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| = Upcoming FreeSurfer courses = | = Virtual FreeSurfer Course = '''The FreeSurfer Team is currently holding Virtual Courses. Please refer to the [[https://surfer.nmr.mgh.harvard.edu/fswiki/CourseDescription|Course Description]] page for info on previous in-person courses. ''' |
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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>> |
###'''The next virtual FreeSurfer course is still being scheduled. The official date is to be confirmed. Stay tuned for more updates.''' '''### ###'''The course date will be announced on our [[https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer|Freesurfer mailing list]] and our [[https://x.com/FreeSurferMRI|Twitter Page]]. '''### ###'''The dates written below reflect those from last year's course. '''### -------- The next virtual !FreeSurfer course is scheduled for '''June 9th, 10th, and 12th, 2025'''. '''The course will take place between 9:00am and 5:00pm Eastern Daylight Time (EDT) on these days. '''''' ''' |
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| The next virtual !FreeSurfer course is scheduled for '''September 12-13th, 2022'''. The payment deadline is '''September 6, 2022'''. '''Note:''' As long as there are empty spots in the course, we will accept late registrations. If you register after the payment deadline has passed, payment is due immediately. | 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 '''June 9th 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. ''' ''' |
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| Registration is not yet open. This page will be updated once registration has opened. | '''Registration is now CLOSED for the 2025 course.''' |
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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>> This is a two day course that offers a basic introduction to FreeSurfer. Review the tentative schedule below before registering. |
###'''Registration is open for the 2025 course, and will be open until Monday, June 9th at 9:00am EDT. [[https://education.martinos.org/freesurfer-tutorial-workshop/|Click here to Register!]] ''' ###'''Please note that we will not be able to provide technical assistance after Friday, June 6th at 5:00pm EDT.''' ###'''Registration is OPEN for the 2025 virtual course! [[https://education.martinos.org/freesurfer-tutorial-workshop/|Click here to Register!]] ''' Computer verification deadline: '''June 9th, 2025 at 3:00pm EDT''' ''' ''' 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 mgb.org). ''' ''' -------- ''' ''' ''' ''' == Course Details == '''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>> ''' ''' ''' === 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 [[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 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 [[https://surfer.nmr.mgh.harvard.edu/fswiki/CourseDescription/Remote_Qualify|here]] which must be checked prior to registering for the course. '''The VM will not work on M1 Model Macs or newer, and it may not work on other computers.''' You will be required to verify your computer can properly host the course software by the deadline ('''June 9th 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. 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. ''' ''' = All times listed are Eastern Daylight Time (EDT) = ==== Monday, June 9th - Gathertown Social & Instructions ==== ||Time ''' ''' ||Title ''' ''' ||Type ''' ''' ||Lecturer ''' ''' || ||3:30-4:00pm ||** [[attachment:gathertownslides_forDemo_2025.pptx|Social Gathering & Gathertown Demo]] ||demo ||Liam Sennott & FS staff || ||4:00 - 4:30 ||** [[attachment:Linux_slides_final_2025.pptx|Intro to Linux for FreeSurfer Users]] ||talk/demo ||Jackson Nolan || ||4:30 - 4:50 ||** [[attachment:fsjargon.pptx|Intro to FreeSurfer Jargon]] ||talk ||Allison McKenzie || |
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| == General Information == Additional details about the Virtual Course can be found [[http://surfer.nmr.mgh.harvard.edu/fswiki/CourseDescription#BostonCourseDetails|below]]. Information about international courses can be found on their respective websites. |
** optional talks ''' ''' |
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| 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). | ==== Tuesday, June 10th - Introduction / Single Subject Analysis / Troubleshooting ==== ||Time ''' ''' ||Title ''' ''' ||Type ''' ''' ||Lecturer ''' ''' || ||9:00 - 9:10 ||Welcome ''' ''' ||social ||staff || ||9:10 - 9:55 ||[[attachment:freesurfer.intro.june.2025.revised_ver2.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 ||[[FsTutorial/FreeviewDemo|Freeview Demo]] ||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/PracticeV6.0|Practice Working with Data]] or finish other tutorials ||tutorial ||staff || |
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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>> |
