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###'''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 9am and 5pm Eastern Daylight Time (EDT) on these days. Registration will be opening on Wednesday, May 21st at 10am EDT.'''''' ''' |
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| ###'''The next virtual FreeSurfer course is still being scheduled. The official date is to be confirmed. Stay tuned for more updates.''' '''### | 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 5th''' in order to stay enrolled in the course. If your computer cannot run the course materials, your course registration will be cancelled and a full refund issued to you. ''' ''' |
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| ###'''The 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]]. '''### | '''Registration is OPEN for the 2025 virtual course! [[https://education.martinos.org/freesurfer-tutorial-workshop/|Click here to Register!]] '''### |
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| ###'''The dates written below reflect those from last year's course. '''### |
Computer verification deadline: '''June 5th, 2025''' ''' ''' 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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The next virtual !FreeSurfer course is scheduled for '''June 9th, 10th, and 12th, 2025'''. '''The course will take place between 9am and 5pm Eastern Daylight Time (EDT) on these days. Registration will be opening on Wednesday, May 21st at 10am EDT.'''''' ''' 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 5th''' 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 for this virtual course will be open today at 10am Eastern Daylight Time. [[https://education.martinos.org/freesurfer-tutorial-workshop/|This link will be live at 10am]] ###Registration is now open for the June 2025 Virtual FreeSurfer Course! [[https://education.martinos.org/freesurfer-tutorial-workshop/|Click here to register!]]### '''Computer verification deadline: '''June 5th, 2025''' ''' '''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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| 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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| '''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 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 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 ('''June 5th, 2025''') 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 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 ('''June 5th, 2025''') 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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| ||Time''' ''' ||Title''' ''' ||Type''' ''' ||Lecturer''' ''' || | ||Time ''' ''' ||Title ''' ''' ||Type ''' ''' ||Lecturer ''' ''' || |
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| '''** optional talks ''' | ** optional talks ''' ''' |
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||Time''' ''' ||Title''' ''' ||Type''' ''' ||Lecturer''' ''' || ||9:00 - 9:10 ||Welcome''' ''' ||social ||staff || |
||Time ''' ''' ||Title ''' ''' ||Type ''' ''' ||Lecturer ''' ''' || ||9:00 - 9:10 ||Welcome ''' ''' ||social ||staff || |
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| ||11:05 - 11:25 ||20 minute break''' ''' || || || | ||11:05 - 11:25 ||20 minute break ''' ''' || || || |
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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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| ||Time''' ''' ||Title''' ''' ||Type''' ''' ||Lecturer''' ''' || | ||Time ''' ''' ||Title ''' ''' ||Type ''' ''' ||Lecturer ''' ''' || |
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| ||10:45 - 11:05 ||20 minute break''' ''' || || || | ||10:45 - 11:05 ||20 minute break ''' ''' || || || |
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| ||12:35 - 1:35 ||Lunch''' ''' ||||<style="text-align:center"> || | ||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 $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!'' ''' | 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 mgh dot harvard dot edu) ''' | 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 the Friday prior to the start of the course (June 5th). 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 5th, you will not be issued a refund. If you do not show your computer is unable to run the software by April 3rd, you will not be issued a refund. ''' | Course fees are refundable, minus a $200 fee, up to the Friday prior to the start of the course (June 5th). 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 5th, you will not be issued a refund. If you do not show your computer is unable to run the software by April 3rd, you will not be issued a refund. ''' ''' |
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| '''Partial Refund Cancellation deadline: '''June 5th, 2025''' <<BR>> Computer verification deadline: '''June 5th, 2025''' ''' | Partial Refund Cancellation deadline: '''June 5th, 2025''' <<BR>> Computer verification deadline: '''June 5th, 2025''' ''' ''' |
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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. ''' |
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. 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. ''' |
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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* 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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* 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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| ''' ''' | ''' ''' ''' ''' |
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| '''<<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>> ''' | <<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 9am and 5pm Eastern Daylight Time (EDT) on these days. Registration will be opening on Wednesday, May 21st at 10am EDT.
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 5th 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 OPEN for the 2025 virtual course! Click here to Register! ###
Computer verification deadline: June 5th, 2025
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 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 (June 5th, 2025) 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 |
Doug Greve & 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 - 9:30 |
talk |
Malte Hoffmann |
|
9:30 - 10:15 |
tutorial |
staff |
|
10:15 - 10:45 |
talk |
Divya Varadarajan |
|
10:45 - 11:05 |
20 minute break |
|
|
11:05 - 11:50 |
talk |
Martin Reuter |
|
11:50 - 12:35 |
tutorial |
staff |
|
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
Course fees are refundable, minus a $200 fee, up to the Friday prior to the start of the course (June 5th). 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 5th, you will not be issued a refund. If you do not show your computer is unable to run the software by April 3rd, you will not be issued a refund.
Partial Refund Cancellation deadline: June 5th, 2025
Computer verification deadline: June 5th, 2025
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.