| Deletions are marked like this. | Additions are marked like this. |
| Line 3: | Line 3: |
| = Upcoming FreeSurfer courses = | = Virtual FreeSurfer Course = |
| Line 17: | Line 17: |
| Additional details about the Virtual Course can be found [[http://surfer.nmr.mgh.harvard.edu/fswiki/CourseDescription#BostonCourseDetails|below]]. Information about international courses can be found on their respective websites. | Additional details about the Virtual Course can be found [[http://surfer.nmr.mgh.harvard.edu/fswiki/CourseDescription#CourseDetails|below]]. |
| Line 29: | Line 29: |
|
== Boston 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#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>> [[http://surfer.nmr.mgh.harvard.edu/fswiki/CourseDescription#LecturersandStaff|Lecturers and Staff]] <<BR>> [[http://surfer.nmr.mgh.harvard.edu/fswiki/CourseDescription#Accommodations|Accommodations]] <<BR>> [[http://surfer.nmr.mgh.harvard.edu/fswiki/CourseDescription#Directions|Directions]] <<BR>> [[http://surfer.nmr.mgh.harvard.edu/fswiki/CourseDescription#Parking|Parking]] <<BR>> [[http://surfer.nmr.mgh.harvard.edu/fswiki/CourseDescription#Map|Map of the Course Location]]''' |
== 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>> [[http://surfer.nmr.mgh.harvard.edu/fswiki/CourseDescription#LecturersandStaff|Lecturers and Staff]] <<BR>> ''' |
| Line 33: | Line 34: |
| The !FreeSurfer Development Team hosts a '''four-day, rigorous''' course for beginner and experienced users of !FreeSurfer. | The two day course consists of talks and tutorials that run throughout the day. Attendees are expected to attend all talks and tutorials. A VM package has been prepared to give attendees access to the tutorial data. |
| Line 35: | Line 36: |
| '''Day 1''' caters to beginners and will cover: |
=== Schedule === ==== Monday, September 12th - Introduction / Single Subject Analysis / ROI Analysis ==== ||'''Time''' ||'''Title''' ||'''Type''' ||'''Lecturer''' || ||8:30 - 8:40 ||** Intro to Linux for !FreeSurfer Users ||talk/demo || || ||8:40 - 9:00 ||** [[https://surfer.nmr.mgh.harvard.edu/fswiki/UnixTutorial|Unix for FreeSurfer Users]] ||tutorial || || ||9:00 - 9:15 ||** [[http://surfer.nmr.mgh.harvard.edu/pub/docs/fsjargon_clean.pptx|Intro to FreeSurfer Jargon]] || talk || || ||9:15 - 9:25 ||'''break''' || || || ||9:25 - 10:10 ||[[attachment:freesurfer.intro.apr.2019.ppt|Introduction to Freesurfer]] ||talk ||Bruce Fischl || ||10:10 - 11:20 ||[[http://surfer.nmr.mgh.harvard.edu/pub/docs/fsrecon.pptx|Analyzing the Individual Subject]] ||talk ||Doug Greve || ||11:20 - 11:40 ||'''break''' || || || ||11:40 - 12:00 ||[[https://www.youtube.com/watch?v=Mv-ECowxq2o|Freeview demonstration]] ||[[FsTutorial/FreeviewDemo|demo]] || || ||12:00 - 12:30 ||[[FsTutorial/OutputData_freeview|Introduction to FreeSurfer Output]] ||tutorial ||staff || ||12:30 - 1:30 ||'''Lunch''' |||||| ||1:30 - 1:45 ||[[FsTutorial/OutputData_freeview|Introduction to FreeSurfer Output]] ||tutorial ||staff || ||1:45 - 2:15 ||[[http://surfer.nmr.mgh.harvard.edu/pub/docs/fs.surface-based-analysis.ppt |Surface-based Analysis: Intersubject Registration & Smoothing ]] ||talk || Diyva Varadarajan || ||2:15 - 2:35 ||'''break''' || || || ||2:35 - 3:05 ||[[http://surfer.nmr.mgh.harvard.edu/pub/docs/fs.roi.EB_wiki.pptx|ROI Analysis]] ||talk || Doug Greve || ||3:05 - 3:50 ||[[FsTutorial/AnatomicalROIV6.0|ROI Analysis Tutorial]] ||tutorial ||staff || ||4:20 - 4:50 ||[[FsTutorial/Practice|Practice Working with Data]] ||tutorial ||staff || |
| Line 37: | Line 56: |
| . An introduction to !FreeSurfer <<BR>> Single Subject Surface-based analysis <<BR>> MRI Acquisition Tips <<BR>> ROI analysis <<BR>> |
