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The virtual !FreeSurfer course is scheduled for '''April 29th, 30th & May 1st, 2024'''. 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 [[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 '''April 1st''' 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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##'''Registration is now open for the Fall 2022 Virtual FreeSurfer Course!''' [[https://forms.gle/uGGk2EaaZFgtWicF9|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>>		 Registration is not yet open. This page will be updated once registration has opened.
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The next virtual !FreeSurfer course is scheduled for '''September 14-15th, 2022'''. The payment deadline is '''September 6, 2022'''. ##'''Registration is now open for the April/May 2024 Virtual !FreeSurfer Course!''' [[https://education.martinos.org/freesurfer-tutorial-workshop/|Click here to register!]] <<BR>>
##'''Registration is now FULL for the April/May 2024 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>>
Computer verification deadline: '''April 1st, 2024'''
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Registration is not yet open. This page will be updated once registration has opened.

##'''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>>
This is a two day course that offers a basic introduction to FreeSurfer. Review the tentative schedule below before registering.


== General Information ==
Additional details about the Virtual Course can be found [[http://surfer.nmr.mgh.harvard.edu/fswiki/CourseDescription#CourseDetails|below]].

If you have a specific question about the !FreeSurfer courses that was not answered by our [[http://surfer.nmr.mgh.harvard.edu/fswiki/CourseDescription#FAQ|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 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]].		 If you have a specific question about the !FreeSurfer courses that was not answered by this website and our [[http://surfer.nmr.mgh.harvard.edu/fswiki/CourseDescription#FAQ|FAQ]] or would like to host a course in your area, you can email one of the course organizers (fscourse AT nmr.mgh.harvard.edu).
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'''Click on any of the topics below for more information: <<BR>> [[http://surfer.nmr.mgh.harvard.edu/fswiki/CourseDescription#Overview|Overview]] <<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>> [[http://surfer.nmr.mgh.harvard.edu/fswiki/CourseDescription#LecturersandStaff|Lecturers and Staff]] <<BR>> '''		 '''Click on any of the topics below for more information: <<BR>>  [[http://surfer.nmr.mgh.harvard.edu/fswiki/VirtualCourse#Overview|Overview]] <<BR>>  [[http://surfer.nmr.mgh.harvard.edu/fswiki/VirtualCourse#TechnicalRequirements|Technical Requirements]] <<BR>> [[http://surfer.nmr.mgh.harvard.edu/fswiki/VirtualCourse#Schedule|Schedule]] <<BR>> [[http://surfer.nmr.mgh.harvard.edu/fswiki/VirtualCourse#Payment|Payment]] <<BR>>  [[http://surfer.nmr.mgh.harvard.edu/fswiki/VirtualCourse#FAQ|FAQ]] <<BR>>  [[http://surfer.nmr.mgh.harvard.edu/fswiki/VirtualCourse#CourseTopics|Topics Covered During the Course]] <<BR>> '''
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##[[https://surfer.nmr.mgh.harvard.edu/cgi-bin/fsurfer/questions.cgi|Submit Questions Online]]
##[[https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/QuestionAnswers|Answers to Submitted Questions]]
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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.

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 [[https://www.gather.town/|gather.town]] while tutorials will be accessible via Virtual Machine (VM). A tentative schedule is below.

=== Technical Requirements ===
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 [[https://surfer.nmr.mgh.harvard.edu/fswiki/CourseDescription/Remote_Qualify|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 ('''April 1st, 2024''') 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. See the payment section below for more details on cancellations and refunds. A strong internet connection is a must for the best workshop experience.
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==== Monday, September 12th - Introduction / Single Subject Analysis / ROI Analysis ==== '''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.

