FreeSurfer Tutorial and Workshop

April 2-4, 2012

Martinos Center for Biomedical Imaging

114 Thirteenth Street, Charlestown, MA 02129

The next course at the Martinos Center will be held on April 2nd, 3rd, & 4th.
The Registration and Payment deadline is February 13, 2012. There are 60 available spots for the course.
The course will be held at the Martinos Center for Biomedical Imaging in Boston (114 Thirteenth Street, Charlestown, MA 02129).

The tentative course schedule can be found here.

Registration is now open! Click here to register!

June 27-29, 2012

Dept. of Radiology, VU University Medical Center

Amsterdam, Netherlands

The Department of Radiology at VU University Medical Center will host a FreeSurfer Tutorial and Workshop in Amsterdam this June! Questions about this course should be directed to Veronica Popescu (v.popescu AT vumc DOT nl). The tentative schedule for the course can be found here.

Registration is now open! Click here to register!

If you are interested in being notified about future course offerings, sign up for our mailing list (here).
If you have a specific question about the FreeSurfer courses or would like to host one in your area, you can email Allison Player (astevens at nmr dot mgh dot harvard dot edu) who organizes the courses.

Information about previous courses can be found below:

The FreeSurfer Development Team is hosting a three-day course for beginner and experienced users of FreeSurfer.

Day 1 will cover:

• An introduction to FreeSurfer
  Surface-based analysis
  Troubleshooting
  

Day 2 will cover:

• ROI analysis
  Longitudinal analysis
  Multi-modal integration
  Group analysis
  

Day 3 will cover:

• Functional analysis
  Diffusion processing

The three days will run roughly from 8am-6pm. Laptops are provided with FreeSurfer and the tutorial data already installed. Attendees will work in pairs (sharing a laptop). The tentative course schedule can be found here. Please check back for updates.

Additional topics and more detail on each topic is provided below.

Information on the following is covered below:
Payment
FAQ
Topics Covered During the Course
Lecturers and Staff
Accommodations
Directions
Parking
Map of the Course Location

Payment

The fee for the course is $650. A reduced rate of $450 is available to graduate students. MDs, PhDs, and post-docs do not qualify for the graduate student rate!
Payment is due immediately upon registration. Payment and all questions about payment should go to Stacey Ladieu (sladieu at nmr dot mgh dot harvard dot edu).

Check and cash are the only forms of accepted payment.
Credit cards are not accepted.

Make checks payable to: Massachusetts General Hospital

Mail checks to:
Stacey Ladieu
Athinoula A. Martinos Center for Biomedical Imaging
149 Thirteenth Street - Room 2301
Charlestown, MA 02129

Please be sure the NAME OF PARTICIPANT is listed on the check.

If payment has not been received by February 13, 2012 or your institution has not contacted Stacey Ladieu (sladieu at nmr dot mgh dot harvard dot edu) with details of their payment arrangement by that date (in the case of an institutional check), 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.

Course fees are refundable up to the payment deadline. A $200 fee will be deducted, should you request a refund up to 2 weeks prior to the program. After that, the tuition can be applied to a future program or you can send someone in your place. In the case there are less than 10 registrants for the course, the course will be cancelled and the registration fee will be refunded to the registrant.

FAQ

1. Do postdocs qualify for the student rate?

   • No, sorry.

2. Is there a discount for MGH or Martinos Center employees?

   • Sorry, no.

3. I can only pay for the course with credit card so that I can be reimbursed later. Is this okay?

   • Sorry, we have not found a way to be able to accept credit cards. Payment must be by check or cash.

4. I cannot pay by check and you don't accept credit card. Do I have any other options?

   • If you are local, you may bring a cash payment to Allison Player (astevens at nmr dot mgh dot harvard dot edu) before the deadline. If you are not local, services like Western Union and Moneygram are a possibility in extreme cases. Please contact Allison for details.

5. Payment is required with registration but my institution will take several weeks to cut a check. Does this mean I cannot attend?

   • You may still attend the course. Have the person at your institution that is responsible for arranging your payment contact Stacey Ladieu (sladieu at nmr dot mgh dot harvard dot edu) to verify that a request for payment has been submitted and is being processed.

6. The course is full. Can you register me for the next one?

   • You can sign up for our course mailing list and you will be notified when registration for the next course opens (that list is here). You can also register for the currently full course to be put on the waiting list for it. This does not however automatically get you a spot in the next course.

7. Can I get a receipt for the course?

   • Sure! Receipts will be available on the last day of the course.

8. How do I know if my payment went through?

   • If it hasn't we will contact you.

9. Do I get any credits for taking this course?

   • Nope, but we will give you a certificate to prove you took it.

10. Do you serve any food at the course?

    • There will be a continental breakfast each morning and coffee supplied in the afternoon. There is also a cafeteria in the building where the course is held and two cafes 1-2 blocks from the building.

11. I have some data I would like to get your opinion on. Can I show it to you?

    • Sure! But please do so during the optional "process your own data" session on the first day or during breaks, not during the tutorial sessions. Questions about the tutorial currently being worked on will have to take priority over personal data questions.

12. I need some help installing FreeSurfer on my laptop - I can't seem to get it to work. Can you help with that?

    • Sure! Please see the response to the question above.

13. Can I bring my own laptop to work on instead of sharing with someone else?

    • We strongly discourage this. If any issues arise during the tutorial sessions which are unique to your laptop, we will not be able to troubleshoot those issues for you (it takes staff away from answering general tutorial questions). Problems with the FreeSurfer installation on your laptop can be worked out during the optional installation session at the end of the first day. If you insist on working on your laptop, please thoroughly test your installation ahead of time - guidelines for this can be found on the TestingFreeSurfer wiki. It might also be a good idea to try to run all the commands in the tutorials (here).