==== Tuesday, September 13th - Group Analysis / Longitudinal Analysis / Troubleshooting ==== ||'''Time''' ||'''Title''' ||'''Type''' ||'''Lecturer''' || ||8:00 - 9:00 ||*** Morning Help Session|| || research technicians || ||9:00 - 9:45 ||[[http://surfer.nmr.mgh.harvard.edu/pub/docs/GLM.pptx|Group Analysis]] ||talk || || ||9:45 - 10:25 ||[[FsTutorial/GroupAnalysisV6.0|Group Analysis Tutorial]] ([[FsgdExamples|FSGD Examples]]) ||tutorial ||staff || ||10:25 - 10:45 ||'''break''' || || || ||10:45 - 11:30 ||[[http://surfer.nmr.mgh.harvard.edu/pub/docs/freesurfer.troubleshooting.apr2019.ppt|FreeSurfer Troubleshooting]] ||talk || || ||11:30 - 12:30 ||[[FsTutorial/TroubleshootingDataV6.0|Troubleshooting Tutorial]] ||tutorial ||staff || ||12:30 - 1:30 ||'''Lunch''' || || || ||1:30 - 2:15 ||[[https://youtu.be/AR83_Bt04VQ|Quality Checking a Recon]] || [[https://zoom.us/wc/join/369478461?pwd=|talk]] || || ||2:15 - 2:55 ||[[http://surfer.nmr.mgh.harvard.edu/pub/docs/multiplecomparisons.ppt|Multiple Comparisons]] ||talk ||Doug Greve|| ||2:55 - 3:25 ||[[FsTutorial/MultipleComparisonsV6.0Perm|Multiple Comparisons Tutorial]] ||tutorial ||staff || ||3:25 - 4:05 ||'''break''' || || || ||4:05 - 4:50 ||[[http://surfer.nmr.mgh.harvard.edu/pub/docs/fs.longitudinal.pptx|Longitudinal FreeSurfer]] ||talk ||Malte Hoffmann || ||4:50 - 5:30 || [[FsTutorial/LongitudinalTutorial|LongitudinalTutorial]] ||tutorial ||staff || ##||5:30 - 6:15 ||*** Optional time to work on tutorials / work on your own data / ask basic questions ||-- || staff|| |
| Line 39: | Line 73: |
|
'''Day 2''' will cover: . Group analysis <<BR>> Longitudinal analysis<<BR>> Troubleshooting '''Day 3''' will cover: . Multi-modal integration <<BR>> fMRI <<BR>> Diffusion '''Day 4''' will cover: . Multi-modal integration <<BR>> Future directions ##The four days will run roughly from '''9am-5pm''' with the last day ending early (~3pm). The four days consist of talks/tutorials that run all day, roughly from '''9am-5pm'''. There will be extra time to work on tutorials or data before 9am and after 5pm. Attendees are expected to attend all talks and tutorials aside from the ones scheduled as "optional". Attendees may opt out of either the fMRI or Diffusion lectures if it is not applicable to them. Laptops are provided with !FreeSurfer and the tutorial data already installed. Attendees will work in pairs (sharing a laptop). '''The schedule of talks and links to tutorials can be found [[http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial|here]].''' Please check back for updates. Additional topics and more detail on each topic is provided [[http://surfer.nmr.mgh.harvard.edu/fswiki/CourseDescription#CourseTopics|below]]. |
|
| Line 121: | Line 139: |
|
1. '''Do I get any credits for taking this course?''' * Nope, but we will give you a certificate to prove you took it. 1. '''Do you serve any food at the course?''' * There will be a continental breakfast each morning & coffee and some snacks supplied in the afternoon. There is also a cafeteria nearby where the course is held and two cafes 2-3 blocks from the building. |
|
| Line 129: | Line 143: |
|
1. '''Can I bring my own laptop to work on instead of sharing with someone else? ''' * If any issues arise during the tutorial sessions which are unique to your laptop, we will not be able to troubleshoot those issues for you (it takes staff away from answering general tutorial questions). We strongly discourage using your own laptop instead of the ones we provide. If you insist on working on your laptop, please thoroughly test your installation ahead of time - guidelines for this can be found on the TestingFreeSurfer wiki. It might also be a good idea to try to run all the commands in the tutorials ([[https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial|here]]). 1. '''How far is the airport from the course location? ''' * About 20 minutes by taxi and 1 hour by public transportation (there are several transfers). The taxi will cost $20-$25. Public transportation will cost under $3. 1. '''Would it work if I scheduled a flight for the evening of the 3rd or 4th day of the class?''' * Certainly. You can bring your luggage to the room where the course is held and leave straight from there. Traffic can be bad after 3pm, so you may need 45 minutes to an hour to get to the airport. To attend all the talks on the 3rd day, your flight will need to be 8pm or later. |
