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| The virtual !FreeSurfer course is scheduled for '''September 14-15th, 2022'''. This is a two day course that offers a basic introduction to !FreeSurfer. A !FreeSurfer Virtual Machine (VM) will be provided to course participants so that they can easily work with !FreeSurfer and practice data during the course. Before registering, review the tentative [[http://surfer.nmr.mgh.harvard.edu/fswiki/CourseDescription#Schedule|schedule]] to make sure it will work for you and review the [[https://surfer.nmr.mgh.harvard.edu/fswiki/CourseDescription/Remote_Qualify|technical requirements]] to be sure your computer can run the course software. You will be required to verify your computer can properly host the course software by Sept 7th in order to stay enrolled in the course. If your computer cannot run the course materials, your course registration will be cancelled and a full refund issued to you. | '''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 Fall 2022 Virtual FreeSurfer Course!''' [[https://education.martinos.org/freesurfer-tutorial-workshop/|Click here to register!]] <<BR>> ##'''Registration is now FULL for the Fall 2022 Virtual FreeSurfer Course!''' You may still register to be added to the wait-list!''' [[https://education.martinos.org/freesurfer-tutorial-workshop/|Click here to register!]] <<BR>> |
###'''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.'''''' ''' 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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| 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, Allison Stevens or Liam Sennott (freesurferlab@gmail.com). | ###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). ''' -------- ''' ''' == 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 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 ||** [[attachment:fs_slidese_KG.pptx|Intro to Linux for FreeSurfer Users]] ||talk/demo ||Jackson Nolan || ||4:30 - 4:50 ||** [[attachment:fs_slidese_KG.pptx|Intro to FreeSurfer Jargon]] ||talk ||Allison McKenzie || |
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| -------- | '''** optional talks ''' |
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| == 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#Schedule|Schedule]] <<BR>> [[http://surfer.nmr.mgh.harvard.edu/fswiki/CourseDescription#Payment|Payment]] <<BR>> [[http://surfer.nmr.mgh.harvard.edu/fswiki/CourseDescription#FAQ|FAQ]] <<BR>> [[http://surfer.nmr.mgh.harvard.edu/fswiki/CourseDescription#CourseTopics|Topics Covered During the Course]] <<BR>> ''' === Overview === The two day course consists of talks and tutorials that run throughout the day. Attendees are expected to attend all talks and tutorials. === Schedule === ==== Wednesday, September 14th - Introduction / Single Subject Analysis / ROI Analysis / Troubleshooting ==== ||'''Time''' ||'''Title''' ||'''Type''' ||'''Lecturer''' || ||8:30 - 9:00 ||** Intro to Linux for !FreeSurfer Users ||talk/demo || Dev || ||9:00 - 9:15 ||** [[http://surfer.nmr.mgh.harvard.edu/pub/docs/fsjargon_clean.pptx|Intro to FreeSurfer Jargon]] || talk || Allison, and Lillia or Caroline if they want? || ||9:15 - 10:00 ||[[attachment:freesurfer.intro.apr.2019.ppt|Introduction to Freesurfer]] ||talk ||Doug or Bruce Fischl || ||10:00 - 10:15 ||'''break''' || || || ||10:15 - 11:25 ||[[http://surfer.nmr.mgh.harvard.edu/pub/docs/fsrecon.pptx|Analyzing the Individual Subject]] ||talk ||Doug Greve || ||11:25 - 11:45 ||[[https://www.youtube.com/watch?v=Mv-ECowxq2o|Freeview demonstration]] ||[[FsTutorial/FreeviewDemo|demo]] || Jackson || ||11:45 - 12:00 ||'''break''' || || || ||12:00 - 12:45 ||[[FsTutorial/OutputData_freeview|Individual Subject Output]] ||tutorial || Allison, RA#2 RA#3 || ||12:45 - 1:45 ||'''Lunch''' |||||| ||1:45 - 2:15 ||[[http://surfer.nmr.mgh.harvard.edu/pub/docs/fs.roi.EB_wiki.pptx|ROI Analysis]] ||talk || Doug Greve || ||2:15 - 3:00 ||[[FsTutorial/AnatomicalROIV6.0|ROI Analysis Tutorial]] ||tutorial ||RA#1 RA#2 RA#3 || ||3:00 - 3:15 ||'''break''' || || || ||3:15 - 4:00 ||[[http://surfer.nmr.mgh.harvard.edu/pub/docs/freesurfer.troubleshooting.apr2019.ppt|FreeSurfer Troubleshooting]] ||talk || Allison? Bruce?|| ||4:00 - 5:00 ||[[FsTutorial/TroubleshootingDataV6.0|Troubleshooting Freesurfer]] ||tutorial ||Dev, Allison, RA#3|| ||5:00 - 5:45 || QA Demo ||talk || Allison? Leah? || |
