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= The next Freesurfer course will be held virtually on April 29th, 30th, and May 1st. The course will take place on Gather.Town and will run from 9am-5pm EST. This page is work in progress. =
The virtual !FreeSurfer course is scheduled for '''June 21st, 22nd & 27th, 2023'''. ''Note: These are not two consecutive dates''. 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 '''May 22nd''' 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.		 '''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 not yet open. This page will be updated once registration has opened.
'''Registration is now open for the June 2023 Virtual !FreeSurfer Course!''' [[https://education.martinos.org/freesurfer-tutorial-workshop/|Click here to register!]] <<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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##'''Registration is now FULL for the June 2023 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: '''May 22nd, 2023'''		 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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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). '''Registration is now CLOSED for the 2025 course.'''

###'''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). ''' '''
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''' ''' ''' '''
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'''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>> ''' '''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. 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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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. 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. ''' '''
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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 ('''May 22nd, 2023''') 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. 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. ''' '''
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'''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. '''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. ''' '''
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==== Wednesday, June 21st - Gathertown Social & Instructions ====
||'''Time''' ||'''Title''' ||'''Type''' ||'''Lecturer''' ||
||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 ||		 = 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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** optional talks ** optional talks ''' '''
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==== Thursday, June 22nd - Introduction / Single Subject Analysis / Troubleshooting ====
||'''Time''' ||'''Title''' ||'''Type''' ||'''Lecturer''' ||
||9:00 - 9:10 ||'''Welcome''' ||social ||staff ||
||9:10 - 9:55 ||[[attachment:freesurfer.intro.june.2023.pptx|Introduction to Freesurfer]] ||talk ||Bruce Fischl ||		 ==== 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 ||
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||11:05 - 11:25 ||'''20 minute break''' || || ||
||11:25 - 11:45 ||Freeview demonstration ||[[FsTutorial/FreeviewDemo|demo]] ||Nathan Draudt ||		 ||11:05 - 11:25 ||20 minute break ''' ''' || || ||
||11:25 - 11:45 ||[[FsTutorial/FreeviewDemo|Freeview Demo]] ||demo ||Nathan Draudt ||
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||12:30 - 1:30 ||'''Lunch''' ||||<style="text-align:center"> || ||12:30 - 1:30 ||Lunch ''' ''' ||||<style="text-align:center"> ||
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||3:25 - 3:45 ||'''20 minute break''' || || || ||3:25 - 3:45 ||20 minute break ''' ''' || || ||
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||4:30 - 5:00 ||[[FsTutorial/Practice|Practice Working with Data]] or finish other tutorials ||tutorial ||staff || ||4:30 - 5:00 ||[[FsTutorial/PracticeV6.0|Practice Working with Data]] or finish other tutorials ||tutorial ||staff ||
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==== Tuesday, June 27th - 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"> ||		 ==== 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"> ||
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||3:05 - 3:25 ||'''20 minute break''' || || || ||3:05 - 3:25 ||20 minute break ''' ''' || || ||
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 * 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]]		  * 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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 * 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.		  * 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 $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!'' 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: 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. 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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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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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 June 8th, you will not be issued a refund. If you do not show your computer is unable to run the software by May 22nd, you will not be issued a refund. ### 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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Partial Refund Cancellation deadline: '''June 8th, 2023''' <<BR>> Computer verification deadline: '''May 22nd, 2023''' 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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 1. '''How many individuals are accepted into the Virtual course?'''
  * 35 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 (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. '''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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## 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. '''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.
 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 nmr.mgh.harvard.edu) for assistance.		  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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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. 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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 * '''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.		  * '''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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## * '''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.
 * '''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.		  * '''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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## * '''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.
 * '''Question and Answer Session'''
  * Open forum to resolve any unanswered questions		  * '''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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== 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]]. == 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

** Social Gathering & Gathertown Demo

demo

Liam Sennott & 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 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

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 Demo

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

Thursday, June 12th - ROI Analysis / Group Analysis / Longitudinal Analysis

Time

Title

Type

Lecturer

9:00 - 9:45

Longitudinal FreeSurfer

talk

Martin Reuter

9:45 - 10:30

Tutorial: LongitudinalTutorial

tutorial

staff

10:30 - 10:50

20 minute break

10:50 - 11:20

ROI Analysis

talk

Malte Hoffmann

11:20 - 12:05

Tutorial: ROI Analysis

tutorial

staff

12:05 - 12:35

Surface Based Analysis

talk

Divya Varadarajan

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 $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

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

    • 45 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 (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.

  5. 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.

  6. 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.

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

    • If it hasn't we will contact you.

  8. 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.

  9. 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.

VirtualCourse (last edited 2025-06-09 08:57:28 by LiamrSennott)