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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	** Intro to FreeSurfer Jargon	talk	Allison, and Lillia or Caroline if they want?
9:15 - 10:00	Introduction to Freesurfer	talk	Doug or Bruce Fischl
10:00 - 10:15	break
10:15 - 11:25	Analyzing the Individual Subject	talk	Doug Greve
11:25 - 11:45	Freeview demonstration	demo	Jackson
11:45 - 12:00	break
12:00 - 12:45	Individual Subject Output	tutorial	Allison, RA#2 RA#3
12:45 - 1:45	Lunch
1:45 - 2:15	ROI Analysis	talk	Doug Greve
2:15 - 3:00	ROI Analysis Tutorial	tutorial	RA#1 RA#2 RA#3
3:00 - 3:15	break
3:15 - 4:00	FreeSurfer Troubleshooting	talk	Allison? Bruce?
4:00 - 5:00	Troubleshooting Freesurfer	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	Group Analysis	talk	Doug
11:15 - 11:30	break
11:30 - 12:10	Group Analysis Tutorial (FSGD Examples)	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	Longitudinal FreeSurfer	talk	Malte? Doug?
4:15 - 4:55	LongitudinalTutorial	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

SUBSCRIBE:
If you are interested in being notified about future course offerings, sign up for our mailing list (here).

UNSUBSCRIBE:
To unsubscribe from the course mailing list please click here.

-Deletions are marked like this.
+Additions are marked like this.
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-'''Registration is now open for the Fall 2022 Virtual FreeSurfer Course!''' [[https://education.martinos.org/freesurfer-tutorial-workshop/|Click here to register!]] <<BR>> 

##'''Registration is now FULL for the Fall 2022 Virtual  FreeSurfer Course!''' But, you can still register for the waitlist [[https://forms.gle/ViDGSMrGEbR8XwgX9|here]] for a good chance at getting into the course.  <<BR>>
+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 [[http://surfer.nmr.mgh.harvard.edu/fswiki/CourseDescription#Schedule|schedule]] to make sure it will work for you and review the [[https://surfer.nmr.mgh.harvard.edu/fswiki/CourseDescription/Remote_Qualify|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.
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-The virtual !FreeSurfer course is scheduled for '''September 14-15th, 2022'''. This is a two day course that offers a basic introduction to !FreeSurfer. Before registering, review the tentative schedule to make sure it will work for you and review the [[https://surfer.nmr.mgh.harvard.edu/fswiki/CourseDescription/Remote_Qualify|technical requirements]] to be sure your computer can run the course software.
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-##'''If our upcoming course is full, you may still register to be added to the wait-list!''' [[https://surfer.nmr.mgh.harvard.edu/cgi-bin/fsurfer/register.1224.cgi|Click here to register!]] <<BR>>
+'''Registration is now open for the Fall 2022 Virtual FreeSurfer Course!''' [[https://education.martinos.org/freesurfer-tutorial-workshop/|Click here to register!]] <<BR>> 

##'''Registration is now FULL for the Fall 2022 Virtual  FreeSurfer Course!''' You may still register to be added to the wait-list!''' [[https://education.martinos.org/freesurfer-tutorial-workshop/|Click here to register!]] <<BR>>
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-----

== Course Mailing List ==

'''SUBSCRIBE''':<<BR>> If you are interested in being notified about future course offerings, sign up for our mailing list ([[http://surfer.nmr.mgh.harvard.edu/cgi-bin/fsurfer/interest.cgi|here]]). <<BR>>



