Upcoming FreeSurfer Workshops

Next Boston course?

We are currently making plans for the next Boston course to occur in April 2013. To be notified of the final dates and when registration opens, sign up for the course mailing list.

Course Mailing List

If you are interested in being notified about future course offerings, sign up for our mailing list (here).
If you have a specific question about the FreeSurfer courses or would like to host one in your area, you can email Allison Stevens (astevens at nmr dot mgh dot harvard dot edu) who organizes the courses.

Information about previous courses can be found below:

Boston Course Overview

The FreeSurfer Development Team hosts a three-day course for beginner and experienced users of FreeSurfer.

Day 1 will cover:

• An introduction to FreeSurfer
  Surface-based analysis
  Troubleshooting
  

Day 2 will cover:

• ROI analysis
  Longitudinal analysis
  Multi-modal integration
  Group analysis
  

Day 3 will cover:

• Functional analysis
  Diffusion processing

The three days will run roughly from 8am-6pm. Laptops are provided with FreeSurfer and the tutorial data already installed. Attendees will work in pairs (sharing a laptop). The most recent Boston course schedule can be found here. Please check back for updates.

Additional topics and more detail on each topic is provided below.

Boston Course Details

Click on any of the topics below for more information:
Payment
FAQ
Topics Covered During the Course
Lecturers and Staff
Accommodations
Directions
Parking
Map of the Course Location

Payment

The fee for the course is $650. A reduced rate of $450 is available to graduate students. MDs, PhDs, and post-docs do not qualify for the graduate student rate!
Payment is due immediately upon registration. Payment and all questions about payment should go to Stacey Ladieu (sladieu at nmr dot mgh dot harvard dot edu).

Check and cash are the only forms of accepted payment.
Credit cards are not accepted.

Make checks payable to: Massachusetts General Hospital

Mail checks to:
Stacey Ladieu
Athinoula A. Martinos Center for Biomedical Imaging
149 Thirteenth Street - Room 2301
Charlestown, MA 02129

Please be sure the NAME OF PARTICIPANT is listed on the check.

If payment has not been received by February 13, 2012 or your institution has not contacted Stacey Ladieu (sladieu at nmr dot mgh dot harvard dot edu) with details of their payment arrangement by that date (in the case of an institutional check), 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 $200 fee will be deducted, should you request a refund up to 2 weeks prior to the program. After that, the tuition can be applied to a future program or you can send someone in your place. In the case there are less than 10 registrants for the course, the course will be cancelled and the registration fee will be refunded to the registrant.

FAQ

1. Do postdocs qualify for the student rate?

   • No, sorry.

2. Is there a discount for MGH or Martinos Center employees?

   • Sorry, no.

3. 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.

4. I cannot pay by check and you don't accept credit card. Do I have any other options?

   • If you are local, you may bring a cash payment to Allison Player (astevens at nmr dot mgh dot harvard dot edu) before the deadline. If you are not local, services like Western Union and Moneygram are a possibility in extreme cases. Please contact Allison for details.

5. 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.

6. 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.

7. Can I get a receipt for the course?

   • Sure! Receipts will be available on the last day of the course.

8. How do I know if my payment went through?

   • If it hasn't we will contact you.

9. Do I get any credits for taking this course?

   • Nope, but we will give you a certificate to prove you took it.

10. Do you serve any food at the course?

    • There will be a continental breakfast each morning and coffee supplied in the afternoon. There is also a cafeteria in the building where the course is held and two cafes 1-2 blocks from the building.

11. I have some data I would like to get your opinion on. Can I show it to you?

    • Sure! But please do so during the optional "process your own data" session on the first day or during breaks, not during the tutorial sessions. Questions about the tutorial currently being worked on will have to take priority over personal data questions.

12. 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.

13. Can I bring my own laptop to work on instead of sharing with someone else?

    • Unless you have made arrangements with Allison to share your laptop at the course, we strongly discourage using your own laptop instead of the ones we provide. 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). Problems with the FreeSurfer installation on your laptop can be worked out during the optional installation session at the end of the first day. 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 (here).

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 Unix is necessary to run and work with FreeSurfer.

Day 1: Introduction / Single Subject / Registration / Troubleshooting

• Unix Tutorial (optional)

  • This unix 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 UNIX, 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 UNIX 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.

• Surface-based Smoothing/Surface-based Registration

  • Volume vs. Surface-based analysis

• 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.

• 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.

• FreeSurfer Installation on Personal Laptops (optional)

  • Help with the installation of FreeSurfer on your personal laptop. Downloading the software ahead of time is recommended.

• Start Processing Your Own Data (optional)

  • Guidance on how to run a recon on your own subject data. Please come with FreeSurfer installed on your laptop and with data you would like to process.

Day 2: ROIs / Longitudinal / Multimodal / Group 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.

• MRI Acquisition Methods for Morphometry (optional)

  • A description of how using different scan protocols can affect data quality and FreeSurfer reconstruction.

• Longitudinal Analysis in FreeSurfer

  • How to process longitudinal data with FreeSurfer and what's going on behind the scenes.

• Multi-Modal Integration - Talk and Tutorial

  • Introduction on how FreeSurfer output can be used with other modalities (i.e. fMRI data, diffusion data)

• Registration Methods

  • 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).

