FreeSurfer Tutorial and Workshop
April 6 & 7, 2009
Martinos Center for Biomedical Imaging
149 Thirteenth Street, Charlestown, MA 02129
The FreeSurfer Development Team is hosting a two-day course for beginner and experienced users of FreeSurfer. Day 1 will be an introduction to FreeSurfer (or a refresher for those more experienced). Day 2 will cover everything you need to know for analyzing your data. Topics are listed below. The two days will roughly run from 8:30am-6pm. Registration deadline is March 20, 2009. There are only 34 available spots for this course.
Laptops will be provided to the first 12 pairs of registrants, which will have FreeSurfer and data already installed. Attendees will work in pairs (sharing a laptop). For the additional 10 pairs of registrants, you must bring your own laptop, and you must install FreeSurfer and tutorial data on it and test it ahead of time. There will be time at the end of Day 1 to learn how to install FreeSurfer but please keep in mind that there might not be enough time to resolve any specific technical issues that may arise.
The course will be held at the Martinos Center for Biomedical Imaging in Boston.
Schedule
Day 1: Introduction to FreeSurfer
- Unix Tutorial (optional - starts at 8am)
Introduction to FreeSurfer
FreeSurfer Applications
Reliability/Validation of FreeSurfer
- Analyzing the Individual Subject
- Interaction with Individual Subject Data
- Group Analysis/GLM
- QDEC
- Multiple Comparisons
- Group Analysis Interactive Tutorial
FreeSurfer Installation on Personal Laptops (optional)
- Start Processing Your Own Data (optional)
Day 2: Advanced FreeSurfer: Working with Various Data Types
- Registration for Multi-Modal Integration
- Working with fMRI and Diffusion Data
- Working with Different Format Types
- Segmentation/ROI Analysis
Working with FreeSurfer Stats
- Surface-Based Multi-Modal Analysis
- Bug Reporting
- Question and Answer Session
Future Directions of FreeSurfer
- Inferring architectonic boundaries from in-vivo MRI - Bruce Fischl
- Combined Volume and Surface Registration - Lilla Zollei
- Tractography of Underlying Anatomy (TRACULA) - Anastasia Yendiki
Lecturers and Staff
- Bruce Fischl
- Doug Greve
- Sita Kakunoori
- David Salat
- Nick Schmansky
- Allison Stevens
- Krish Subramaniam
- Koen Van Leemput
- Anastasia Yendiki
- Lilla Zollei
Accomodations
We encourage attendees to stay at either of these two locations:
The Constitution Inn is located adjacent to our research building in Charlestown. Rooms at the Inn are simple and relatively inexpensive. The proximity of this accommodation was found to be a major benefit for other NMR Center course attendees. The facility was recently renovated and guests can use the health club and pool. The Inn has free wireless internet access. To reserve a room at the Constitution Inn, call (617) 241-8400, or visit them on the web at www.constitutioninn.org.
Marriott Residence Inn at Tudor Wharf, a short walk through the Navy Yard to the classroom. The MGH/Partners shuttle bus also has a stop just steps from the hotel, at Gate 1, and it runs every 15 minutes during the day, and every half an hour in the evening. The hotel is a new all-suite hotel that offers complimentary high-speed and wireless internet access and a complimentary breakfast buffet daily.
Directions
The FreeSurfer Course is being held at:
- Building 149, Conference Room A
- 149 Thirteenth Street
- Charlestown Navy Yard (CNY)
- Charlestown, MA 02129-2020
Conference Room A is closest to the 9th Street Entrance.
If you are coming by T, there is a shuttle bus that picks up at North Station (across from TD Banknorth Garden). The schedule is here: http://www.partners.org/ourhosp/shuttleschedule/mgh_cny.html
From North Station, you want to look at the side that says Arrive/Depart MGH Main Campus. It comes every 15 minutes and it takes about 5 minutes for it to get to North Station from the Main Campus. You want to get off at Building 149 (usually the third stop).