FreeSurfer courses

The FreeSurfer team is currently hosting virtual courses. Please visit the Virtual Course Page for more details:

Virtual Course Page

Currently, we are holding virtual courses periodically. See details here. We are not yet sure when we will return to in-person courses.

Next International course?

If you would like to host a FreeSurfer course, contact Allison Stevens (astevens at martinos dot org).

General Information

Information about our virtual courses can be found here. Details about the Boston Course we have held in the past can be found below. Information about international courses can be found on their respective websites.

If you have a specific question about the FreeSurfer courses that was not answered by our FAQ or would like to host a course in your area, you can email one of the course organizers, ( fscourse@mgb.org ).

Boston Course Details

Click on any of the topics below for more information:
Overview
Payment
FAQ
Topics Covered During the Course
Lecturers and Staff
Accommodations
Directions
Parking
Map of the Course Location

Overview

The FreeSurfer Development Team hosts a four-day, rigorous course for beginner and experienced users of FreeSurfer.

Day 1 caters to beginners and will cover:

• An introduction to FreeSurfer
  Single Subject Surface-based analysis
  MRI Acquisition Tips
  ROI analysis
  

Day 2 will cover:

• Group analysis
  Longitudinal analysis
  Troubleshooting

Day 3 will cover:

• Multi-modal integration
  fMRI
  Diffusion

Day 4 will cover:

• Multi-modal integration
  Future directions

The four days consist of talks/tutorials that run all day, roughly from 9am-5pm. There will be extra time to work on tutorials or data before 9am and after 5pm. Attendees are expected to attend all talks and tutorials aside from the ones scheduled as "optional". Attendees may opt out of either the fMRI or Diffusion lectures if it is not applicable to them. Laptops are provided with FreeSurfer and the tutorial data already installed. Attendees will work in pairs (sharing a laptop). The schedule of talks and links to tutorials can be found here. Please check back for updates.

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

Payment

Cost

The fee for the course is $950. A reduced rate of $625 is available to undergraduate and graduate students. MDs, PhDs, RAs and Post-docs do not qualify for the student rate!

Deadlines & Accepted Payment Types

The Payment deadline is February 24, 2020 for all payment forms except for institutional check. The payment deadline for those sending an institutional check is March 9,2020, with the expectation that we will be contacted by your financial institution by February 24, 2020 to confirm a check is being issued. As long as there are empty spots in the course, we will accept late registrations (regardless of the payment deadline). If you register after the payment deadline has passed, payment is due immediately. Payment and all questions about payment should sent to Stacey Ladieu (sladieu at martinos dot org). Please cc the course organizers ( fscourse@mgb.org ) on your emails with Stacey so she can update your payment status accordingly.

Credit cards, checks, and cash are the only forms of accepted payment.

Credit Cards

Please use the website below to make a payment via credit card.

Once live, on this website, you will see two payment amounts to choose from; the reduced fee for students and the standard course fee. Select the relevant category for your payment which takes you to a new page. Then select your quantity and Add to cart. Select View Cart and the Proceed to Checkout. Enter your billing address and click continue, then enter your credit card details. This is a new website, so please contact Stacey ( sladieu@mgh.harvard.edu ) and CC the course organizer's email ( fscourse@mgb.org ) for any issues.

Click here to pay by Credit Card

Checks

Make checks payable to: Massachusetts General Hospital

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

Please be sure the name of the person taking the course is listed on the check.

Cash

There are two options for paying by cash:

1. Make an appointment with Allison Stevens (astevens at martinos dot org) to deliver cash in person
2. Contact Stacey (sladieu at martinos dot org) to send cash via Western Union or Moneygram. The transfer must be made out to Stacey Ladieu.

Missed Deadlines & Cancellations

If payment has not been received by the payment deadline or in the case of an institutional check, your institution has not contacted Stacey Ladieu (sladieu at martinos dot org) with details of their payment arrangement by that date, 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 $300 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 within one year of the course for which you registered and paid for, or you can send someone in your place.

FAQ

1. How many individuals are accepted into the Boston course?

   • 50 people

2. Do postdocs qualify for the student rate?

   • No, sorry.

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

   • Sorry, no.

4. I cannot pay by check or credit card. Do I have any other options?

   • If you are local, you may bring a cash payment to Allison Stevens (astevens at nmr dot mgh dot harvard dot edu) before the deadline. If you are not local, you can pay via Western Union and Moneygram if it is addressed to Stacey Ladieu. Please contact Stacey (sladieu at nmr dot mgh dot harvard dot edu) first 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! Paper receipts will be available on the first day of the course. If you need a receipt or invoice before then to get a check issued or reimbursed, please use the confirmation email you received when you registered for 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 & coffee and some snacks supplied in the afternoon. There is also a cafeteria nearby where the course is held and two cafes 2-3 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 know that if you show us during a tutorial, questions from students about that tutorial will have to take priority over personal data questions. If you email Allison or Emma prior to the course, they can try to arrange some help.

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?

    • 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). We strongly discourage using your own laptop instead of the ones we provide. 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).

14. How far is the airport from the course location?

    • About 20 minutes by taxi and 1 hour by public transportation (there are several transfers). The taxi will cost $20-$25. Public transportation will cost under $3.

15. Would it work if I scheduled a flight for the evening of the 3rd or 4th day of the class?

    • Certainly. You can bring your luggage to the room where the course is held and leave straight from there. Traffic can be bad after 3pm, so you may need 45 minutes to an hour to get to the airport. To attend all the talks on the 3rd day, your flight will need to be 8pm or later.

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 Linux is necessary to run and work with FreeSurfer.