== Exact times and speakers are TBD ==
==== Monday, April 29th - Gathertown Social & Instructions ====
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||8:30 - 8:40 ||** Intro to Linux for !FreeSurfer Users ||talk/demo || ||
||8:40 - 9:00 ||** [[https://surfer.nmr.mgh.harvard.edu/fswiki/UnixTutorial|Unix for FreeSurfer Users]] ||tutorial || ||
||9:00 - 9:15 ||** [[http://surfer.nmr.mgh.harvard.edu/pub/docs/fsjargon_clean.pptx|Intro to FreeSurfer Jargon]] || talk || ||
||9:15 - 9:25 ||'''break''' || || ||
||9:25 - 10:10 ||[[attachment:freesurfer.intro.apr.2019.ppt|Introduction to Freesurfer]] ||talk ||Bruce Fischl ||
||10:10 - 11:20 ||[[http://surfer.nmr.mgh.harvard.edu/pub/docs/fsrecon.pptx|Analyzing the Individual Subject]] ||talk ||Doug Greve ||
||11:20 - 11:40 ||'''break''' || || ||
||11:40 - 12:00 ||[[https://www.youtube.com/watch?v=Mv-ECowxq2o|Freeview demonstration]] ||[[FsTutorial/FreeviewDemo|demo]] || ||
||12:00 - 12:30 ||[[FsTutorial/OutputData_freeview|Introduction to FreeSurfer Output]] ||tutorial ||staff ||
||12:30 - 1:30 ||'''Lunch''' ||||||
||1:30 - 1:45 ||[[FsTutorial/OutputData_freeview|Introduction to FreeSurfer Output]] ||tutorial ||staff ||
||1:45 - 2:15 ||[[http://surfer.nmr.mgh.harvard.edu/pub/docs/fs.surface-based-analysis.ppt |Surface-based Analysis: Intersubject Registration & Smoothing ]] ||talk || Diyva Varadarajan ||
||2:15 - 2:35 ||'''break''' || || ||
||2:35 - 3:05 ||[[http://surfer.nmr.mgh.harvard.edu/pub/docs/fs.roi.EB_wiki.pptx|ROI Analysis]] ||talk || Doug Greve ||
||3:05 - 3:50 ||[[FsTutorial/AnatomicalROIV6.0|ROI Analysis Tutorial]] ||tutorial ||staff ||
||4:20 - 4:50 ||[[FsTutorial/Practice|Practice Working with Data]] ||tutorial ||staff ||		 ||3:30-4:00pm ||Social Gathering & Gathertown Demo ||demo ||Doug Greve & FS staff ||
||4:00 - 4:30 ||** [[attachment:Linux_slides_final.pptx|Intro to Linux for FreeSurfer Users]] ||talk/demo ||Jackson Nolan ||
||4:30 - 4:50 ||** [[http://surfer.nmr.mgh.harvard.edu/pub/docs/fsjargon.pptx|Intro to FreeSurfer Jargon]] ||talk ||Allison Player ||
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==== Tuesday, September 13th - Group Analysis / Longitudinal Analysis / Troubleshooting ====
** optional talks