==== 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.spring.2024.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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| ==== Thursday, September 15th - Group Analysis / Longitudinal Analysis ==== ||'''Time''' ||'''Title''' ||'''Type''' ||'''Lecturer''' || ||10:00 - 10:30 || Surface Based Analysis ||talk || Divya / Doug || ||10:30 - 11:15 ||[[http://surfer.nmr.mgh.harvard.edu/pub/docs/GLM.pptx|Group Analysis]] ||talk || Doug || ||11:15 - 11:30 ||'''break''' || || || ||11:30 - 12:10 ||[[FsTutorial/GroupAnalysisV6.0|Group Analysis Tutorial]] ([[FsgdExamples|FSGD Examples]]) ||tutorial || RA#1 RA#2 RA#3 || ||12:10 - 1:10 ||'''Lunch''' |||||| ||1:10 - 1:55 || Corrections for MC ||talk || Doug || ||1:55 - 2:25 || Tutorial: Corrections ||tutorial ||RA#1 RA#2 RA#3 || ||2:25 - 3:40 ||'''break''' || || || ||3:40 - 4:15 ||[[http://surfer.nmr.mgh.harvard.edu/pub/docs/fs.longitudinal.pptx|Longitudinal FreeSurfer]] ||talk ||Malte? Doug?|| ||4:15 - 4:55 || [[FsTutorial/LongitudinalTutorial|LongitudinalTutorial]] ||tutorial ||Dev, RA#2 RA#3 || ||4:55 - 5:15 || Q&A with FreeSurfer Team||talk || Doug? Bruce?|| |
==== Thursday, June 12th - ROI Analysis / Group Analysis / Longitudinal Analysis ==== ||Time''' ''' ||Title''' ''' ||Type''' ''' ||Lecturer''' ''' || ||9:00 - 9:30 ||[[http://surfer.nmr.mgh.harvard.edu/pub/docs/fs.roi.EB_wiki.pptx|ROI Analysis]] ||talk ||Malte Hoffmann || ||9:30 - 10:15 ||[[FsTutorial/AnatomicalROIV6.0|Tutorial: ROI Analysis]] ||tutorial ||staff || ||10:15 - 10:45 ||[[attachment:fs.surface-based-analysis.ppt|Surface Based Analysis]] ||talk ||Divya Varadarajan || ||10:45 - 11:05 ||20 minute break''' ''' || || || ||11:05 - 11:50 ||[[http://surfer.nmr.mgh.harvard.edu/pub/docs/fs.longitudinal.pptx|Longitudinal FreeSurfer]] ||talk ||Martin Reuter || ||11:50 - 12:35 ||[[FsTutorial/LongitudinalTutorial|Tutorial: LongitudinalTutorial]] ||tutorial ||staff || ||12:35 - 1:35 ||Lunch''' ''' ||||<style="text-align:center"> || ||1:35 - 2:20 ||[[attachment:GLM.pptx|Group Analysis]] ||talk ||Doug Greve || ||2:20 - 3:05 ||[[FsTutorial/GroupAnalysisV6.0|Tutorial: Group Analysis]] ([[FsgdExamples|FSGD Examples]]) ||tutorial ||staff || ||3:05 - 3:25 ||20 minute break''' ''' || || || ||3:25 - 4:10 ||[[http://surfer.nmr.mgh.harvard.edu/pub/docs/multiplecomparisons.ppt|Corrections for Multiple Comparisons]] ||talk ||Doug Greve || ||4:10 - 4:40 ||[[https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/MultipleComparisonsV6.0Perm|Tutorial: Corrections for Multiple Comparisons]] ||tutorial ||staff || ||4:40 - 5:00 ||Q&A with !FreeSurfer Team ||talk ||Bruce Fischl, Doug Greve, & FS Team || |
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| === Additional Useful Information === ==== During the Course ==== * '''Using a Mac & need a text editor? Download gedit, [[http://ftp.gnome.org/pub/GNOME/binaries/mac/gedit/3.2/gedit-3.2.6-3_SnowLeopard_64bit.dmg|here]]. ''' * '''Some basic information on text editors can be found [[FsTutorial/CreatingTextfiles|here]]. ''' * '''The tutorials often refer to keyboard shortcuts (such as Alt+v) which do not work on a Mac. For a list of equivalent keyboard commands on a Mac, please refer to MacCommands. ''' * '''[[FsTutorial/Scripts|Scripts & aliases]] ''' * '''[[FsTutorial/Glossary|Glossary]] ''' ==== After the Course ==== * '''A full list of all [[Tutorials|FreeSurfer tutorials]], including ones that may not have been included at this course ''' * '''[[https://www.zotero.org/freesurfer|Publications]] ''' * '''How to cite !FreeSurfer is on the FreeSurferMethodsCitation page. ''' |
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| The fee for the course is $400. A reduced rate of $275 is available to undergraduate and graduate students. ''MDs, !PhDs, RAs and Post-docs do not qualify for the student rate!'' |
'''The fee for the course is $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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| Payment Coordinator/Contact: Stacey Ladieu (sladieu at martinos dot org) | '''Accepted Payment types: credit card, MGB internal fund, cash (contact the course organizers to arrange how to pay with cash)<<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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| 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) ''' |
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| Cancellation deadline: '''August 31st, 2022''' <br> Computer verification deadline: '''September 7th, 2022''' |
'''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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| Course fees are refundable, minus a $100 fee, up to 2 weeks prior to the program. If you verify your computer is ''unable'' to host the course software & data by September 7th, you will be issued a full refund. If you do not cancel your registration by August 31st or do not show your computer is unable to run the software by September 7th, you will not be issued a refund. | '''Partial Refund Cancellation deadline: '''June 5th, 2025''' <<BR>> Computer verification deadline: '''June 5th, 2025''' ''' |
