= Virtual FreeSurfer Course =
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.



'''Registration is now FULL for the Fall 2022 Virtual  [[https://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurfer|FreeSurfer]] Course!'''

Cancellation deadline: '''August 31st, 2022'''
  Computer verification deadline: '''September 7th, 2022'''

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#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.

During  the tutorial sessions, you will be shown a variety of commands.  Only  those that appear in a box should be copy-and-pasted into the terminal.  They will look like this:

{{{
command arg1 arg2
}}}


=== Schedule ===

==== Wednesday, September 14th - Introduction / Single Subject Analysis / Troubleshooting ====
||'''Time''' ||'''Title''' ||'''Type''' ||'''Lecturer''' ||
||9:00 - 9:15 ||'''Welcome (for optional talks)''' ||social ||staff ||
||9:15 - 9:45 ||** Intro to Linux for FreeSurfer Users ||talk/demo ||Jackson Nolan ||
||9:45 - 10:00 ||** [[http://surfer.nmr.mgh.harvard.edu/pub/docs/fsjargon_clean.pptx|Intro to FreeSurfer Jargon]] ||talk ||Allison Player & Lilla Zollei ||
||10:00 - 10:10 ||'''Welcome/10 minute break''' || || ||
||10:10 - 10:55 ||[[http://surfer.nmr.mgh.harvard.edu/pub/docs/freesurfer.intro.sep.2022.pptx|Introduction to Freesurfer]] ||talk ||Bruce Fischl ||
||10:55 - 12:05 ||[[http://surfer.nmr.mgh.harvard.edu/pub/docs/fsrecon.sep2022.pptx|Analyzing the Individual Subject]] ||talk ||Doug Greve ||
||12:05 - 12:10 ||'''5 minute break''' || || ||
||12:10 - 12:15 ||[[https://www.youtube.com/watch?v=Mv-ECowxq2o|Freeview demonstration]] ||[[https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/FreeviewDemo|demo]] ||Devani Cordero ||
||12:15 - 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 - 1:45 ||[[https://www.youtube.com/watch?v=Mv-ECowxq2o|Continued: Freeview demonstration]] ||[[https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/FreeviewDemo|demo]] ||Devani Cordero ||
||1:45 - 2:15 ||[[https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/OutputData_freeview|Continue Tutorial: Individual Subject Output]] ||tutorial ||staff ||
||2:15 - 3:00 ||[[http://surfer.nmr.mgh.harvard.edu/pub/docs/freesurfer.troubleshooting.sep2022.ppt|FreeSurfer Troubleshooting]] ||talk ||Doug Greve ||
||3:00 - 3:15 ||'''15 minute break''' || || ||
||3:15 - 4:15 ||[[https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TroubleshootingDataV6.0|Tutorial: Troubleshooting Freesurfer]] ||tutorial ||staff ||
||4:15 - 5:00 ||Quality Checking a Recon ||talk ||Nathan Draudt ||


** optional talks

==== Thursday, September 15th - 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 ||Doug Greve ||
||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 - 11:00 ||'''15 minute break''' || || ||
||11:00 - 11:45 ||[[http://surfer.nmr.mgh.harvard.edu/pub/docs/GLM.pptx|Group Analysis]] ||talk ||Doug Greve ||
||11:45 - 12:30 ||[[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 ||
||12:30 - 1:30 ||'''Lunch''' ||||<style="text-align: center"> ||
||1:30 - 2:15 ||[[http://surfer.nmr.mgh.harvard.edu/pub/docs/multiplecomparisons.ppt|Corrections for Multiple Comparisons]] ||talk ||Doug Greve ||
||2:15 - 2:45 ||Tutorial: Corrections for Multiple Comparisons ||tutorial ||staff ||
||2:45 - 3:00 ||'''15 minute break''' || || ||
||3:00 - 3:45 ||[[http://surfer.nmr.mgh.harvard.edu/pub/docs/fs.longitudinal.pptx|Longitudinal FreeSurfer]] ||talk ||Malte Hoffmann ||
||3:45 - 4:25 ||[[https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/LongitudinalTutorial|Tutorial: LongitudinalTutorial]] ||tutorial ||staff ||
||4:25 - 4:45 ||Q&A with [[https://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurfer|FreeSurfer]] Team ||talk ||Bruce Fischl ||




=== 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 $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!''

==== 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 $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.

Cancellation deadline: '''August 31st, 2022'''
  Computer verification deadline: '''September 7th, 2022'''

=== FAQ ===
 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 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]].