==== Tuesday, April 30th - Introduction / Single Subject Analysis / Troubleshooting ====
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||8:00 - 9:00 ||*** Morning Help Session|| || research technicians ||
||9:00 - 9:45 ||[[http://surfer.nmr.mgh.harvard.edu/pub/docs/GLM.pptx|Group Analysis]] ||talk || ||
||9:45 - 10:25 ||[[FsTutorial/GroupAnalysisV6.0|Group Analysis Tutorial]] ([[FsgdExamples|FSGD Examples]]) ||tutorial ||staff ||
||10:25 - 10:45 ||'''break''' || || ||
||10:45 - 11:30 ||[[http://surfer.nmr.mgh.harvard.edu/pub/docs/freesurfer.troubleshooting.apr2019.ppt|FreeSurfer Troubleshooting]] ||talk || ||
||11:30 - 12:30 ||[[FsTutorial/TroubleshootingDataV6.0|Troubleshooting Tutorial]] ||tutorial ||staff ||
||12:30 - 1:30 ||'''Lunch''' || || ||
||1:30 - 2:15 ||[[https://youtu.be/AR83_Bt04VQ|Quality Checking a Recon]] || [[https://zoom.us/wc/join/369478461?pwd=|talk]] || ||
||2:15 - 2:55 ||[[http://surfer.nmr.mgh.harvard.edu/pub/docs/multiplecomparisons.ppt|Multiple Comparisons]] ||talk ||Doug Greve||
||2:55 - 3:25 ||[[FsTutorial/MultipleComparisonsV6.0Perm|Multiple Comparisons Tutorial]] ||tutorial ||staff ||
||3:25 - 4:05 ||'''break''' || || ||
||4:05 - 4:50 ||[[http://surfer.nmr.mgh.harvard.edu/pub/docs/fs.longitudinal.pptx|Longitudinal FreeSurfer]] ||talk ||Malte Hoffmann ||
||4:50 - 5:30 || [[FsTutorial/LongitudinalTutorial|LongitudinalTutorial]] ||tutorial ||staff ||
##||5:30 - 6:15 ||*** Optional time to work on tutorials / work on your own data / ask basic questions ||-- || staff||		 ||9:00 - 9:10 ||'''Welcome''' ||social ||staff ||
||9:10 - 9:55 ||[[attachment:freesurfer.intro.june.2023.pptx|Introduction to Freesurfer]] ||talk ||Bruce Fischl ||
||9:55 - 11:05 ||[[attachment:fsrecon.sep2022.pptx|Analyzing the Individual Subject]] ||talk ||Doug Greve ||
||11:05 - 11:25 ||'''20 minute break''' || || ||
||11:25 - 11:45 ||Freeview demonstration ||[[FsTutorial/FreeviewDemo|demo]] ||Nathan Draudt ||
||11:45 - 12:30 ||[[FsTutorial/OutputData_freeview|Tutorial: Individual Subject Output]] ||tutorial ||staff ||
||12:30 - 1:30 ||'''Lunch''' ||||<style="text-align:center"> ||
||1:30 - 2:15 ||[[attachment:freesurfer.troubleshooting.sep2022.ppt|FreeSurfer Troubleshooting]] ||talk ||Doug Greve ||
||2:15 - 3:25 ||[[FsTutorial/TroubleshootingDataV6.0|Tutorial: Troubleshooting Freesurfer]] ||tutorial ||staff ||
||3:25 - 3:45 ||'''20 minute break''' || || ||
||3:45 - 4:30 ||Quality Checking a Recon ||talk ||Nathan Draudt ||
||4:30 - 5:00 ||[[FsTutorial/Practice|Practice Working with Data]] or finish other tutorials ||tutorial ||staff ||
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==== Wednesday, May 1st - ROI Analysis / Group Analysis / Longitudinal Analysis ====
||'''Time''' ||'''Title''' ||'''Type''' ||'''Lecturer''' ||
||9:00 - 9:30 ||[[http://surfer.nmr.mgh.harvard.edu/pub/docs/fs.roi.EB_wiki.pptx|ROI Analysis]] ||talk ||Malte Hoffmann ||
||9:30 - 10:15 ||[[FsTutorial/AnatomicalROIV6.0|Tutorial: ROI Analysis]] ||tutorial ||staff ||
||10:15 - 10:45 ||[[attachment:fs.surface-based-analysis.ppt|Surface Based Analysis]] ||talk ||Divya Varadarajan ||
||10:45 - 11:05 ||'''20 minute break''' || || ||
||11:05 - 11:50 ||[[http://surfer.nmr.mgh.harvard.edu/pub/docs/fs.longitudinal.pptx|Longitudinal FreeSurfer]] ||talk ||Martin Reuter ||
||11:50 - 12:35 ||[[FsTutorial/LongitudinalTutorial|Tutorial: LongitudinalTutorial]] ||tutorial ||staff ||
||12:35 - 1:35 ||'''Lunch''' ||||<style="text-align:center"> ||
||1:35 - 2:20 ||[[attachment:GLM.pptx|Group Analysis]] ||talk ||Doug Greve ||
||2:20 - 3:05 ||[[FsTutorial/GroupAnalysisV6.0|Tutorial: Group Analysis]] ([[FsgdExamples|FSGD Examples]]) ||tutorial ||staff ||
||3:05 - 3:25 ||'''20 minute break''' || || ||
||3:25 - 4:10 ||[[http://surfer.nmr.mgh.harvard.edu/pub/docs/multiplecomparisons.ppt|Corrections for Multiple Comparisons]] ||talk ||Doug Greve ||
||4:10 - 4:40 ||[[https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/MultipleComparisonsV6.0Perm|Tutorial: Corrections for Multiple Comparisons]] ||tutorial ||staff ||
||4:40 - 5:00 ||Q&A with !FreeSurfer Team ||talk ||Bruce Fischl, Doug Greve, & FS Team ||


