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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 Course, October 4 and 5, 2010

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

Monday, October 4th - Introduction / Single Subject / 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	optional - Intro to FreeSurfer Jargon	talk	Allison Stevens
8:30 - 9:00	Course Registration	sign-in	staff
9:00 - 9:30	Introduction to Freesurfer	talk	Bruce Fischl
9:30 - 10:00	Accuracy, Reliability and Validation	talk	David Salat
10:00 - 11:00	Analyzing the Individual Subject	talk	Doug Greve
11:00 - 11:15	break
11:15 - 11:45	Tkmedit/Tksurfer demonstration	demo	Doug Greve
11:45 - 12:15	Interaction with Individual Subject Data Tutorial	tutorial	staff
12:15 - 1:15	Lunch	--	--
12:30 - 1:00	Optional Lunch Talk- MRI Acquisition Methods for Morphometry	talk	Andre van der Kouwe
1:15 - 2:00	FreeSurfer Applications	talk	David Salat
2:00 - 2:30	Surface-based Smoothing/Surface-based Registration	talk	Doug Greve
2:30 - 2:45	break
2:45 - 3:30	Group Analysis / GLM / Multiple Comparisons	talk	Mert Sabuncu
3:30 - 4:30	Group Analysis / Multiple Comparisons - mri_glmfit Tutorial	tutorial	staff
4:30 - 4:45	QDEC demonstration	demo	Nick Schmansky
4:45 - 5:30	Group Analysis - qdec Tutorial	tutorial	staff
5:30 -	optional - FreeSurfer Installation on Personal Laptops	one-on-one	Nick Schmansky
5:30 -	optional - Start Processing Your Own Data	one-on-one	Allison Stevens

Boston Beer Works location information here.
Meet us at 6:10pm at the front of Building 149 (the entrance on the opposite side of the building from where the Course is held).
If you miss us, we are taking the 6:15pm MGH/Navy Yard shuttle to North Station. From there, you cross the street and go down Canal Street. Boston Beer Works will be on your left.

Time	Title	Type	Lecturer
9:00 - 10:00	ROI Analysis	talk	Doug Greve
10:00 - 10:30	ROI Analysis Tutorial	tutorial	staff
10:30 - 11:00	Longitudinal FreeSurfer see also: LongitudinalProcessing	talk	Martin Reuter
11:00 - 11:15	break
11:15 - 11:45	Failure Modes	talk	Bruce Fischl
11:45 - 12:45	Troubleshooting Demonstration, Troubleshooting Tutorial	tutorial	staff, Allison
12:45 - 1:45	Lunch	--	--
12:45 - 1:15	Optional Lunch Talk- Quality Checking a Recon	demo	Allison Stevens
1:45 - 3:00	Multi-Modal Integration	talk	Doug Greve
3:00 - 3:45	Multi-Modal Integration Tutorial	tutorial	staff
3:45 - 4:00	break
4:00 - 4:20	Combined Volume and Surface Registration	talk	Lilla Zollei
4:20 - 5:30	Future Directions of FreeSurfer:
4:20 - 4:40	Motion-compensated neuroanatomical imaging	talk	Dylan Tisdall
4:40 - 5:10	Inferring architectonic boundaries from in-vivo MRI	talk	Bruce Fischl
5:10- 5:30	TRActs Constrained by UnderLying Anatomy (TRACULA)	talk	Lilla Zollei
5:30 - 6:00	Question and Answer Session, FsQuiz............FsQuizAnswers	talk	staff

The FreeSurfer Evaluation is here!

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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