Upcoming FreeSurfer courses
If you would like to be notified about upcoming FreeSurfer courses, sign up for the course mailing list.. We host two Boston courses each year, typically in the first week of April and thhttps://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Spring2019CourseSchedulee last week of September.
Next Boston course?
Registration is full for the next FreeSurfer Course ##but you can still sign up to our waiting list here: Click here to register! The next Boston course is scheduled for For your own planning purposes, we plan to open registration for the September course on This is a rigorous four day course that offers structural, functional and diffusion MRI topics. You may find a prospective schedule for the upcoming Fall 2019 course here. Please note that this schedule is not yet final and subject to change. The course will be held at the Martinos Center for Biomedical Imaging in Boston (114 Sixteenth Street, Charlestown, MA 02129).
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 or Leah Morgan (freesurferlab@gmail.com).
The FreeSurfer Development Team hosts a An introduction to FreeSurfer Group analysis Multi-modal integration Multi-modal integration The four days consist of talks/tutorials that run all day, roughly from 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!
The Payment deadline is Credit cards, checks, and cash are the only forms of accepted payment.
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 (freesurferlab@gmail.com) for any issues. Click here to pay by Credit Card
Make checks payable to: Massachusetts General Hospital Mail checks to this address: Please be sure the
There are two options for paying by cash:
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.
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. 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. 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).
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. This Linux tutorial is very basic. Overview of FreeSurfer's abilities. Description of each step of the FreeSurfer processing stream. Using FreeSurfer's visualization tools to look at FreeSurfer output. Discussion of the possible errors one may find in their FreeSurfer output and how to fix them. Live demo of how to scroll through FreeSurfer output and look for errors. 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). Introduction on how FreeSurfer output can be used with other modalities (i.e. fMRI data, diffusion data) How to process diffusion MRI data to extract basic diffusion measures and to reconstruct white-matter pathways using FreeSurfer's tractography tool. A description of how using different scan protocols can affect data quality and FreeSurfer reconstruction. How to process longitudinal data with FreeSurfer and what's going on behind the scenes.
For discounted hotel options, please see this website. We have also reserved a block of discounted hotel rooms at the Constitution Inn (at $166.25/night) for the Spring 2019 course attendees. Further instructions are below: Please be sure to contact Elizabeth Benner to reserve a room via email: ebenner@ymcaboston.org or at 617-286-1209. She generally does not answer phone calls and will no longer be accepting international phone calls, so we recommend contacting her via email for the least amount of hassle. The deadline for reserving a room at the Constitution Inn's discount price is 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 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.
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.) 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 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.
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.
Next International course?
General Information
Course Mailing List
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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
Day 2 will cover:
Single Subject Surface-based analysis
MRI Acquisition Tips
ROI analysis
Day 3 will cover:
Longitudinal analysis
Troubleshooting
Day 4 will cover:
fMRI
Diffusion
Future directions Payment
Cost
Deadlines & Accepted Payment Types
Credit Cards
Checks
Stacey Ladieu
Athinoula A. Martinos Center for Biomedical Imaging
149 Thirteenth Street - Room 2301
Charlestown, MA 02129
Cash
Missed Deadlines & Cancellations
FAQ's
How many individuals are accepted into the Boston course? Course Topics
Linux Demo/Tutorial (optional)
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.
Structural and Functional Integration Lecturers and Staff
Accommodations
Directions
114 Sixteenth Street
Charlestown Navy Yard (CNY)
Charlestown, MA 02129-2020 Map
Public Transportation & Shuttle
Parking
Directions from Parking Garage