= Virtual FreeSurfer Course June 2025 = '''The [[https://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurfer|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. ''' -------- 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 [[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. ''' ''' '''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 [[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: <
> [[http://surfer.nmr.mgh.harvard.edu/fswiki/VirtualCourse#Overview|Overview]] <
> [[http://surfer.nmr.mgh.harvard.edu/fswiki/VirtualCourse#TechnicalRequirements|Technical Requirements]] <
> [[http://surfer.nmr.mgh.harvard.edu/fswiki/VirtualCourse#Schedule|Schedule]] <
> [[http://surfer.nmr.mgh.harvard.edu/fswiki/VirtualCourse#Payment|Payment]] <
> [[http://surfer.nmr.mgh.harvard.edu/fswiki/VirtualCourse#FAQ|FAQ]] <
> [[http://surfer.nmr.mgh.harvard.edu/fswiki/VirtualCourse#CourseTopics|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 [[https://www.gather.town/|gather.town]] while tutorials will be accessible via Virtual Machine (VM). A tentative schedule is below. ''' ''' === Technical Requirements === Prior to the course, attendees will be provided with instructions on how to download & install the VM software package and course data necessary to participate in the course. These downloads require 70GB of free storage space on your computer or an external hard drive. The computer also needs to have a minimum of 16GB of RAM (total) to function properly while working with the course data during tutorials. There are additional technical requirements listed [[https://surfer.nmr.mgh.harvard.edu/fswiki/CourseDescription/Remote_Qualify|here]] which must be checked prior to registering for the course. '''The VM will not work on M1 Model Macs or newer, and it may not work on other computers.''' You will be required to verify your computer can properly host the course software by the deadline ('''June 9th at 3:00pm EDT''') in order to stay enrolled in the course. If your computer cannot run the course materials, your course registration will be cancelled and a full refund issued to you. See the payment section below for more details on cancellations and refunds. A strong internet connection is a must for the best workshop experience. ''' ''' === Schedule === '''WARNING''': The hyperlinks in the tables below used to download slides will NOT WORK in Google Chrome. Please use a different browser to access these slides. ''' ''' = All times listed are Eastern Daylight Time (EDT) = ==== Monday, June 9th - Gathertown Social & Instructions ==== ||Time ''' ''' ||Title ''' ''' ||Type ''' ''' ||Lecturer ''' ''' || ||3:30-4:00pm ||** [[attachment:gathertownslides_forDemo_2025.pptx|Social Gathering & Gathertown Demo]] ||demo ||Liam Sennott & FS staff || ||4:00 - 4:30 ||** [[attachment:Linux_slides_final_2025.pptx|Intro to Linux for FreeSurfer Users]] ||talk/demo ||Jackson Nolan || ||4:30 - 4:50 ||** [[attachment:fsjargon.pptx|Intro to FreeSurfer Jargon]] ||talk ||Allison [[https://surfer.nmr.mgh.harvard.edu/fswiki/McKenzie|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 ||[[attachment:freesurfer.intro.june.2025.revised_ver2.pptx|Introduction to Freesurfer]] ||talk ||Bruce Fischl || ||9:55 - 11:05 ||[[attachment:fsrecon.sep2022.pptx|Analyzing the Individual Subject]] ||talk ||Doug Greve || ||11:05 - 11:25 ||20 minute break ''' ''' || || || ||11:25 - 11:45 ||[[https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/FreeviewDemo|Freeview Demo]] ||demo ||Nathan Draudt || ||11:45 - 12:30 ||[[https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/OutputData_freeview|Tutorial: Individual Subject Output]] ||tutorial ||staff || ||12:30 - 1:30 ||Lunch ''' ''' |||| || ||1:30 - 2:15 ||[[attachment:freesurfer.troubleshooting.sep2022.ppt|FreeSurfer Troubleshooting]] ||talk ||Doug Greve || ||2:15 - 3:25 ||[[https://surfer.nmr.mgh.harvard.edu/fswiki/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 ||[[https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/PracticeV6.0|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 ||[[http://surfer.nmr.mgh.harvard.edu/pub/docs/fs.longitudinal.pptx|Longitudinal FreeSurfer]] ||talk ||Martin Reuter || ||9:45 - 10:30 ||[[https://surfer.nmr.mgh.harvard.edu/fswiki/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 ||[[https://surfer.nmr.mgh.harvard.edu/fswiki/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 ''' ''' |||| || ||1:35 - 2:20 ||[[attachment:GLM.pptx|Group Analysis]] ||talk ||Doug Greve || ||2:20 - 3:05 ||[[https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysisV6.0|Tutorial: Group Analysis]] ([[https://surfer.nmr.mgh.harvard.edu/fswiki/FsgdExamples|FSGD Examples]]) ||tutorial ||staff || ||3:05 - 3:25 ||20 minute break ''' ''' || || || ||3:25 - 4:10 ||[[http://surfer.nmr.mgh.harvard.edu/pub/docs/multiplecomparisons.ppt|Corrections for Multiple Comparisons]] ||talk ||Doug Greve || ||4:10 - 4:40 ||[[https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/MultipleComparisonsV6.0Perm|Tutorial: Corrections for Multiple Comparisons]] ||tutorial ||staff || ||4:40 - 5:00 ||Q&A with FreeSurfer Team ||talk ||Bruce Fischl, Doug Greve, & FS Team || === Additional Useful Information === ==== During the Course ==== * Using a Mac & need a text editor? Download gedit, [[http://ftp.gnome.org/pub/GNOME/binaries/mac/gedit/3.2/gedit-3.2.6-3_SnowLeopard_64bit.dmg|here]]. ''' ''' * Some basic information on text editors can be found [[https://surfer.nmr.mgh.harvard.edu/fswiki/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 [[https://surfer.nmr.mgh.harvard.edu/fswiki/MacCommands|MacCommands]]. ''' ''' * [[https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Scripts|Scripts & aliases]] ''' ''' * [[https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Glossary|Glossary]] ''' ''' ==== After the Course ==== * A full list of all [[https://surfer.nmr.mgh.harvard.edu/fswiki/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 [[https://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferMethodsCitation|FreeSurferMethodsCitation]] page. ''' ''' === Payment === ==== Cost ==== The fee for the course is $450. A reduced rate of $300 is available to undergraduate and graduate students. ''MDs, PhDs, RAs and Post-docs do not qualify for the student rate!'' ''' ''' ==== Accepted Payment Types ==== Accepted Payment types: credit card, MGB internal fund, cash (contact the course organizers to arrange how to pay with cash) . As long as there are empty spots in the course, we will accept late registrations (regardless of the cancellation deadline). Payment and all questions about payment should be sent to Stacey. ''' ''' Payment Coordinator/Contact: Stacey Ladieu (sladieu at mgh dot harvard dot edu) ''' ''' ==== Cancellations, Refunds, and Deadlines ==== Partial Refund Cancellation deadline: '''June 9th, 2025 at 3:00pm EDT''' . Computer verification deadline: '''June 9th, 2025 at 3:00pm EDT''' ''' ''' === FAQ === 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. '''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. ''' ''' === 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 [[https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer|Freesurfer mailing list]] and our [[https://x.com/FreeSurferMRI|Twitter Page]].