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| '''UNSUBSCRIBE''':<<BR>> To unsubscribe from the course mailing list please click [[https://surfer.nmr.mgh.harvard.edu/cgi-bin/fsurfer/unsubscribe.cgi|here]]. | ==== Thursday, June 12th - ROI Analysis / Group Analysis / Longitudinal Analysis ==== ||Time ''' ''' ||Title ''' ''' ||Type ''' ''' ||Lecturer ''' ''' || ||9:00 - 9:45 ||[[http://surfer.nmr.mgh.harvard.edu/pub/docs/fs.longitudinal.pptx|Longitudinal FreeSurfer]] ||talk ||Martin Reuter || ||9:45 - 10:30 ||[[FsTutorial/LongitudinalTutorial|Tutorial: LongitudinalTutorial]] ||tutorial ||staff || ||10:30 - 10:50 ||20 minute break ''' ''' || || || ||10:50 - 11:20 ||[[http://surfer.nmr.mgh.harvard.edu/pub/docs/fs.roi.EB_wiki.pptx|ROI Analysis]] ||talk ||Malte Hoffmann || ||11:20 - 12:05 ||[[FsTutorial/AnatomicalROIV6.0|Tutorial: ROI Analysis]] ||tutorial ||staff || ||12:05 - 12:35 ||[[attachment:fs.surface-based-analysis.ppt|Surface Based Analysis]] ||talk ||Divya Varadarajan || ||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 || |
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| -------- | |
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| == Boston Course Details == '''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#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#Accommodations|Accommodations]] <<BR>> [[http://surfer.nmr.mgh.harvard.edu/fswiki/CourseDescription#Directions|Directions]] <<BR>> [[http://surfer.nmr.mgh.harvard.edu/fswiki/CourseDescription#Parking|Parking]] <<BR>> [[http://surfer.nmr.mgh.harvard.edu/fswiki/CourseDescription#Map|Map of the Course Location]]''' |
=== 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]] ''' ''' |
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| === Overview === The !FreeSurfer Development Team hosts a '''four-day, rigorous''' course for beginner and experienced users of !FreeSurfer. '''Day 1''' caters to beginners and will cover: . An introduction to !FreeSurfer <<BR>> Single Subject Surface-based analysis <<BR>> MRI Acquisition Tips <<BR>> ROI analysis <<BR>> '''Day 2''' will cover: . Group analysis <<BR>> Longitudinal analysis<<BR>> Troubleshooting '''Day 3''' will cover: . Multi-modal integration <<BR>> fMRI <<BR>> Diffusion '''Day 4''' will cover: . Multi-modal integration <<BR>> Future directions ##The four days will run roughly from '''9am-5pm''' with the last day ending early (~3pm). The four days consist of talks/tutorials that run all day, roughly from '''9am-5pm'''. There will be extra time to work on tutorials or data before 9am and after 5pm. Attendees are expected to attend all talks and tutorials aside from the ones scheduled as "optional". Attendees may opt out of either the fMRI or Diffusion lectures if it is not applicable to them. Laptops are provided with !FreeSurfer and the tutorial data already installed. Attendees will work in pairs (sharing a laptop). '''The schedule of talks and links to tutorials can be found [[http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial|here]].''' Please check back for updates. Additional topics and more detail on each topic is provided [[http://surfer.nmr.mgh.harvard.edu/fswiki/CourseDescription#CourseTopics|below]]. |
==== 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 $450. A reduced rate of $300 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 ==== Payment Coordinator/Contact: Stacey Ladieu (sladieu at martinos dot org) |
Payment Coordinator/Contact: Stacey Ladieu (sladieu at mgh dot harvard dot edu) ''' ''' |
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| Payment deadline: '''September 6, 2022''' | ==== Cancellations, Refunds, and Deadlines ==== ### As of 5-21-25 Liam took out the 'minus a $200 fee' portion from this next sentence since Doug wanted to fully refund students for the June 2025 course ### The following sentences were also removed for this course: "If you do not cancel your registration by June 5th, you will not be issued a refund. If you do not show your computer is unable to run the software by June 5th, you will not be issued a refund" ###Course fees are refundable up to 30 minutes prior to the start of the course (June 9th at 3:00pm EDT). ###Course fees are refundable up to 30 minutes prior to the start of the course (June 9th at 3:00pm). 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. ''' ''' |
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| Accepted Payment types: credit card, cash, or institutional check (see sections below for details on each) | Partial Refund Cancellation deadline: '''June 9th, 2025 at 3:00pm EDT''' <<BR>> Computer verification deadline: '''June 9th, 2025 at 3:00pm EDT''' ''' ''' |
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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>> |
=== FAQ === 1. '''How many individuals are accepted into the Virtual course?''' ''' ''' * 45 people ''' ''' 1. '''Do postdocs qualify for the student rate?''' ''' ''' * No, sorry. ''' ''' 1. '''Is there a discount for MGH or Martinos Center employees?''' ''' ''' * Sorry, no. ''' ''' 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 (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. ''' ''' |
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| ==== Credit Cards ==== Please use the website below to make a payment via credit card. |
