Virtual FreeSurfer Course
The virtual FreeSurfer course is scheduled for September 14-15th, 2022. 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 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 Sept 7th 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 open for the Fall 2022 Virtual FreeSurfer Course! Click here to register!
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, Allison Stevens or Liam Sennott (freesurferlab@gmail.com).
Course Details
Click on any of the topics below for more information:
Overview
Schedule
Payment
FAQ
Topics Covered During the Course
Overview
The two day course consists of talks and tutorials that run throughout the day. Attendees are expected to attend all talks and tutorials.
Schedule
Wednesday, September 14th - Introduction / Single Subject Analysis / ROI Analysis / Troubleshooting
Time |
Title |
Type |
Lecturer |
8:30 - 9:00 |
** Intro to Linux for FreeSurfer Users |
talk/demo |
Dev |
9:00 - 9:15 |
talk |
Allison, and Lillia or Caroline if they want? |
|
9:15 - 10:00 |
talk |
Doug or Bruce Fischl |
|
10:00 - 10:15 |
break |
|
|
10:15 - 11:25 |
talk |
Doug Greve |
|
11:25 - 11:45 |
Jackson |
||
11:45 - 12:00 |
break |
|
|
12:00 - 12:45 |
tutorial |
Allison, RA#2 RA#3 |
|
12:45 - 1:45 |
Lunch |
||
1:45 - 2:15 |
talk |
Doug Greve |
|
2:15 - 3:00 |
tutorial |
RA#1 RA#2 RA#3 |
|
3:00 - 3:15 |
break |
|
|
3:15 - 4:00 |
talk |
Allison? Bruce? |
|
4:00 - 5:00 |
tutorial |
Dev, Allison, RA#3 |
|
5:00 - 5:45 |
QA Demo |
talk |
Allison? Leah? |
Thursday, September 15th - Group Analysis / Longitudinal Analysis
Time |
Title |
Type |
Lecturer |
10:00 - 10:30 |
Surface Based Analysis |
talk |
Divya / Doug |
10:30 - 11:15 |
talk |
Doug |
|
11:15 - 11:30 |
break |
|
|
11:30 - 12:10 |
tutorial |
RA#1 RA#2 RA#3 |
|
12:10 - 1:10 |
Lunch |
||
1:10 - 1:55 |
Corrections for MC |
talk |
Doug |
1:55 - 2:25 |
Tutorial: Corrections |
tutorial |
RA#1 RA#2 RA#3 |
2:25 - 3:40 |
break |
|
|
3:40 - 4:15 |
talk |
Malte? Doug? |
|
4:15 - 4:55 |
tutorial |
Dev, RA#2 RA#3 |
|
4:55 - 5:15 |
Q&A with FreeSurfer Team |
talk |
Doug? Bruce? |
Payment
Cost
The fee for the course is $400. 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
Payment Coordinator/Contact: Stacey Ladieu (sladieu at martinos dot org)
Accepted Payment types: credit card, MGB internal fund, cash (contact the course organizers to arrange how to pay with cash)
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
Cancellation deadline: August 31st, 2022 <br> Computer verification deadline: September 7th, 2022
Course fees are refundable, minus a $100 fee, up to 2 weeks prior to the program. If you verify your computer is unable to host the course software & data by September 7th, you will be issued a full refund. If you do not cancel your registration by August 31st or do not show your computer is unable to run the software by September 7th, you will not be issued a refund.
Cancellations
Course fees are refundable up to the cancellation deadline. A $100 fee will be deducted, should you request a refund up to 2 weeks prior to the program. Course fees are refundable minus a $100 fee up to 2 weeks prior to the program. If you verify your computer is unable to host the course software & data by September 7th, you will be issued a full refund.
FAQ's
How many individuals are accepted into the Virtual course?
- 20 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?
- Contact the payment coordinator, Stacey (sladieu at nmr dot mgh dot harvard dot edu) to arrange getting a receipt.
How do I know if my payment went through?
- If it hasn't we will contact you.
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.
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)
Question and Answer Session
- Open forum to resolve any unanswered questions
Course Mailing List
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