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| ||4:40 - 5:00 ||Q&A with !FreeSurfer Team ||talk ||Bruce Fischl, Doug Greve, & FS Team || | ||4:40 - 5:00 ||Q&A with !FreeSurfer Team ||talk ||Doug Greve & FS Team || |
2-Day Virtual FreeSurfer Course
The FreeSurfer Team is currently holding Virtual Courses. Please refer to the Course Description page for info on previous in-person courses.
The next virtual FreeSurfer course is scheduled for June 2nd, 3rd, and 5th, 2026. The course will take place between 9:00am and 5:00pm Eastern Daylight Time (EDT) on these days. This is a two day course that offers a basic introduction to FreeSurfer. A FreeSurfer Virtual Machine (VM) will be provided to course participants so that they can easily work with FreeSurfer and practice data during the course. Before registering, review the tentative schedule (listed below) to make sure it will work for you and review the technical requirements to be sure your computer can run the course software. You will be required to verify your computer can properly host the course software by May 22nd at 3:00pm EDT in order to stay enrolled in the course. If your computer cannot run the course materials, your course registration will be cancelled and a full refund issued to you.
Registration is now CLOSED for the 2026 course. If you have a specific question about the FreeSurfer courses that was not answered by this website and our FAQ or would like to host a course in your area, you can email one of the course organizers (fscourse AT mgb.org).
The two day course consists of talks and tutorials that run throughout the day. Attendees are expected to attend all talks and tutorials. This course will cover the basics of using FreeSurfer, including how to process subjects through the FreeSurfer pipeline, how to inspect processed data for accuracy, how to intervene if results are inaccurate, and how to conduct various analyses including group analysis, ROI analysis, and longitudinal analysis. Lectures & virtual meetings will be hosted on gather.town while tutorials will be accessible via Virtual Machine (VM). A tentative schedule is below.
Prior to the course, attendees will be provided with instructions on how to download & install the VM software package and course data necessary to participate in the course. These downloads require 70GB of free storage space on your computer or an external hard drive. The computer also needs to have a minimum of 16GB of RAM (total) to function properly while working with the course data during tutorials. There are additional technical requirements listed here which must be checked prior to registering for the course.
Time Title Type Lecturer 3:30-4:00pm demo Liam Sennott & FS staff 4:00 - 4:30 talk/demo Jackson Nolan 4:30 - 4:50 talk Allison McKenzie ** optional talks
Time Title Type Lecturer 9:15 - 9:30 Welcome social staff 9:30 - 10:15 talk Doug Greve 10:15 - 11:25 talk Doug Greve 11:25 - 11:45 20 minute break 11:45 - 12:05 demo Nathan Draudt 12:05 - 12:50 tutorial staff 12:50 - 1:50 Lunch 1:50 - 2:35 talk Doug Greve 2:35 - 3:45 tutorial staff 3:45 - 4:05 20 minute break 4:05 - 4:50 Quality Checking a Recon talk Nathan Draudt 4:50 - 5:20 Practice Working with Data or finish other tutorials tutorial staff
Time Title Type Lecturer 9:00 - 9:45 talk Martin Reuter 9:45 - 10:30 tutorial staff 10:30 - 10:50 20 minute break 10:50 - 11:30 talk Malte Hoffmann 11:30 - 12:10 tutorial staff 12:10 - 12:40 talk Divya Varadarajan 12:40 - 1:40 Lunch 1:40 - 2:25 talk Doug Greve 2:25 - 3:05 tutorial staff 3:05 - 3:25 20 minute break 3:25 - 4:10 talk Doug Greve 4:10 - 4:40 tutorial staff 4:40 - 5:00 Q&A with FreeSurfer Team talk Doug Greve & FS Team
Using a Mac & need a text editor? Download gedit, here. Some basic information on text editors can be found here. The tutorials often refer to keyboard shortcuts (such as Alt+v) which do not work on a Mac. For a list of equivalent keyboard commands on a Mac, please refer to MacCommands.
A full list of all FreeSurfer tutorials, including ones that may not have been included at this course How to cite FreeSurfer is on the FreeSurferMethodsCitation page.