'''UNSUBSCRIBE''':<<BR>> To unsubscribe from the course mailing list please click [[https://surfer.nmr.mgh.harvard.edu/cgi-bin/fsurfer/unsubscribe.cgi|here]].
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-[[http://surfer.nmr.mgh.harvard.edu/fswiki/CourseDescription#Schedule|Schedule]] <<BR>> [[http://surfer.nmr.mgh.harvard.edu/fswiki/CourseDescription#Payment|Payment]] <<BR>> [[http://surfer.nmr.mgh.harvard.edu/fswiki/CourseDescription#FAQ|FAQ]] <<BR>> [[http://surfer.nmr.mgh.harvard.edu/fswiki/CourseDescription#CourseTopics|Topics Covered During the Course]]  <<BR>> [[http://surfer.nmr.mgh.harvard.edu/fswiki/CourseDescription#LecturersandStaff|Lecturers and Staff]] <<BR>> '''
+[[http://surfer.nmr.mgh.harvard.edu/fswiki/CourseDescription#Schedule|Schedule]] <<BR>> [[http://surfer.nmr.mgh.harvard.edu/fswiki/CourseDescription#Payment|Payment]] <<BR>> [[http://surfer.nmr.mgh.harvard.edu/fswiki/CourseDescription#FAQ|FAQ]] <<BR>> [[http://surfer.nmr.mgh.harvard.edu/fswiki/CourseDescription#CourseTopics|Topics Covered During the Course]]  <<BR>> '''
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-The two day course consists of talks and tutorials that run throughout the day. Attendees are expected to attend all talks and tutorials.  A VM package has been prepared to give attendees access to the tutorial data.
+The two day course consists of talks and tutorials that run throughout the day. Attendees are expected to attend all talks and tutorials.
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-==== Monday, September 12th - Introduction / Single Subject Analysis / ROI Analysis  ====
+==== Wednesday, September 14th - Introduction / Single Subject Analysis / ROI Analysis / Troubleshooting  ====
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-==== Tuesday, September 13th - Group Analysis / Longitudinal Analysis / Troubleshooting ====
+==== Thursday, September 15th - Group Analysis / Longitudinal Analysis  ====
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-==== Deadlines & Accepted Payment Types ====
+==== Accepted Payment Types ====
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-Payment deadline: '''September 6, 2022''' <br>

'''Note:''' If you register after the payment deadline has passed, payment is due immediately.
+Accepted Payment types: credit card, MGB internal fund, cash (contact the course organizers to arrange how to pay with cash)
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-Accepted Payment types: credit card, cash, or institutional check (see sections below for details on each)
+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.
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-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. 

##Please cc the course organizers (freesurferlab@gmail.com) on your emails with Stacey so we can update your payment status accordingly.  <<BR>>
+==== Cancellations, Refunds, and Deadlines ====

Cancellation deadline: '''August 31st, 2022''' <br>

Computer verification deadline: '''September 7th, 2022'''
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-==== Credit Cards ====

Please use the website below to make a payment via credit card.
+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.
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-Choose the box with the payment fee that applies to you:

2022 Virtual FreeSurfer Course

OR

2022 Virtual FreeSurfer Course STUDENT FEE
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-Select the correct quantity of registrations and 'Add to cart'. Select 'View Cart' and then 'Proceed to Checkout'. Enter your billing address and click continue, then enter your credit card details. Please contact Stacey (sladieu@mgh.harvard.edu) and CC the course organizer's email (freesurferlab@gmail.com) if there are any issues.  <<BR>>
+==== 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.
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-[[http://payment.martinos.org/|Click here to pay by Credit Card]]



==== Checks ====

For those sending an institutional check, we understand these can take some time to produce. Please have your financial institution contact our payment coordinator, Stacey Ladieu, to confirm a check is being issued prior to the payment deadline. 



Make checks payable to: Massachusetts General Hospital



Mail checks to this address:<<BR>> Stacey Ladieu<<BR>> Athinoula A. Martinos Center for Biomedical Imaging<<BR>> 149 Thirteenth Street - Room 2301<<BR>> Charlestown, MA 02129<<BR>>



Please be sure the '''name of the person taking the course''' is listed on the check.



==== Cash ====

There are two options for paying by cash:



 1. Make an appointment with Allison Stevens (astevens at martinos dot org) to deliver cash in person

 1. Contact Stacey (sladieu at martinos dot org) to send cash via Western Union or Moneygram. The transfer must be made out to Stacey Ladieu.



==== 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 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.
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-==== Lecturers and Staff ====

 * Bruce Fischl

 * Doug Greve

 * Andre van der Kouwe

 * Allison Stevens

 * Anastasia Yendiki

 * Caroline Magnain

 * Lilla Zollei

 * David Salat

 * Iman Aganj

 * Paul Wighton

 * Robert Frost

 * Leah Morgan

 * Andrew Hoopes

 * Matthew Vera

 * Devani Cordero 

 * Jonathan Polimeni

 * Malte Hoffmann
+----

== Course Mailing List ==

'''SUBSCRIBE''':<<BR>> If you are interested in being notified about future course offerings, sign up for our mailing list ([[http://surfer.nmr.mgh.harvard.edu/cgi-bin/fsurfer/interest.cgi|here]]). <<BR>>



'''UNSUBSCRIBE''':<<BR>> To unsubscribe from the course mailing list please click [[https://surfer.nmr.mgh.harvard.edu/cgi-bin/fsurfer/unsubscribe.cgi|here]].