|
Size: 714
Comment:
|
Size: 3137
Comment:
|
| Deletions are marked like this. | Additions are marked like this. |
| Line 1: | Line 1: |
| = FreeSurfer Tutorial = | [[FreeSurferWiki|top]] |
| Line 3: | Line 3: |
| [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: |
| Line 10: | Line 7: |
| [wiki:Self:FsTutorial/Exercises Exercise Overview] [wiki:Self:FsTutorial/FileFormats File Formats] [wiki:Self:FsTutorial/Tools FreeSurfer Tools] [wiki:Self:FsTutorial/Glossary Glossary] |
* 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 }}} ---- '''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, [[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 [[http://spreadsheets.google.com/viewform?formkey=cHJlMFNVZDFNeDltbUE0RkNhaTBuWFE6MA..|here]]. You can fill it in throughout the course. == Course Schedule == ## select one of the course schedules, comment-out the others: ##<<Include(FsTutorial/Jan2009CourseSchedule)>> ##<<Include(FsTutorial/April2009CourseSchedule)>> ##<<Include(FsTutorial/BrazilCourseSchedule)>> ##<<Include(FsTutorial/FslCourseSchedule)>> <<Include(FsTutorial/MultiModal2009CourseSchedule)>> == 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]] * [[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
Laptop damage policy: If liquid is spilled on a provided laptop, then you are liable for payment of the repair costs!
Course Schedule
FreeSurfer/FS-FAST Course, June 4 and 5, 2009
MGH, Charlestown Navy Yard, Conference Room A
Thursday, June 4th - Introduction / Single Subject / Troubleshooting
Time |
Title |
Type |
Lecturer |
2:00 - 2:30 |
talk |
Bruce Fischl |
|
2:30 - 3:30 |
talk |
Doug Greve |
|
3:30 - 3:45 |
talk |
Bruce Fischl |
|
3:45 - 4:00 |
Tkmedit/Tksurfer demonstration |
demo |
Doug Greve |
4:00 - 4:15 |
break |
|
|
4:15 - 5:00 |
tutorial |
staff |
|
5:00 - 6:00 |
Troubleshooting, Troubleshooting demonstration |
tutorial |
staff, Allison Stevens |
Friday, June 5th - Surface-based Smoothing and Registration / Group Analysis / FS-FAST
Time |
Title |
Type |
Lecturer |
9:00 - 9:30 |
talk |
Doug Greve |
|
9:30 - 10:30 |
talk |
Doug Greve |
|
10:30 - 11:00 |
QDEC demonstration |
demo |
Nick Schmansky |
11:00 - 11:15 |
break |
|
|
11:15 - 12:15 |
tutorial |
staff |
|
12:15 - 1:00 |
tutorial |
staff |
|
1:00 - 2:00 |
lunch |
|
|
2:00 - 3:00 |
talk |
Doug Greve |
|
3:00 - 3:15 |
break |
|
|
3:15 - 6:00 |
tutorial |
staff |
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)