The fee for the course is $475. A reduced rate of $325 is available to undergraduate and graduate students. MDs, PhDs, RAs and Post-docs do not qualify for the student rate!
Accepted Payment types: credit card, MGB internal fund, cash (contact the course organizers to arrange how to pay with cash) Payment Coordinator/Contact: Stacey Ladieu (sladieu at mgh dot harvard dot edu)
Course fees are refundable, minus a $200 fee, up to 1 week 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. If you do not cancel your registration by May 26th, you will not be issued a refund. Partial Refund Cancellation deadline:
How many individuals are accepted into the Virtual course? Do postdocs qualify for the student rate? Is there a discount for MGH or Martinos Center employees? I cannot pay by internal fund or credit card. Do I have any other options? The course is full. Can you register me for the next one? Can I get a receipt for the course? How do I know if my payment went through? I have some data I would like to get your opinion on. Can I show it to you? I need some help installing FreeSurfer on my laptop - I can't seem to get it to work. Can you help with that?
Linux Demo/Tutorial (optional) Introduction to FreeSurfer Jargon (optional) Introduction to FreeSurfer Analyzing the Individual Subject in FreeSurfer Freeview demonstration Interaction with Individual Subject Output - Tutorial Region of Interest (ROI) Analysis - Talk and Tutorial FreeSurfer Troubleshooting - Talk and Tutorial Quality Checking a Recon Surface-based Analysis: Intersubject Registration & Smoothing Group Analysis/GLM/Multiple Comparisons (mri_glmfit)- Talk and Tutorial Longitudinal Analysis in FreeSurfer Question and Answer Session
Course Details
Click on any of the topics below for more information:
Overview
Technical Requirements
Schedule
Payment
FAQ
Topics Covered During the Course
Overview
Technical Requirements
Schedule
WARNING: The hyperlinks in the tables below used to download slides will NOT WORK in Google Chrome. Please use a different browser to access these slides. All times listed are Eastern Daylight Time (EDT)
Tuesday, June 2nd - Gathertown Social & Instructions
Wednesday, June 3rd - Introduction / Single Subject Analysis / Troubleshooting
Friday, June 5th - ROI Analysis / Group Analysis / Longitudinal Analysis
Additional Useful Information
During the Course
After the Course
Payment
Cost
Accepted Payment Types
As long as there are empty spots in the course, we will accept late registrations (regardless of the cancellation deadline).
Payment and all questions about payment should be sent to Stacey. Cancellations, Refunds, and Deadlines
FAQ
40 people
No, sorry.
Sorry, no.
If you are local, you may bring a cash payment to Allison Stevens (allison.stevensplayer at mgh dot harvard dot edu) before the deadline. If you are not local, you may be able to pay via Western Union and Moneygram if it is addressed to Stacey Ladieu. Please contact Stacey (sladieu at mgh dot harvard dot edu) first for details.
You can sign up for the Freesurfer mailing list and follow our BlueSky Page and Twitter Page to see announcements of when registration for the next course opens. 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.
Contact the payment coordinator, Stacey (sladieu at mgh dot harvard dot edu) to arrange getting a receipt.
If it hasn't we will contact 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 the course organizers (fscourse AT mgb.org) prior to the course, they can try to arrange a time to discuss your data.
Sure! Please email the course organizers (fscourse AT mgb.org) for assistance. 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.
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.
Intended for those new to imaging software. Explains basic vocabulary such as voxel, surface, vertex, volume, segmentation, parcellation, registration, and recon.
Overview of FreeSurfer's abilities.
Description of each step of the FreeSurfer processing stream.
A live walk-through for how to use the Freeview GUI.
Using FreeSurfer's visualization tools to look at FreeSurfer output.
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).
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.
Volume vs. Surface-based analysis
Covers the basics of group analysis in the context of imaging data.
How to process longitudinal data with FreeSurfer and what's going on behind the scenes.
Open forum to resolve any unanswered questions Future Courses
We will announce future courses via our Freesurfer mailing list, our BlueSky Page, and our Twitter Page.