=== Additional Useful Information ===
==== During the Course ====
 * Using a Mac & need a text editor? Download gedit, [[http://ftp.gnome.org/pub/GNOME/binaries/mac/gedit/3.2/gedit-3.2.6-3_SnowLeopard_64bit.dmg|here]].
 * Some basic information on text editors can be found [[FsTutorial/CreatingTextfiles|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.
 * [[FsTutorial/Scripts|Scripts & aliases]]
 * [[FsTutorial/Glossary|Glossary]]

==== After the Course ====
 * A full list of all [[Tutorials|FreeSurfer tutorials]], including ones that may not have been included at this course
 * [[https://www.zotero.org/freesurfer|Publications]]
 * How to cite !FreeSurfer is on the FreeSurferMethodsCitation page.
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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!'' 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!''
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==== Accepted Payment Types ====
Accepted Payment types: credit card, MGB internal fund, cash (contact the course organizers to arrange how to pay with cash)<<BR>> As long as there are empty spots in the course, we will accept late registrations (regardless of the cancellation deadline). <<BR>> Payment and all questions about payment should be sent to Stacey.
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==== Deadlines & 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.		 ==== Cancellations, Refunds, and Deadlines ====
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 1st, you will not be issued a refund.
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Accepted Payment types: credit card, cash, or institutional check (see sections below for details on each) Partial Refund Cancellation deadline: '''April 16th, 2024''' <<BR>> Computer verification deadline: '''April 1st, 2024'''
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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>>

==== Credit Cards ====
Please use the website below to make a payment via credit card.

Choose the box with the payment fee that applies to you:
2022 Virtual FreeSurfer Course
OR
2022 Virtual FreeSurfer Course STUDENT FEE

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>>

[[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.
##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.

==== FAQ's ====		 === FAQ ===
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  * 20 people   * 40 people
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 1. '''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.
 1. '''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.		  1. '''I cannot pay by internal fund 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 may be able to 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.

## 1. '''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.
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  * 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.   * 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 nmr.mgh.harvard.edu) prior to the course, they can try to arrange a time to discuss your data.
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  * Sure! Please see the response to the question above.   * Sure! Please email the course organizers (fscourse AT nmr.mgh.harvard.edu) for assistance.
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==== Course Topics ====		 === Course Topics ===
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 * '''Interaction with Individual Subject Data - Tutorial'''  * '''Freeview demonstration'''
  * A live walk-through for how to use the Freeview GUI.
 * '''Interaction with Individual Subject Output - Tutorial'''
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 * '''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.
## * '''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.
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 * '''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'''		 ## * '''Structural and Functional Integration'''
## * An explanation of why structural information is critical for functional imaging research.
 * '''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).
 * '''!FreeSurfer Troubleshooting - Talk and Tutorial'''
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 * '''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).
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 * '''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)
## * '''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)
 * '''Longitudinal Analysis in !FreeSurfer'''
  * How to process longitudinal data with !FreeSurfer and what's going on behind the scenes.
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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]].

Virtual FreeSurfer Course

The virtual FreeSurfer course is scheduled for April 29th, 30th & May 1st, 2024. 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 April 1st 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 not yet open. This page will be updated once registration has opened.

Computer verification deadline: April 1st, 2024

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 nmr.mgh.harvard.edu).

Course Details

Click on any of the topics below for more information:
Overview
Technical Requirements
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.

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.

Technical Requirements

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 (April 1st, 2024) 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. See the payment section below for more details on cancellations and refunds. A strong internet connection is a must for the best workshop experience.

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.

