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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 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/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 }}} ---- |
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| [wiki:Self:FsTutorial/Tools FreeSurfer Tools] | == Course Schedule == |
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| [wiki:Self:FsTutorial/Glossary Glossary] | ## select one of the course schedules, comment-out the others: ##<<Include(FsTutorial/Jan2009CourseSchedule)>> ##<<Include(FsTutorial/April2009CourseSchedule)>> <<Include(FsTutorial/BrazilCourseSchedule)>> ##<<Include(FsTutorial/FslCourseSchedule)>> |
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[wiki:Self:FsTutorial/FuncRegistration Functional Registration] |
== 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 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.
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
Course Schedule
FreeSurfer Tutorial and Workshop in São Paulo, Brazil
16, 17, & 18 (Sat.,Sun.,Mon.) April 2011
The FreeSurfer Development Team is hosting a three-day course for beginner and experienced users of FreeSurfer. Topics are listed below. There are 40 available spots for this course (see course registration).
Computers will be provided to all pairs of registrants, which will have FreeSurfer and data already installed. Attendees will work in pairs (sharing a computer).
The course will be held at São Paulo healthcare complex of HCFMUSP.
Contact: Pedro Paulo de M. Oliveira Jr. ( ppj at netfilter dot com dot br )
Location
Hospital das Clínicas - Avenida Dr Eneas de Carvalho Aguiar, 44 - São Paulo - SP - Brazil - (hotel,map)
The course will be held at the Radiology Center Building, in the Amphitheatre C.
Saturday, 16 April - Introduction / Single Subject / Troubleshooting
Time |
Title |
Type |
Lecturer |
8:30 - 9:00 |
Course Registration |
sign-in |
|
9:00 - 9:30 |
tutorial |
Pedro Paulo de M. Oliveira Jr. |
|
9:30 - 10:00 |
talk |
Pedro Paulo de M. Oliveira Jr. |
|
10:00 - 10:30 |
talk |
Nick Schmansky |
|
10:30 - 11:00 |
talk |
Nick Schmansky |
|
11:00 - 11:30 |
break |
|
|
11:30 - 12:30 |
talk |
Allison Stevens |
|
12:30 - 1:30 |
lunch |
-- |
-- |
1:30 - 2:00 |
Tkmedit/Tksurfer demonstration |
demo |
Nick Schmansky |
2:00 - 3:00 |
tutorial |
staff |
|
3:00 - 3:30 |
break |
|
|
3:30- 4:00 |
talk |
Allison Stevens |
|
4:00 - 4:30 |
Quality Checking a Recon |
demo |
Allison Stevens |
4:30 - 5:30 |
Troubleshooting Demonstration, Troubleshooting Tutorial |
tutorial |
staff, Allison |
Sunday, 17 April - Group Analysis / Registration / Longitudinal / ROIs
Time |
Title |
Type |
Lecturer |
9:00 - 10:00 |
talk |
Lilla Zollei |
|
10:00 - 10:30 |
QDEC demonstration |
demo |
Nick Schmansky |
10:30 - 10:45 |
break |
|
|
10:45 - 11:15 |
tutorial |
staff |
|
11:15 - 11:45 |
tutorial |
staff |
|
11:45 - 1:00 |
lunch |
-- |
-- |
1:00 - 1:45 |
talk |
Lilla Zollei |
|
2:15 - 2:45 |
talk |
Lilla Zollei |
|
2:45 - 3:00 |
break |
|
|
3:00 - 3:30 |
talk |
Allison Stevens |
|
3:30 - 4:00 |
talk |
Andre van der Kouwe |
|
4:00 - 4:30 |
tutorial |
staff |
|
4:30 - 5:00 |
tutorial |
staff |
Monday, 18 April - Diffusion / Tracula / MRI basics / Apps / Q&A
Time |
Title |
Type |
Lecturer |
9:00 - 9:30 |
talk |
Lilla Zollei |
|
9:30 - 10:30 |
tutorial |
staff |
|
10:30 - 11:00 |
break and group photo |
|
|
11:00 - 11:30 |
talk |
Lilla Zollei |
|
11:30 - 12:30 |
tutorial |
staff |
|
12:30 - 1:30 |
lunch |
-- |
-- |
1:30 - 2:00 |
talk |
Andre van der Kouwe |
|
2:00 - 2:30 |
break and evaluations |
|
|
2:30 - 3:00 |
talk |
Andre van der Kouwe |
|
3:00 - 3:30 |
talk |
Pedro Paulo de M. Oliveira Jr. |
|
3:30 - 4:00 |
Question and Answer Session, FsQuiz |
talk |
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)