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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 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	staff
9:00 - 9:30	Unix Tutorial for FreeSurfer Users 1. Surrey, 2. O'Reilly	tutorial	Pedro Paulo de M. Oliveira Jr.
9:30 - 10:00	Intro to FreeSurfer Jargon	talk	Pedro Paulo de M. Oliveira Jr.
10:00 - 10:30	Introduction to Freesurfer	talk	Nick Schmansky
10:30 - 11:00	FreeSurfer Applications, Publications	talk	Nick Schmansky
11:00 - 11:30	break
11:30 - 12:30	Analyzing the Individual Subject	talk	Allison Stevens
12:30 - 1:30	lunch	--	--
1:30 - 2:00	Tkmedit/Tksurfer demonstration	demo	Nick Schmansky
2:00 - 3:00	Interaction with Individual Subject Data Tutorial	tutorial	staff
3:00 - 3:30	break
3:30- 4:00	Failure Modes	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	Group Analysis / GLM / Multiple Comparisons	talk	Lilla Zollei
10:00 - 10:30	QDEC demonstration	demo	Nick Schmansky
10:30 - 10:45	break
10:45 - 11:15	Group Analysis / Multiple Comparisons - mri_glmfit Tutorial	tutorial	staff
11:15 - 11:45	Group Analysis - qdec Tutorial	tutorial	staff
11:45 - 1:00	lunch	--	--
1:00 - 1:45	Registration Methods	talk	Lilla Zollei
2:15 - 2:45	Longitudinal FreeSurfer see also: LongitudinalProcessing	talk	Lilla Zollei
2:45 - 3:00	break
3:00 - 3:30	ROI Analysis	talk	Allison Stevens
3:30 - 4:00	A Non-physicist's Intro to MR SpinBench	talk	Andre van der Kouwe
4:00 - 4:30	ROI Analysis Tutorial	tutorial	staff
4:30 - 5:00	Longitudinal Tutorial	tutorial	staff

Monday, 18 April - Diffusion / Tracula / MRI basics / Apps / Q&A

Time	Title	Type	Lecturer
9:00 - 9:30	Diffusion Data Processing,dtrecon intro	talk	Lilla Zollei
9:30 - 10:30	Diffusion Processing Tutorial	tutorial	staff
10:30 - 11:00	break and group photo
11:00 - 11:30	TRActs Constrained by UnderLying Anatomy (TRACULA)	talk	Lilla Zollei
11:30 - 12:30	Tracula Tutorial	tutorial	staff
12:30 - 1:30	lunch	--	--
1:30 - 2:00	MRI Acquisition Methods for Morphometry	talk	Andre van der Kouwe
2:00 - 2:30	break and evaluations
2:30 - 3:00	Motion-compensated neuroanatomical imaging	talk	Andre van der Kouwe
3:00 - 3:30	iSurf and local FreeSurfer Applications	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)

iSurf - iPhone/iPad app to view FreeSurfer segmentations
Glossary
References
System Requirements for Installation

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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]
 [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 [[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)>>

== 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]]
 * [[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)]]