Exact times and speakers are TBD

Monday, April 29th - Gathertown Social & Instructions

Time

Title

Type

Lecturer

3:30-4:00pm

Social Gathering & Gathertown Demo

demo

Doug Greve & FS staff

4:00 - 4:30

** Intro to Linux for FreeSurfer Users

talk/demo

Jackson Nolan

4:30 - 4:50

** Intro to FreeSurfer Jargon

talk

Allison Player

** optional talks

Tuesday, April 30th - Introduction / Single Subject Analysis / Troubleshooting

Time

Title

Type

Lecturer

9:00 - 9:10

Welcome

social

staff

9:10 - 9:55

Introduction to Freesurfer

talk

Bruce Fischl

9:55 - 11:05

Analyzing the Individual Subject

talk

Doug Greve

11:05 - 11:25

20 minute break

11:25 - 11:45

Freeview demonstration

demo

Nathan Draudt

11:45 - 12:30

Tutorial: Individual Subject Output

tutorial

staff

12:30 - 1:30

Lunch

1:30 - 2:15

FreeSurfer Troubleshooting

talk

Doug Greve

2:15 - 3:25

Tutorial: Troubleshooting Freesurfer

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

Wednesday, May 1st - ROI Analysis / Group Analysis / Longitudinal Analysis

Time

Title

Type

Lecturer

9:00 - 9:30

ROI Analysis

talk

Malte Hoffmann

9:30 - 10:15

Tutorial: ROI Analysis

tutorial

staff

10:15 - 10:45

Surface Based Analysis

talk

Divya Varadarajan

10:45 - 11:05

20 minute break

11:05 - 11:50

Longitudinal FreeSurfer

talk

Martin Reuter

11:50 - 12:35

Tutorial: LongitudinalTutorial

tutorial

staff

12:35 - 1:35

Lunch

1:35 - 2:20

Group Analysis

talk

Doug Greve

2:20 - 3:05

Tutorial: Group Analysis (FSGD Examples)

tutorial

staff

3:05 - 3:25

20 minute break

3:25 - 4:10

Corrections for Multiple Comparisons

talk

Doug Greve

4:10 - 4:40

Tutorial: Corrections for Multiple Comparisons

tutorial

staff

4:40 - 5:00

Q&A with FreeSurfer Team

talk

Bruce Fischl, Doug Greve, & FS Team

Additional Useful Information

During the Course

  • 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.

  • Scripts & aliases

  • Glossary

After the Course

Payment

Cost

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

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.

Payment Coordinator/Contact: Stacey Ladieu (sladieu at martinos dot org)

Cancellations, Refunds, and Deadlines

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 1st, you will not be issued a refund.

Partial Refund Cancellation deadline: April 16th, 2024
Computer verification deadline: April 1st, 2024

FAQ

  1. How many individuals are accepted into the Virtual course?

    • 40 people

  2. Do postdocs qualify for the student rate?

    • No, sorry.

  3. Is there a discount for MGH or Martinos Center employees?

    • Sorry, no.

  4. I cannot pay by internal fund 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 may be able to 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.

  1. 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.

  2. 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.

  3. How do I know if my payment went through?

    • If it hasn't we will contact you.

  4. 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 the course organizers (fscourse AT nmr.mgh.harvard.edu) prior to the course, they can try to arrange a time to discuss your data.

  5. 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 email the course organizers (fscourse AT nmr.mgh.harvard.edu) 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.

  • 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.

  • Freeview demonstration

    • A live walk-through for how to use the Freeview GUI.

  • Interaction with Individual Subject Output - Tutorial

    • Using FreeSurfer's visualization tools to look at FreeSurfer output.

  • 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).

  • FreeSurfer Troubleshooting - 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

  • Group Analysis/GLM/Multiple Comparisons (mri_glmfit)- Talk and Tutorial

    • Covers the basics of group analysis in the context of imaging data.

  • Longitudinal Analysis in FreeSurfer

    • How to process longitudinal data with FreeSurfer and what's going on behind the scenes.

  • 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.

VirtualCourse (last edited 2026-02-16 14:06:21 by DougGreve)