1. '''The course is full. Can you register me for the next one?''' ''' ''' * You can sign up for the [[https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer|Freesurfer mailing list]] and follow our [[https://x.com/FreeSurferMRI|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. ''' ''' 1. '''Can I get a receipt for the course?''' ''' ''' * Contact the payment coordinator, Stacey (sladieu at mgh dot harvard dot edu)) to arrange getting a receipt. ''' ''' 1. '''How do I know if my payment went through?''' ''' ''' * If it hasn't we will contact you. ''' ''' 1. '''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 mgb.org) prior to the course, they can try to arrange a time to discuss your data. ''' ''' 1. '''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 mgb.org) for assistance. ''' ''' |
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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 |
=== 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. ''' ''' |
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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>> | * '''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. ''' ''' |
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| [[http://payment.martinos.org/|Click here to pay by Credit Card]] | * '''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. ''' ''' |
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| ==== 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. |
* '''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 ''' ''' |
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| Make checks payable to: Massachusetts General Hospital | ---- ''' ''' ''' ''' |
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| 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 ==== 1. '''How many individuals are accepted into the Virtual course?''' * 20 people 1. '''Do postdocs qualify for the student rate?''' * No, sorry. 1. '''Is there a discount for MGH or Martinos Center employees?''' * Sorry, no. 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. '''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 [[http://surfer.nmr.mgh.harvard.edu/cgi-bin/fsurfer/interest.cgi|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. 1. '''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. 1. '''How do I know if my payment went through?''' * If it hasn't we will contact you. 1. '''Do I get any credits for taking this course?''' * Nope, but we will give you a certificate to prove you took it. 1. '''Do you serve any food at the course?''' * There will be a continental breakfast each morning & coffee and some snacks supplied in the afternoon. There is also a cafeteria nearby where the course is held and two cafes 2-3 blocks from the building. 1. '''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. 1. '''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. 1. '''Can I bring my own laptop to work on instead of sharing with someone else? ''' * If any issues arise during the tutorial sessions which are unique to your laptop, we will not be able to troubleshoot those issues for you (it takes staff away from answering general tutorial questions). We strongly discourage using your own laptop instead of the ones we provide. If you insist on working on your laptop, please thoroughly test your installation ahead of time - guidelines for this can be found on the TestingFreeSurfer wiki. It might also be a good idea to try to run all the commands in the tutorials ([[https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial|here]]). 1. '''How far is the airport from the course location? ''' * About 20 minutes by taxi and 1 hour by public transportation (there are several transfers). The taxi will cost $20-$25. Public transportation will cost under $3. 1. '''Would it work if I scheduled a flight for the evening of the 3rd or 4th day of the class?''' * Certainly. You can bring your luggage to the room where the course is held and leave straight from there. Traffic can be bad after 3pm, so you may need 45 minutes to an hour to get to the airport. To attend all the talks on the 3rd day, your flight will need to be 8pm or later. ## 1. '''I can only pay for the course with credit card so that I can be reimbursed later. Is this okay?''' ## * Sorry, we have not found a way to be able to accept credit cards. Payment must be by check or cash. ==== 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. ## * '''Running !FreeSurfer in the cloud with AWS batch''' ## * This talk will cover how to run FreeSufer's recon-all pipeline in the cloud using AWS Batch. It begins with a ##brief overview of relevant AWS components and terminology as well as an introduction to docker: a tool to help ##create, deploy and run software in a consistent and reproducible environment. This will be followed by a ##demonstration of how to use docker on a local machine and finally how to execute recon-all inside a docker container ##on AWS using AWS Batch. * '''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) * '''Basics of fMRI Analysis''' * Covers