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 still being scheduled. The official date will be confirmed in late Spring. Stay tuned for more updates. The course date will be announced on our Freesurfer mailing list and our Twitter Page. The dates written below reflect those from last year's course. 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 Computer verification deadline: 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 64GB 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. The VM may not work on all computers (including the newer Mac laptops). You will be required to verify your computer can properly host the course software by the deadline (
Time Title Type Lecturer 3:30-4:00pm Social Gathering & Gathertown Demo demo Doug Greve & FS staff 4:00 - 4:30 talk/demo Karthik Gopinath 4:30 - 4:50 talk Karthik Gopinath ** optional talks
Time Title Type Lecturer 9:00 - 9:10 Welcome social staff 9:10 - 9:55 talk Bruce Fischl 9:55 - 11:05 talk Doug Greve 11:05 - 11:25 20 minute break 11:25 - 11:45 demo Nathan Draudt 11:45 - 12:30 tutorial staff 12:30 - 1:30 Lunch 1:30 - 2:15 talk Doug Greve 2:15 - 3:25 tutorial staff 3:25 - 3:45 20 minute break 3:45 - 4:30 Quality Checking a Recon talk Nathan Draudt 4:30 - 5:00 Practice Working with Data or finish other tutorials tutorial staff
Time Title Type Lecturer 9:00 - 9:30 talk Malte Hoffmann 9:30 - 10:15 tutorial staff 10:15 - 10:45 talk Divya Varadarajan 10:45 - 11:05 20 minute break 11:05 - 11:50 talk Martin Reuter 11:50 - 12:35 tutorial staff 12:35 - 1:35 Lunch 1:35 - 2:20 talk Doug Greve 2:20 - 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 Bruce Fischl, 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 $425. A reduced rate of $275 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 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. If you do not cancel your registration by April 16th, you will not be issued a refund. If you do not show your computer is unable to run the software by April 3rd, you will not be issued a refund. Partial Refund Cancellation deadline:
You can sign up for the Freesurfer mailing list and follow our 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.
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. 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. How to process longitudinal data with FreeSurfer and what's going on behind the scenes.
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)
Monday, April 29th - Gathertown Social & Instructions
Tuesday, April 30th - Introduction / Single Subject Analysis / Troubleshooting
Wednesday, May 1st - 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
Computer verification deadline: April 3rd, 2024 FAQ
How many individuals are accepted into the Virtual course?
The course is full. Can you register me for the next one? 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.
Region of Interest (ROI) Analysis - Talk and Tutorial
Longitudinal Analysis in FreeSurfer Future Courses
We will announce future courses via our Freesurfer mailing list and our Twitter Page.