FreeSurfer Tutorial and Workshop

February 1 & 2, 2010

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 and analysis (or a refresher for those more experienced). Day 2 will cover troubleshooting and multimodal applications. More detail on the topics to be discussed is provided below. The two days will run roughly from 9am-6pm. The complete schedule can be found here.

Note: fMRI analysis is not a component that is taught in this course.
Refer to the Martinos Center Training and Events page for courses covering fMRI.

The course will be held at the Martinos Center for Biomedical Imaging in Boston.

Information on the following is covered below:

• Cost
• Topics Covered During the Course
• Lecturers and Staff
• Accommodations
• Directions
• Parking

• Map of the Course Location

Cost

Payment and all questions about payment should go to Stacey Ladieu (sladieu at nmr dot mgh dot harvard dot edu). The fee for the course is $300 for students, $450 for all others. Check is the only form of accepted payment except for internal employees. If you are from within the Partners network, you can pay via fund transfer. Credit cards are not accepted.

Checks should be made out to Massachusetts General Hospital and include the name of the participant. Send checks to:
Stacey Ladieu
Athinoula A. Martinos Center for Biomedical Imaging
149 Thirteenth Street - Room 2301
Charlestown, MA 02129

Payment must be arranged by January 8, 2010. Payment must be received by that date or you must have at least discussed your method of payment with Stacey Ladieu by that date in order to remain enrolled in the course. Otherwise, your spot will be opened to the waiting list. There is no need to contact us to check whether your payment has gone through - your spot is safe unless we contact you.

There are no refunds if you cannot attend the course. If you cannot attend, you can either apply the tuition payment towards the next course or send someone else in your spot. In the case there are less than 10 registrants for the course, the course will be canceled and the registration fee will be refunded to the registrant.

Course Topics

Below is the list of topics. A more detailed schedule can be found here.

Day 1: Introduction to FreeSurfer

• Unix Tutorial (optional - starts at 8am)

• Introduction to FreeSurfer Jargon

• Introduction to FreeSurfer

• Analyzing the Individual Subject in FreeSurfer

• Interaction with Individual Subject Data - Tutorial
• Introduction to Diffusion Processing (optional)
• MRI Acquisition Methods for Morphometry (optional)
• Surface-based Smoothing/Surface-based Registration
• Region of Interest (ROI) Analysis - Talk and Tutorial
• Group Analysis/GLM/Multiple Comparisons (mri_glmfit)- Talk and Tutorial
• QDEC (group analysis software) - Talk and Tutorial

• FreeSurfer Installation on Personal Laptops (optional)

• Start Processing Your Own Data (optional)

Day 2: Advanced FreeSurfer: Working with Various Data Types

• Accuracy, Reliability, and Validation of Data using FreeSurfer

• Longitudinal Analysis in FreeSurfer

• FreeSurfer Applications - Examples of studies done using FreeSurfer

• Failure Modes and Troubleshooting with FreeSurfer - Talk and Tutorial

• Step-by-Step Through a Recon (optional)
• Combined Gray Matter/White Matter Analysis of the Aging Brain (optional)
• Multi-Modal Integration: ROI and Surface-based Analysis - Talk and Tutorial

• Future Directions of FreeSurfer

  • Inferring architectonic boundaries from in-vivo MRI - Bruce Fischl
  • Combined Volume and Surface Registration - Lilla Zollei

  • TRActs Constrained on UnderLying Anatomy (TRACULA) - Anastasia Yendiki

• Question and Answer Session

Lecturers and Staff

• Bruce Fischl
• Doug Greve
• Sita Kakunoori
• David Salat
• Nick Schmansky
• Allison Stevens
• Krish Subramaniam
• Koen Van Leemput
• Martin Reuter
• Andre van der Kouwe
• Anastasia Yendiki
• Lilla Zollei
• Mert Sabuncu

Accommodations

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. A block of rooms are reserved at $99/night. To request this block, ask for the 'Freesurfer' block.

• 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.

To get to Downtown Boston from Charlestown you can take the shuttle (it runs every 15 minutes during the day on weekends), the water shuttle, or the #93 bus.

Directions

The FreeSurfer Course is being held at the Martinos Center for Biomedical Imaging in Boston:

• Building 149, Conference Room A
• 149 Thirteenth Street
• Charlestown Navy Yard (CNY)
• Charlestown, MA 02129-2020

Public Transportation

If you are coming by T, there is a free Partners shuttle bus that picks you up at North Station (across from TD Banknorth Garden). The schedule is here.

Exit North Station to Causeway Street exit and when you are out in the open ( Causeway St.) walk a few steps to your right. The shuttle stops near the fire hydrant you see in this street view. 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 (the last stop and usually the third stop where everyone exits).

Let security know you are there for the FreeSurfer Course in Conference room A and they will direct you to the location. You will not need an ID or guest pass since you are staying on the first floor.

Parking

Parking near the Center is difficult to get and is either metered (with a 2 hour limit) or expensive ($20+/day for a garage). We can get discounted parking for a group at $5/day ($10 for the 2 days of the course).

If you plan on driving to the course and are interested in purchasing this discounted parking, please let Allison (astevens AT nmr dot mgh dot harvard dot edu) know how many days worth of parking you need.

When you arrive for the course simply pull into the garage and take a ticket. During the Course Registration, you can purchase the discounted parking sticker to put on your ticket. You will have to pay us in cash or by check (made out to MGH) to receive the parking validation sticker(s).

This is very *important*: we cannot wait for checks to be processed by your institution, university, etc. for the price of the parking. You will have to have the check ready on the first day of the course during Registration.

How to determine how many stickers you need: Each parking sticker is good for 24 consecutive hours of parking. Once you park in the garage, you cannot take your car out without needing an additional sticker to pay for your re-entry.

For example, if you are driving on the day of the course, leaving at the end of the course that day, and returning the next day - you only need two stickers to pay for those 2 days. If you are arriving in Boston on Sunday at 6pm and leaving at 8am on Wednesday (62 hours), you will need 3 stickers.

If you are unsure of how many you might need, just tell Allison the maximum amount you would need so she can be sure to have enough stickers on hand during Registration.

Directions from Parking Garage

From the garage, you would walk towards the elevator (away from the ramps you came up on in the car) and take it to the 1st floor. From there, go out the double doors and across the street to enter the building there (Building 149). Let security know you are there for the FreeSurfer Course in Conference room A and they will direct you to the location. You will not need an ID or guest pass since you are staying on the first floor.

Map

Conference Room A is closest to the 9th Street Entrance.