<Include(FsTutorial/Jan2009CourseSchedule)>> ##<<Include(FsTutorial/April2009CourseSchedule)>> ##<<Include(FsTutorial/Brazil2009CourseSchedule)>> ##<<Include(FsTutorial/FslCourseSchedule)>> ##<<Include(FsTutorial/MultiModal2009CourseSchedule)>> ##<<Include(FsTutorial/Sept2009CourseSchedule)>> ##<<Include(FsTutorial/Feb2010CourseSchedule)>> ##<<Include(FsTutorial/MultiModal2010CourseSchedule)>> ##<<Include(FsTutorial/StLouis2010CourseSchedule)>> ##<<Include(FsTutorial/Oct2010CourseSchedule)>> ##<<Include(FsTutorial/April2011CourseSchedule)>> ##<<Include(FsTutorial/Brazil2011CourseSchedule)>> ##<<Include(FsTutorial/MultiModal2011CourseSchedule)>> ##<<Include(FsTutorial/June2011FslCourseSchedule)>> ##<<Include(FsTutorial/Dec2011CourseSchedule)>> ##<<Include(FsTutorial/April2012CourseSchedule)>> <<Include(MultiModal2012CourseSchedule)>> == 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) '''DO NOT attempt this during a course!''' Contact a staff member for instructions on how to get this data locally during the course. ## * [[FsTutorial/Exercises|Listing of all exercises]] ## * [[FsTutorial/Tools|FreeSurfer tools]] * [[http://itunes.apple.com/us/app/isurf-brainview/id381072423?mt=8|iSurf]] - iPhone/iPad app to view !FreeSurfer segmentations * [[FsTutorial/Glossary|Glossary]] * [[Articles|References]] * [[SystemRequirements|System Requirements for Installation]] ## * [[FsTutorial/SnapShot|PDF and HTML snapshot]] ## * 4pp PDFs: [[attachment:intro4pp.pdf]], [[attachment:recon4pp.pdf]], [[attachment:group4pp.pdf]] [[attachment:feat4pp.pdf]] * [[FsTutorial/Acknowledgements|Acknowledgements]] * [[ConferenceRoomA| Conference Room A]] ## * [[FsTutorial/CourseChecklist| Course checklist (internal)]] |
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 describe 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.
Note: 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
Note: Please DO NOT try to download the tutorial data during the course!
We have copies of this data stored on servers located in the course room. Attempting to download this data from the public link (this link) during the course presents excessive and unnecessary load on our network, and likely will fail due to this load. Please contact a staff member for help in getting this data.
Laptop damage policy: If liquid is spilled on a provided laptop, then you are liable for payment of the repair costs!
Question / Suggestion Box
During the course, if you have questions or suggestions, please follow this link to submit them (anonymously, or not). We will process them during the course and give feedback at the end.
Course Schedule
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) DO NOT attempt this during a course! Contact a staff member for instructions on how to get this data locally during the course.
iSurf - iPhone/iPad app to view FreeSurfer segmentations