Course Topics

Below is the list of topics. The course format is composed of lectures followed by hands-on tutorials so that you can gain experience interacting with data processed by FreeSurfer. A basic understanding of Unix is necessary to run and work with FreeSurfer.

Day 1: Introduction to FreeSurfer

• Unix Tutorial (optional)

  • This unix tutorial is very basic. It will only cover how to use cd to navigate through directories, how to copy files, and how to use emacs. Scripting will not be covered. For those who are not familiar with UNIX, this tutorial is meant to get you comfortable enough to at least get through the FreeSurfer tutorials that are part of the course.

• Introduction to FreeSurfer Jargon (optional)

  • Intended for those new to imaging software.

• Introduction to FreeSurfer

  • Overview of FreeSurfer's abilities.

• Analyzing the Individual Subject in FreeSurfer

  • Description of each step of the FreeSurfer processing stream.

• Interaction with Individual Subject Data - Tutorial

  • Using FreeSurfer's visualization tools to look at FreeSurfer output.

• Surface-based Smoothing/Surface-based Registration
  • Volume vs. Surface-based analysis
• A Non-physicist's Intro to MR (optional)
  • A short introduction to the basic processes underlying MR imaging, with an emphasis on intuitive explanations for non-physicist MR users.
• Registration Methods
  • Overview of different registration methods

• Failure Modes and Troubleshooting with FreeSurfer - Talk and Tutorial

  • Discussion of the possible errors one may find in their FreeSurfer output and how to fix them.

• Quality Checking a Recon

  • Live demo of how to scroll through FreeSurfer output and look for errors.

• FreeSurfer Installation on Personal Laptops (optional)

  • Help with installation of FreeSurfer. Downloading the software ahead of time is recommended.

• Start Processing Your Own Data (optional)
  • Guidance on how to run a recon on your own subject data. (You supply the data).

Day 2: FreeSurfer and Diffusion Data

• Region of Interest (ROI) Analysis - Talk and Tutorial

  • A description of the FreeSurfer atlases used in subcortical segmentation and cortical parcellation. Information on creating and analyzing ROIs.

• Longitudinal Analysis in FreeSurfer

  • How to run longitudinal data and what's going on behind the scenes.
• MRI Acquisition Methods for Morphometry (optional)

  • A description of how using different scan protocols can affect data quality and FreeSurfer reconstruction.

• Future Directions of FreeSurfer

  • Inferring architectonic boundaries from in-vivo MRI - Bruce Fischl
• Multi-Modal Integration - Talk and Tutorial

  • Introduction on how FreeSurfer output can be used with other modalities (i.e. functional data, diffusion data)

• Group Analysis/GLM/Multiple Comparisons (mri_glmfit)- Talk and Tutorial
  • Covers the basics of group analysis in the context of imaging data.
• QDEC (group analysis software) - Talk and Tutorial
  • Introduction to a user-friendly tool for conducting group analyses.

Day 3: FreeSurfer and Functional Data

• FSFAST
  • Preprocessing of fMRI (motion correction, slice-timing correction, smoothing, registration to the anatomical, sampling to the common group space in the surface and volume), setting up and running block and event-related analysis, adding nuisance variables to the analysis, performing the individual fMRI time series fMRI analysis, performing group fMRI analysis in the volume and on the surface.
• Motion-compensated neuroanatomical imaging (optional)
  • While real-time fMRI motion correction has been available with some MRI scanners for years (e.g. Siemens' PACE), effective real-time motion correction in neuroanatomical imaging is just now becoming available. This talk focuses on the motion-correction system we have developed for the Siemens platform, but also discusses the current developments on the GE platform.

• Diffusion Data Processing and TRACULA talks and tutorial

  • How to process diffusion MRI data to extract basic diffusion measures and to reconstruct white-matter pathways using FreeSurfer's new tractography tool.

• Question and Answer Session

Lecturers and Staff

• Bruce Fischl
• Doug Greve
• Andre van der Kouwe
• Jon Polimeni
• Martin Reuter
• Mert Sabuncu
• David Salat
• Nick Schmansky
• Allison Stevens Player
• Krish Subramaniam
• Dylan Tisdall
• Anastasia Yendiki
• Lilla Zollei
• Sita Kakunoori
• Michelle Roy
• Louis Vinke
• Priti Srinivasan
• Juan Eugenio Iglesias
• Jonathan Polimeni
• Emma Ben-Avi

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 $109/night. To request this block, ask for the 'MGH Freesurfer' block. Only 20 rooms are available and the deadline for reserving a room at this price is March 2, 2012 by 5pm EST.

• 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.

You can get a discounted rate of $199/night for a studio - speak to the hotel directly and ask for the Partners Healthcare Rate.

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 114, Conference Room D1
• 114 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 114 (the second stop after North Station).

Let security know you are there for the FreeSurfer Course in Conference room D1 and they will direct you to the location.

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).

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 drive in the first day of the course and leave the garage at the end of the day, repeating this for all 3 course days - you will need 3 parking stickers to pay for those 3 days. If you are parking in the garage on Sunday evening at 6pm and take your car out at 8am on Thursday (86 hours), you will need 4 stickers (86/24 = 3.58 round up to 4 stickers to pay for the 3.5 days).

Map

Please check back - the map will be posted soon!