Day 3: fMRI / Diffusion / Q&A

• 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.

• FSFAST

  • 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.

• 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.

• 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 new tractography tool.

• 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

• Question and Answer Session

  • Open forum to resolve any unanswered questions

Lecturers and Staff

• Bruce Fischl
• Doug Greve
• Andre van der Kouwe
• Martin Reuter
• David Salat
• Nick Schmansky
• Allison Stevens Player
• Krish Subramaniam
• Dylan Tisdall
• Anastasia Yendiki
• Lilla Zollei
• Sita Kakunoori
• Michelle Roy
• Louis Vinke
• Priti Srinivasan
• Juan Eugenio Iglesias
• Jonathan Polimeni
• Emma Ben-Avi
• Melanie Ganz

Accommodations

We encourage attendees to stay at either of these two locations:

• The Constitution Inn is located adjacent to our research building in Charlestown. Rooms at the Inn are simple and relatively inexpensive. The proximity of this accommodation was found to be a major benefit for other NMR Center course attendees. The facility was recently renovated and guests can use the health club and pool. The Inn has free wireless internet access. To reserve a room at the Constitution Inn, call (617) 241-8400, or visit them on the web at www.constitutioninn.org.
  

A block of rooms are reserved at $109/night. To request this block, ask for the 'MGH Freesurfer' block. Only 20 rooms are available and the deadline for reserving a room at this price is March 2, 2012 by 5pm EST.

• Marriott Residence Inn at Tudor Wharf, a short walk through the Navy Yard to the classroom. The MGH/Partners shuttle bus also has a stop just steps from the hotel, at Gate 1, and it runs every 15 minutes during the day, and every half an hour in the evening. The hotel is a new all-suite hotel that offers complimentary high-speed and wireless internet access and a complimentary breakfast buffet daily.

You can get a discounted rate of $199/night for a studio - speak to the hotel directly and ask for the Partners Healthcare Rate.

To get to Downtown Boston from Charlestown you can take the shuttle (it runs every 15 minutes during the day on weekends), the water shuttle, or the #93 bus. Shuttle bus stops are marked on the Map at the end of this page.

Directions

The FreeSurfer Course is being held at the Martinos Center for Biomedical Imaging in Boston. Here is a map:

• Building 114, Conference Room D1
  114 Sixteenth Street
  Charlestown Navy Yard (CNY)
  Charlestown, MA 02129-2020

When you enter Building 114, take the door on your left.

Map

Public Transportation & Shuttle

If you are coming via the train (aka the T), there is a free Partners shuttle bus that picks you up at the North Station T stop (across from TD Banknorth Garden) and will take you to the course location in the Navy Yard. The shuttle schedule can be found here here under "MGH Main Campus, North Station, One Constitution Road, Charlestown Navy Yard". (Note: There is a second schedule in the list with a similar name but without "One Constitution Road" in the title. This is the Saturday/Sunday schedule. Be sure to choose the schedule that corresponds to the date you are traveling.)

From inside the train station, exit North Station to the Causeway Street exit. The shuttle stops right outside of the T stop in front of the CVS (where the man is standingin this picture prior to the CVS being built). The shuttle comes every 15 minutes during the day (after 7pm, it comes every half hour and stops around 1am). It will arrive at North Station approximately 5 minutes after the time listed on the schedule under "Arrive/Depart MGH Main Campus". The shuttle stops right in front of Building 114 (the third stop after you board at North Station). Please see the map above for the shuttle bus stop and building location.

Let security know you are there for the FreeSurfer Course in Conference room D1 and they will direct you to the location.

Parking

Parking near the Center is difficult to get and is either metered (with a 2 hour limit) or expensive ($20+/day for a garage). We get discounted parking ($5 for 24 hours) at the parking garage on 5th Avenue (please see the map above for the location).

If you would like to park in the garage at this discounted rate, take a ticket when you enter the garage and bring this ticket with you to the course. During the Course Registration, you can purchase the discounted parking sticker to put on your ticket. You will have to pay us in cash or by check (made out to MGH) to receive the parking validation sticker(s).

This is very *important*: we cannot wait for checks to be processed by your institution, university, etc. for the price of the parking. You will have to have payment ready at the course to receive the parking validation. Please notify the Registration desk if you need a receipt for parking.

How to determine how many stickers you need: Each parking sticker is good for 24 consecutive hours of parking. Once you park in the garage, you cannot take your car out without needing an additional sticker to pay for your re-entry.

For example, if you drive in the first day of the course and leave the garage at the end of the day, repeating this for all 3 course days - you will need 3 parking stickers to pay for those 3 days. If you are parking in the garage on Sunday evening at 6pm and take your car out at 8am on Thursday (86 hours), you will need 4 stickers (86/24 = 3.58 round up to 4 stickers to pay for the 3.5 days).

Directions from Parking Garage

As can be seen on the map above, the parking garage has two exits. The exit at the back of the garage takes you to 16th Street and is closest to Building 114, however, it consists only of stairs. The exit farthest from Building 114 has elevators. If you would prefer to take an elevator, take it to the 1st floor. From there, go out the double doors and make a right. Take another right at the corner onto 5th Avenue. Cross the street at the crosswalk and in front of you will be the entrance to Building 114.