|
| Line 136: | Line 144: |
|
## 1. '''I can only pay for the course with credit card so that I can be reimbursed later. Is this okay?''' ## * Sorry, we have not found a way to be able to accept credit cards. Payment must be by check or cash. |
|
| Line 171: | Line 178: |
|
* '''Basics of fMRI Analysis''' * Covers the basics of functional MRI data analysis, spanning preprocessing to single-subject and group-level analyses. Topics include motion correction, B0 distortion correction, spatial normalization, spatial smoothing, hemodynamic modeling, GLM analysis, contrasts and hypothesis testing, and Random-, Fixed-, and Mixed-Effects group analyses. * '''FS-FAST''' * Preprocessing of fMRI (motion correction, slice-timing correction, smoothing, registration to the anatomical, sampling to the common group space in the surface and volume), setting up and running block and event-related analysis, adding nuisance variables to the analysis, performing the individual fMRI time series fMRI analysis, performing group fMRI analysis in the volume and on the surface. * '''Diffusion Data Processing and TRACULA talks and tutorial''' * How to process diffusion MRI data to extract basic diffusion measures and to reconstruct white-matter pathways using !FreeSurfer's tractography tool. * '''Motion-compensated neuroanatomical imaging (optional)''' * While real-time fMRI motion correction has been available with some MRI scanners for years (e.g. Siemens' PACE), effective real-time motion correction in neuroanatomical imaging is just now becoming available. This talk focuses on the motion-correction system we have developed for the Siemens platform, but also discusses the current developments on the GE platform. * '''MRI Acquisition Methods for Morphometry (optional)''' * A description of how using different scan protocols can affect data quality and !FreeSurfer reconstruction. * '''Registration Methods (optional)''' * Overview of different registration methods discussed so far (flirt, robust_register, bbregister) and introduction of a new registration tool, CVS (combined volume and surface registration). * '''Longitudinal Analysis in !FreeSurfer''' * How to process longitudinal data with !FreeSurfer and what's going on behind the scenes. * '''Future Directions of !FreeSurfer''' * Inferring architectonic boundaries from in-vivo MRI - Bruce Fischl * Techniques for inferring the location of architectonic features in the brain in vivo |
Virtual FreeSurfer Course
The next virtual FreeSurfer course is scheduled for September 12-13th, 2022. The payment deadline is September 6, 2022. Note: As long as there are empty spots in the course, we will accept late registrations. If you register after the payment deadline has passed, payment is due immediately.
Registration is not yet open. This page will be updated once registration has opened.
This is a two day course that offers a basic introduction to FreeSurfer. Review the tentative schedule below before registering.
General Information
Additional details about the Virtual Course can be found below.
If you have a specific question about the FreeSurfer courses that was not answered by our 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).
Course Mailing List
SUBSCRIBE:
If you are interested in being notified about future course offerings, sign up for our mailing list (here).
UNSUBSCRIBE:
To unsubscribe from the course mailing list please click here.
Course Details
Click on any of the topics below for more information:
Overview
Schedule
Payment
FAQ
Topics Covered During the Course
Lecturers and Staff
Overview
The two day course consists of talks and tutorials that run throughout the day. Attendees are expected to attend all talks and tutorials. A VM package has been prepared to give attendees access to the tutorial data.