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| === 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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| ==== Cancellations ==== Course fees are refundable up to the cancellation deadline. A $100 fee will be deducted, should you request a refund up to 2 weeks prior to the program. Course fees are refundable minus a $100 fee up to 2 weeks prior to the program. If you verify your computer is unable to host the course software & data by September 7th, you will be issued a full refund. |
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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| ##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. | === 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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| ==== 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. '''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. |
* 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. ''' |
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| ==== 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) * '''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 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. 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).
Click on any of the topics below for more information:
WARNING
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
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
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
How many individuals are accepted into the Virtual course? Do postdocs qualify for the student rate? Is there a discount for MGH or Martinos Center employees? I cannot pay by internal fund or credit card. Do I have any other options? The course is full. Can you register me for the next one? Can I get a receipt for the course? How do I know if my payment went through? I have some data I would like to get your opinion on. Can I show it to you? I need some help installing FreeSurfer on my laptop - I can't seem to get it to work. Can you help with that?
Linux Demo/Tutorial (optional) Introduction to FreeSurfer Jargon (optional) Introduction to FreeSurfer Analyzing the Individual Subject in FreeSurfer Freeview demonstration Interaction with Individual Subject Output - Tutorial Region of Interest (ROI) Analysis - Talk and Tutorial FreeSurfer Troubleshooting - Talk and Tutorial Quality Checking a Recon Surface-based Analysis: Intersubject Registration & Smoothing Group Analysis/GLM/Multiple Comparisons (mri_glmfit)- Talk and Tutorial Longitudinal Analysis in FreeSurfer Question and Answer Session
Course Details
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
All times listed are Eastern Daylight Time (EDT)
Monday, June 9th - Gathertown Social & Instructions
Tuesday, June 10th - Introduction / Single Subject Analysis / Troubleshooting
Thursday, June 12th - ROI Analysis / Group Analysis / Longitudinal Analysis
Additional Useful Information
During the Course
Using a Mac & need a text editor? Download gedit, here. After the Course
A full list of all FreeSurfer tutorials, including ones that may not have been included at this 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
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
45 people
No, sorry.
Sorry, no.
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.
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.
Contact the payment coordinator, Stacey (sladieu at mgh dot harvard dot edu)) to arrange getting a receipt.
If it hasn't we will contact 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.
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.
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.
Intended for those new to imaging software. Explains basic vocabulary such as voxel, surface, vertex, volume, segmentation, parcellation, registration, and recon.
Overview of FreeSurfer's abilities.
Description of each step of the FreeSurfer processing stream.
A live walk-through for how to use the Freeview GUI.
Using FreeSurfer's visualization tools to look at FreeSurfer output.
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).
Discussion of the possible errors one may find in their FreeSurfer output and how to fix them.
Live demo of how to scroll through FreeSurfer output and look for errors.
Volume vs. Surface-based analysis
Covers the basics of group analysis in the context of imaging data.
How to process longitudinal data with FreeSurfer and what's going on behind the scenes.
Open forum to resolve any unanswered questions Future Courses
We will announce future courses via our Freesurfer mailing list and our Twitter Page.