Upcoming FreeSurfer courses
If you would like to be notified about upcoming FreeSurfer courses, sign up for the course mailing list.
Next Boston course?
The next Boston course is scheduled for April 2-5, 2018.
The Spring 2018 course is full, but you may still register to be added to the wait-list! Click here to register!
We have expanded to a four day course so that we may offer structural, functional and diffusion MRI topics at every course. You may find an example of the schedule here. Please note that this schedule is not yet final.
The course will be held at the Martinos Center for Biomedical Imaging in Boston (114 Sixteenth Street, Charlestown, MA 02129).
We plan to open registration for the April course on January 31, 2018 at 3:30 PM EST. To be notified of when it is open and to receive other course-related emails, sign up for the course mailing list. The payment deadline is February 9, 2018 for all payment forms except for institutional check. The payment deadline for those sending an institutional check is March 5, 2018 with the expectation that we will be contacted by your financial institution by February 9, 2018 to confirm a check is being issued. Note: As long as there are empty spots in the course, we will accept late registrations. If you register after the payment deadline has passed, payment is due immediately.
Next International course?
If you would like to host a FreeSurfer course, contact Allison Stevens (astevens at martinos dot org).
Additional details about the Boston Course 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, Allison Stevens (astevens at martinos dot org) or Emma Boyd (eboyd2 at martinos dot org).
Course Mailing List
If you are interested in being notified about future course offerings, sign up for our mailing list (here).
To unsubscribe from the course mailing list please click here.
Boston Course Details
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
Day 2 will cover:
Day 3 will cover:
Day 4 will cover:
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 most recent Boston course schedule can be found here. Please check back for updates.
Additional topics and more detail on each topic is provided below.
The fee for the course is $900. 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 9, 2018 for all payment forms except for institutional check. The payment deadline for those sending an institutional check is March 5, 2018 with the expectation that we will be contacted by your financial institution by February 9th 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 Emma Boyd (eboyd2 at martinos dot 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.
Make checks payable to: Massachusetts General Hospital
Mail checks to this address:
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.
There are two options for paying by cash:
- Make an appointment with Allison Stevens (astevens at martinos dot org) to deliver cash in person
- Contact Stacey (sladieu at martinos dot org) to send cash via Western Union or Moneygram. The transfer must be made out to Stacey Ladieu.
Please use the website below to make a payment via credit card.
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 or you can send someone in your place.
How many individuals are accepted into the Boston course?
- 50 people
Do postdocs qualify for the student rate?
- No, sorry.
Is there a discount for MGH or Martinos Center employees?
- Sorry, no.
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.
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.
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.
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.
How do I know if my payment went through?
- If it hasn't we will contact you.
Do I get any credits for taking this course?
- Nope, but we will give you a certificate to prove you took it.
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.
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.
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.
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).
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.
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.
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.
Running FreeSurfer in the cloud with AWS batch
This talk will cover how to run FreeSufer's recon-all pipeline in the cloud using AWS Batch. It begins with a brief overview of relevant AWS components and terminology as well as an introduction to docker: a tool to help create, deploy and run software in a consistent and reproducible environment. This will be followed by a demonstration of how to use docker on a local machine and finally how to execute recon-all inside a docker container on AWS using AWS Batch.
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 Smoothing/Surface-based Registration
- 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.
- 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
- Inferring architectonic boundaries from in-vivo MRI - Bruce Fischl
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
- Lilla Zollei
- Jonathan Polimeni
- Caroline Magnain
- Emma Boyd
- Andrew Hoopes
- Iman Aganj
- Isik Karahanoglu
- Paul Wighton
- Viviana Siless
- Giorgia Grisot
- Robert Frost
- Aina Frau-Pascual
- Amod Jog
For discounted hotel options, please see this website. Further instructions are below:
We've had some issues in the past with the Constitution Inn main desk telling attendees that there is no block or no vacancy. As long as the block deadline has not passed and the block is not full, you should be able to reserve a room at the discounted rate without issue. If the deadline has passed or the block is full *but* they still have rooms available, they will give you those rooms at the same discount. Please be sure to contact Elizabeth Benner to reserve a room at 617-286-1209 for the least amount of hassle. If they do not accommodate you or you are told the block is full, please let Stacey Ladieu (sladieu AT martinos DOT org) know.
To get to Downtown Boston from Charlestown you can take the free shuttle (it runs every 15 minutes during the day on weekends), the water shuttle, or the #93 bus. Shuttle bus stops are marked on the Map at the end of this page.
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.
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.
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 at our garage overnight. We will give you parking tickets to be able to do so.
Each parking ticket is good for 24 hours but you will not be able to take your car out of the garage and return it without needing more tickets. If you are parking your car overnight for a few days (say, 3 days), make sure you put enough tickets (3 tickets) in one right after the other. Note: When you are feeding multiple tickets into the meter, make sure you put them in one at a time. They do not go in on a continuous feed.
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.