Schedule
Monday, September 12th - Introduction / Single Subject Analysis / ROI Analysis
Time |
Title |
Type |
Lecturer |
8:30 - 8:40 |
** Intro to Linux for FreeSurfer Users |
talk/demo |
|
8:40 - 9:00 |
tutorial |
|
|
9:00 - 9:15 |
talk |
|
|
9:15 - 9:25 |
break |
|
|
9:25 - 10:10 |
talk |
Bruce Fischl |
|
10:10 - 11:20 |
talk |
Doug Greve |
|
11:20 - 11:40 |
break |
|
|
11:40 - 12:00 |
|
||
12:00 - 12:30 |
tutorial |
staff |
|
12:30 - 1:30 |
Lunch |
||
1:30 - 1:45 |
tutorial |
staff |
|
1:45 - 2:15 |
Surface-based Analysis: Intersubject Registration & Smoothing |
talk |
Diyva Varadarajan |
2:15 - 2:35 |
break |
|
|
2:35 - 3:05 |
talk |
Doug Greve |
|
3:05 - 3:50 |
tutorial |
staff |
|
4:20 - 4:50 |
tutorial |
staff |
|
Tuesday, September 13th - Group Analysis / Longitudinal Analysis / Troubleshooting
Time |
Title |
Type |
Lecturer |
8:00 - 9:00 |
*** Morning Help Session |
|
research technicians |
9:00 - 9:45 |
talk |
|
|
9:45 - 10:25 |
tutorial |
staff |
|
10:25 - 10:45 |
break |
|
|
10:45 - 11:30 |
talk |
|
|
11:30 - 12:30 |
tutorial |
staff |
|
12:30 - 1:30 |
Lunch |
|
|
1:30 - 2:15 |
|
||
2:15 - 2:55 |
talk |
Doug Greve |
|
2:55 - 3:25 |
tutorial |
staff |
|
3:25 - 4:05 |
break |
|
|
4:05 - 4:50 |
talk |
Malte Hoffmann |
|
4:50 - 5:30 |
tutorial |
staff |
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!
Deadlines & Accepted Payment Types
Payment Coordinator/Contact: Stacey Ladieu (sladieu at martinos dot org)
Payment deadline: September 6, 2022
Accepted Payment types: credit card, cash, or institutional check (see sections below for details on each)
As long as there are empty spots in the course, we will accept late registrations (regardless of the payment deadline). If you register after the payment deadline has passed, payment is due immediately. Payment and all questions about payment should sent to Stacey.
Credit Cards
Please use the website below to make a payment via credit card.
Choose the box with the payment fee that applies to you: 2022 Virtual FreeSurfer Course OR 2022 Virtual FreeSurfer Course STUDENT FEE
Select the correct quantity of registrations and 'Add to cart'. Select 'View Cart' and then 'Proceed to Checkout'. Enter your billing address and click continue, then enter your credit card details. Please contact Stacey (sladieu@mgh.harvard.edu) and CC the course organizer's email (freesurferlab@gmail.com) if there are any issues.
Click here to pay by Credit Card
Checks
For those sending an institutional check, we understand these can take some time to produce. Please have your financial institution contact our payment coordinator, Stacey Ladieu, to confirm a check is being issued prior to the payment deadline.
Make checks payable to: Massachusetts General Hospital
Mail checks to this address:
Stacey Ladieu
Athinoula A. Martinos Center for Biomedical Imaging
149 Thirteenth Street - Room 2301
Charlestown, MA 02129
Please be sure the name of the person taking the course is listed on the check.
Cash
There are two options for paying by cash:
- Make an appointment with Allison Stevens (astevens at martinos dot org) to deliver cash in person
- Contact Stacey (sladieu at martinos dot org) to send cash via Western Union or Moneygram. The transfer must be made out to Stacey Ladieu.
Missed Deadlines & Cancellations
If payment has not been received by the payment deadline or in the case of an institutional check, your institution has not contacted Stacey Ladieu with details of their payment arrangement by that date, your spot will be opened to the waiting list. There is no need to contact us to check whether your payment has gone through - your spot is safe unless we contact you.
Course fees are refundable up to the payment deadline. A $300 fee will be deducted, should you request a refund up to 2 weeks prior to the program.
FAQ's
How many individuals are accepted into the Virtual course?
- 20 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 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.
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.
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 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.
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.
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 Allison or Emma prior to the course, they can try to arrange some help.
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.
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.
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
Lecturers and Staff
- Bruce Fischl
- Doug Greve
- Andre van der Kouwe
- Allison Stevens
- Anastasia Yendiki
- Caroline Magnain
- Lilla Zollei
- David Salat
- Iman Aganj
- Paul Wighton
- Robert Frost
- Leah Morgan
- Andrew Hoopes
- Matthew Vera
- Devani Cordero
- Jonathan Polimeni
- Malte Hoffmann