the basics of functional MRI data analysis, spanning preprocessing to single-subject and group-level analyses. Topics include motion correction, B0 distortion correction, spatial normalization, spatial smoothing, hemodynamic modeling, GLM analysis, contrasts and hypothesis testing, and Random-, Fixed-, and Mixed-Effects group analyses. * '''FS-FAST''' * Preprocessing of fMRI (motion correction, slice-timing correction, smoothing, registration to the anatomical, sampling to the common group space in the surface and volume), setting up and running block and event-related analysis, adding nuisance variables to the analysis, performing the individual fMRI time series fMRI analysis, performing group fMRI analysis in the volume and on the surface. * '''Diffusion Data Processing and TRACULA talks and tutorial''' * How to process diffusion MRI data to extract basic diffusion measures and to reconstruct white-matter pathways using !FreeSurfer's tractography tool. * '''Motion-compensated neuroanatomical imaging (optional)''' * While real-time fMRI motion correction has been available with some MRI scanners for years (e.g. Siemens' PACE), effective real-time motion correction in neuroanatomical imaging is just now becoming available. This talk focuses on the motion-correction system we have developed for the Siemens platform, but also discusses the current developments on the GE platform. * '''MRI Acquisition Methods for Morphometry (optional)''' * A description of how using different scan protocols can affect data quality and !FreeSurfer reconstruction. * '''Registration Methods (optional)''' * Overview of different registration methods discussed so far (flirt, robust_register, bbregister) and introduction of a new registration tool, CVS (combined volume and surface registration). * '''Longitudinal Analysis in !FreeSurfer''' * How to process longitudinal data with !FreeSurfer and what's going on behind the scenes. * '''Future Directions of !FreeSurfer''' * Inferring architectonic boundaries from in-vivo MRI - Bruce Fischl * Techniques for inferring the location of architectonic features in the brain in vivo * '''Question and Answer Session''' * Open forum to resolve any unanswered questions ==== 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 |
== Future Courses == <<BR>> We will announce future courses via our [[https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer|Freesurfer mailing list]] and our [[https://x.com/FreeSurferMRI|Twitter Page]]. <<BR>> ''' ''' |
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 9th, 10th, and 12th, 2025. 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 June 9th 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 2025 course.
Computer verification deadline: June 9th, 2025 at 3:00pm EDT
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).
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 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. The VM will not work on M1 Model Macs or newer, and it may not work on other computers. You will be required to verify your computer can properly host the course software by the deadline (June 9th 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. 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.
All times listed are Eastern Daylight Time (EDT)
Monday, June 9th - Gathertown Social & Instructions
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
Tuesday, June 10th - Introduction / Single Subject Analysis / Troubleshooting
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 |
Thursday, June 12th - ROI Analysis / Group Analysis / Longitudinal Analysis
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 - 11:20 |
talk |
Malte Hoffmann |
|
11:20 - 12:05 |
tutorial |
staff |
|
12:05 - 12:35 |
talk |
Divya Varadarajan |
|
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 |
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.
After the Course
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.
Payment
Cost
The fee for the course is $450. A reduced rate of $300 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 mgh dot harvard dot edu)
Cancellations, Refunds, and Deadlines
Partial Refund Cancellation deadline: June 9th, 2025 at 3:00pm EDT
Computer verification deadline: June 9th, 2025 at 3:00pm EDT
FAQ
How many individuals are accepted into the Virtual course?
45 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 internal fund or credit card. Do I have any other options?
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.
The course is full. Can you register me for the next one?
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.
Can I get a receipt for the course?
Contact the payment coordinator, Stacey (sladieu at 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 the course organizers (fscourse AT mgb.org) prior to the course, they can try to arrange a time to discuss your data.
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 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.
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
Future Courses
We will announce future courses via our Freesurfer mailing list and our Twitter Page.