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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!

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 Evaluation

Please fill out our course evaluation 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

FreeSurfer Course, February 1 and 2, 2010

MGH, Charlestown Navy Yard, Building 149, Conference Room A

Monday, February 1st - Introduction / Single Subject / ROIs /Group Analysis

Time	Title	Type	Lecturer
8:00 - 8:30	optional - Unix Tutorial for FreeSurfer Users 1. Surrey, 2. O'Reilly	tutorial	Allison Stevens
8:30 - 9:00	Course Registration	sign-in	staff
9:00 - 9:30	Introduction to Freesurfer	talk	Bruce Fischl
9:30 - 10:30	Analyzing the Individual Subject	talk	Bruce Fischl
10:30 - 10:45	break
10:45 - 11:15	Tkmedit/Tksurfer demonstration	demo	Doug Greve
11:15 - 11:45	Interaction with Individual Subject Data Tutorial	tutorial	staff
11:45 - 12:15	Surface-based Smoothing/Surface-based Registration	talk	Doug Greve
12:15 - 12:45	Working lunch Optional talk - Introduction to Diffusion Processing	talk	Lilla Zollei
12:45 - 1:15	Working lunch Optional talk - MRI Acquisition Methods for Morphometry	talk	Andre van der Kouwe
1:15 - 2:15	ROI Analysis	talk	Doug Greve
2:15 - 2:45	ROI Analysis Tutorial	tutorial	staff
2:45 - 3:00	break
3:00 - 3:45	Group Analysis / GLM / Multiple Comparisons	talk	Mert Sabuncu
3:45 - 4:45	Group Analysis / Multiple Comparisons - mri_glmfit Tutorial	tutorial	staff
4:45 - 5:00	QDEC demonstration	demo	Nick Schmansky
5:00 - 5:45	Group Analysis - qdec Tutorial	tutorial	staff
5:45 -	optional - FreeSurfer Installation on Personal Laptops	one-on-one	Nick Schmansky
5:45 -	optional - Start Processing Your Own Data	one-on-one	Allison Stevens

Tuesday, February 2nd - Troubleshooting / Multi-Modal / Q&A / Future Directions

Time	Title	Type	Lecturer
9:00 - 9:30	Accuracy, Reliability and Validation	talk	David Salat
9:30 - 10:00	Longitudinal FreeSurfer see also: LongitudinalProcessing	talk	Martin Reuter
10:00 - 10:45	FreeSurfer Applications	talk	David Salat
10:45 - 11:00	break
11:00 - 11:30	Failure Modes	talk	Bruce Fischl
11:30 - 12:30	Troubleshooting Tutorial, Troubleshooting Demonstration	tutorial	staff, Allison
12:30 - 1:00	Working lunch Optional demo - Step-by-Step Through a Recon	demo	TBD
1:00 - 1:30	Working lunch Optional talk - Combined Gray Matter/White Matter Analysis of the Aging Brain	talk	David Salat
1:30 - 2:45	Multi-Modal Integration	talk	Doug Greve
2:45 - 3:45	Multi-Modal Integration Tutorial	tutorial	staff
3:45 - 4:00	break
4:00 - 5:00	Future Directions of FreeSurfer:
4:00 - 4:20	Combined Volume and Surface Registration	talk	Lilla Zollei
4:20 - 4:40	TRActs Constrained by UnderLying Anatomy (TRACULA)	talk	Anastasia Yendiki
4:40 - 5:00	Inferring architectonic boundaries from in-vivo MRI	talk	Bruce Fischl
5:00 - 5:30	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)

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+Additions are marked like this.
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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:
-Line 10:
+Line 7:
- [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.
-Line 12:
+Line 13:
- [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
}}}
----
'''Laptop damage policy: If liquid is spilled on a provided laptop, then you are liable for payment of the repair costs!'''
-Line 14:
+Line 21:
- [wiki:Self:FsTutorial/Tools FreeSurfer Tools]
+== 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.
-Line 16:
+Line 24:
- [wiki:Self:FsTutorial/Glossary Glossary]
+== 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/BrazilCourseSchedule)>>
##<<Include(FsTutorial/FslCourseSchedule)>>
##<<Include(FsTutorial/MultiModal2009CourseSchedule)>>
##<<Include(FsTutorial/Sept2009CourseSchedule)>>
<<Include(FsTutorial/Feb2010CourseSchedule)>>

== 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)]]