• Linux Demo/Tutorial (optional)

  • This Linux tutorial is very basic. Scripting will not be covered. This tutorial will cover how to to navigate (cd) through directories, how to copy files, how to make directories, how to use emacs, and how to set variables. For those who are not familiar with Linux, this tutorial is meant to get you comfortable enough to at least get through the FreeSurfer tutorials that are part of the course. If you have never used Linux before, this session is highly recommended.

• Introduction to FreeSurfer Jargon (optional)

  • Intended for those new to imaging software. Explains basic vocabulary such as voxel, surface, vertex, volume, segmentation, parcellation, registration, and recon.

• 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.

• 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.

• Structural and Functional Integration

  • An explanation of why structural information is critical for functional imaging research.

• 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.

• Surface-based Analysis: Intersubject Registration & Smoothing

  • Volume vs. Surface-based analysis

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

  • A description of the FreeSurfer atlases used in subcortical segmentation and cortical parcellation as well as the measures FreeSurfer provides. Information on creating and analyzing ROIs (volume vs. intensity studies).

• 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.

• Multi-Modal Integration - Talk and Tutorial

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

• Basics of fMRI Analysis

  • Covers the basics of functional MRI data analysis, spanning preprocessing to single-subject and group-level analyses. Topics include motion correction, B0 distortion correction, spatial normalization, spatial smoothing, hemodynamic modeling, GLM analysis, contrasts and hypothesis testing, and Random-, Fixed-, and Mixed-Effects group analyses.

• FS-FAST

  • 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.

• 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 tractography tool.

• 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.

• MRI Acquisition Methods for Morphometry (optional)

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

• Registration Methods (optional)

  • Overview of different registration methods discussed so far (flirt, robust_register, bbregister) and introduction of a new registration tool, CVS (combined volume and surface registration).

• Longitudinal Analysis in FreeSurfer

  • How to process longitudinal data with FreeSurfer and what's going on behind the scenes.

• Future Directions of FreeSurfer

  • Inferring architectonic boundaries from in-vivo MRI - Bruce Fischl
    • Techniques for inferring the location of architectonic features in the brain in vivo

• Question and Answer Session

  • Open forum to resolve any unanswered questions

Lecturers and Staff

• Bruce Fischl
• Doug Greve
• Andre van der Kouwe
• Allison Stevens
• Anastasia Yendiki
• Caroline Magnain
• Lilla Zollei
• David Salat
• Iman Aganj
• Paul Wighton
• Robert Frost
• Leah Morgan
• Andrew Hoopes
• Matthew Vera
• Devani Cordero
• Jonathan Polimeni
• Malte Hoffmann

Accommodations

For nearby hotel options, please see this website. We have reserved a block of discounted hotel rooms at the Constitution Inn (at~ $160/night) for FreeSurfer course attendees. The Constitution Inn is the closest accommodation to the course location, but the website lists other hotel options that are also nearby. Please note that we recommend hotels based on their proximity to the course location only and we strongly encourage students to read reviews on the hotel options before booking, to determine if it's the right fit for you.

Directions

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

• Building 114, Conference Room D1
  114 Sixteenth Street
  Charlestown Navy Yard (CNY)
  Charlestown, MA 02129-2020

When you enter Building 114, take the door on your left. Follow the signs or let security know you are there for the FreeSurfer Course in Conference room D1 and they will direct you to the location.

Map

Public Transportation & Shuttle

If you are coming via the train (aka the T), there is a free Partners shuttle bus that picks you up at the MGH main campus and the North Station T stop (across from TD Banknorth Garden) and will take you to the course location in the Navy Yard. If you are taking the 'green line' train to North Station, leave the station via the Causeway Street exit. Shuttles traveling to the Charlestown Navy Yard (CNY) and to the MGH main campus stop on Haverhill St. near the corner of Causeway St.

The shuttle schedule can be found here here under "MGH Main Campus, North Station, One Constitution Road, Charlestown Navy Yard". (Note: There is a second schedule in the list with a similar name but without "One Constitution Road" in the title. This is the Saturday/Sunday schedule. Be sure to choose the schedule that corresponds to the date you are traveling.)
Important Note: Due to construction in the area, the shuttle bus takes a much longer, convoluted path than it used to and thus the ride to North Station can take 20-30 minutes. The ride from the main hospital to CNY takes about 40 minutes. The ride from North Station to CNY takes only about 10-20 minutes.

The shuttle comes every 15 minutes during the day (after 7pm, it comes every half hour and stops around 1am). It will arrive at North Station approximately 5 minutes after the time listed on the schedule under "Arrive/Depart MGH Main Campus". The shuttle stops right in front of Building 114 (the third stop after you board at North Station). Please see the map above for the shuttle bus stop and building location.

There is another shuttle bus that picks up from North Station. It has only one stop - the Spaulding Rehab building in the Navy Yard. This is right next to the course location. The Spaulding shuttle has a limited schedule and only operates between 6:00 AM - 9:00 AM and 3:00 PM - 6:00 PM on weekdays. On weekends, it does not operate in the evening. It runs approximately every 10 minutes.

Parking

If you are driving to the course, you may park in the parking garage at 199 5th Avenue and we will pay for your parking. During registration on the first day of the course, you will be given validated parking.

If you are staying at the Constitution Inn in Charlestown, you may park in a secure garage overngith one block away from the inn at a cost of $10/day. The inn has their own validation machine and therefore course organizers are not able to arrange this parking on your behalf.

Directions from Parking Garage

As can be seen on the map above, the parking garage has two exits. The exit at the back of the garage takes you to 16th Street and is closest to Building 114, however, it consists only of stairs. The exit farthest from Building 114 has elevators. If you would prefer to take an elevator, take it to the 1st floor. From there, go out the double doors and make a right. Take another right at the corner onto 5th Avenue. Cross the street at the crosswalk and in front of you will be the entrance to Building 114.