= Virtual FreeSurfer Course =
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.

'''Registration is now open for the June 2023 Virtual FreeSurfer Course!''' [[https://education.martinos.org/freesurfer-tutorial-workshop/|Click here to register!]]

Computer verification deadline: '''May 22nd, 2023'''

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).

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== 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 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.

=== 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.

==== 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 ||


** optional talks

==== 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 ||
||9:55 - 11:05 ||[[http://surfer.nmr.mgh.harvard.edu/pub/docs/fsrecon.sep2022.pptx|Analyzing the Individual Subject]] ||talk ||Doug Greve ||
||11:05 - 11:25 ||'''20 minute break''' || || ||
||11:25 - 11:45 ||Freeview demonstration ||[[https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/FreeviewDemo|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''' ||||<style="text-align:center"> ||
||1:30 - 2:15 ||[[http://surfer.nmr.mgh.harvard.edu/pub/docs/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/Practice|Practice Working with Data]] or finish other tutorials ||tutorial ||staff ||




==== 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 ||[[https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/AnatomicalROIV6.0|Tutorial: ROI Analysis]] ||tutorial ||staff ||
||10:15 - 10:45 ||[[http://surfer.nmr.mgh.harvard.edu/pub/docs/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 ||[[https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/LongitudinalTutorial|Tutorial: LongitudinalTutorial]] ||tutorial ||staff ||
||12:35 - 1:35 ||'''Lunch''' ||||<style="text-align:center"> ||
||1:35 - 2:20 ||[[http://surfer.nmr.mgh.harvard.edu/pub/docs/multiplecomparisons.ppt|Corrections for Multiple Comparisons]] ||talk ||Doug Greve ||
||2:20 - 2:50 ||[[https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/MultipleComparisonsV6.0Perm|Tutorial: Corrections for Multiple Comparisons]] ||tutorial ||staff ||
||2:50 - 3:10 ||'''20 minute break''' || || ||
||3:10 - 3:55 ||[[http://surfer.nmr.mgh.harvard.edu/pub/docs/GLM.pptx|Group Analysis]] ||talk ||Doug Greve ||
||3:55 - 4:40 ||[[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 ||
||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 $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!''

==== 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 martinos dot org)

==== Cancellations, Refunds, and Deadlines ====
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.

Partial Refund Cancellation deadline: '''June 8th, 2023'''
  Computer verification deadline: '''May 22nd, 2023'''

=== FAQ ===
 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. '''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.

=== 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

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== Course Mailing List ==
'''SUBSCRIBE''':
  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]]).

'''UNSUBSCRIBE''':
  To unsubscribe from the course mailing list please click [[https://surfer.nmr.mgh.harvard.edu/cgi-bin/fsurfer/unsubscribe.cgi|here]].