FreeSurfer Tutorial and Workshop
Course Policies |
Getting the tutorial data |
Please DO NOT try to download the tutorial data during the course! We have copies of this data stored on servers located in the course room. Attempting to download this data from the public link (this link) during the course presents excessive and unnecessary load on our network, and likely will fail due to this load. Please contact a staff member for help in getting this data if needed outside of the course. |
Wifi
You may connect to any of the following wifi networks in the classroom area (all networks use the same password):
Name: nmrclass1_wifi_2.4Ghz, nmrclass1_wifi_5Ghz, lcn_guest2, lcn_guest5
Password: brain.map
About the Course
The FreeSurfer tools deal with two main types of data: volumetric data (volumes of voxels) and surface data (polygons that tile a surface). The talks and tutorials should familiarize you with FreeSurfer's volume and surface processing streams. The tutorials also describe some of FreeSurfer's tools for registering volumetric datasets, performing group analysis on morphology data, and integrating multi-modal output with FreeSurfer (overlaying color-coded parametric maps onto the cortical surface and visualizing plotted results).
Note: 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
Tip for Mac users: 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 MacCommands.
Online Question Forum |
Videos of Lectures |
Throughout the course, you may post questions here (anonymously or not). |
You can find videos of the lectures here. |
Course Schedule
FreeSurfer Course, April 1-4, 2019
Our awesome FreeSurfer shirts can be purchased here.
8:00 - 9:30am Registration Desk Open
* Indicates an optional technical talk. These talks have great content. They are related to, but not directly about, the FreeSurfer processing stream.
** Indicates an optional talk that covers basic/beginner material.
*** Indicates optional extra time to work on tutorials and/or ask questions about your own data.
Monday, April 1st - Introduction / Single Subject Analysis / ROI Analysis
Time |
Title |
Type |
Lecturer |
8:30 - 9:00 |
talk/demo |
Andrew Hoopes |
|
9:00 - 9:15 |
talk |
Caroline Magnain |
|
9:15 - 9:30 |
break |
|
|
9:30 - 10:15 |
talk |
Bruce Fischl |
|
10:15 - 11:25 |
talk |
Doug Greve |
|
11:25 - 11:45 |
break |
|
|
11:45 - 12:00 |
Bram Diamond |
||
12:00 - 12:30 |
tutorial |
||
12:30 - 1:30 |
-- |
-- |
|
1:30 - 1:45 |
tutorial |
||
1:45 - 2:15 |
Surface-based Analysis: Intersubject Registration & Smoothing |
talk |
Iman Aganj |
2:15 - 2:35 |
break |
|
|
2:35 - 3:05 |
talk |
Emma Boyd |
|
3:05 - 3:50 |
tutorial |
staff |
|
3:50 - 4:20 |
talk |
David Salat |
|
4:20 - 4:50 |
tutorial |
staff |
Answers to online questions here
Tuesday, April 2nd - Group Analysis / Longitudinal Analysis / Troubleshooting
Time |
Title |
Type |
Lecturer |
8:00 - 9:00 |
*** Optional session, extra support for structural processing and ROI analysis |
-- |
Research Techs |
9:00 - 9:50 |
talk |
Viviana Siless |
|
9:50 - 10:30 |
tutorial |
staff |
|
10:30 - 10:50 |
break |
|
|
10:50 - 11:30 |
talk |
Doug Greve |
|
11:30 - 12:00 |
tutorial |
staff |
|
12:00 - 1:00 |
Lunch |
-- |
-- |
1:00 - 1:45 |
talk |
Bruce Fischl |
|
1:45 - 2:45 |
tutorial |
staff |
|
2:45 - 3:05 |
break |
|
|
3:05 - 4:05 |
demo |
Leah Morgan, Allison Stevens |
|
4:05 - 4:50 |
talk |
Malte Hoffmann |
|
4:50 - 5:30 |
tutorial |
staff |
|
5:30 - 7:30 |
Social Night in the atrium of Bldg. 149 |
Snacks and Beverages Served |
you! |
Answers to online questions here
Wednesday, April 3rd - Multimodal Analysis / Diffusion Analysis / fMRI Analysis / MR Acquisition
Time |
Title |
Type |
Lecturer |
8:00 - 9:00 |
*** Optional session, extra support for questions on longitudinal processing and working with pediatric data |
-- |
Lilla Zöllei, other staff |
9:00 - 9:30 |
** Intro to MR (SpinBench) |
talk |
Robert Frost |
9:30 - 10:00 |
talk |
Aina Frau-Pascual |
|
10:00 - 10:30 |
tutorial |
staff |
|
10:30 - 10:50 |
break |
|
|
10:50 - 11:05 |
talk |
Robert Frost |
|
11:05 - 11:45 |
talk |
Anastasia Yendiki |
|
11:45 - 12:30 |
tutorial |
staff |
|
12:30 - 1:30 |
Lunch |
-- |
-- |
1:30 - 2:20 |
talk |
Anastasia Yendiki |
|
2:20 - 3:20 |
tutorial |
staff |
|
3:20 - 3:40 |
break |
|
|
3:40 - 3:50 |
talk |
Anastasia Yendiki |
|
3:50 - 4:50 |
talk |
Jingyuan Chen |
|
4:50 - 5:30 |
talk |
Paul Wighton |
Answers to online questions here
The FreeSurfer Evaluation is here!
Thursday, April 4th - fMRI Analysis / Multimodal Analysis / Future Directions
Time |
Title |
Type |
Lecturer |
8:00 - 9:00 |
*** Optional session, extra support for fMRI and Diffusion Questions |
-- |
staff |
9:00 - 9:30 |
talk |
Doug Greve |
|
9:30 - 10:00 |
tutorial |
staff |
|
10:00 - 10:20 |
break & Evaluation |
|
|
10:20 - 11:20 |
talk |
Doug Greve |
|
11:20 - 12:00 |
tutorial |
staff |
|
12:00 - 1:00 |
Lunch |
-- |
-- |
1:00 - 1:30 |
talk |
Lilla Zöllei |
|
1:30 - 1:45 |
talk |
Doug Greve |
|
1:45 - 2:15 |
talk |
Doug Greve |
|
2:15 - 3:00 |
tutorial |
staff |
|
3:00 - 3:15 |
break |
|
|
3:15 - 3:30 |
talk |
Doug Greve |
|
3:30 - 4:30 |
Future Directions |
talk |
FS Development Team |
4:30 - 5:00 |
Question & Answer Session |
-- |
staff |
Answers to online questions here
* Indicates an optional technical talk. These talks have great content. They are related to, but not directly about, the FreeSurfer processing stream.
** Indicates an optional talk covering basic/beginner material. *** Optional sessions are a time where you can work on finishing tutorials / work on your own data / ask basic questions in the presence of a few staff members
Additional Useful Information
During the Course
Getting the tutorial data (necessary only if you are not taking a formal course where data is provided) DO NOT attempt this during a course! Contact a staff member for instructions on how to get this data locally during the course.
Using a Mac & need a text editor? Download gedit, here.
Some basic information on text editors can be found here.
Taxi phone numbers can be found here.
After the Course
Home page: http://surfer.nmr.mgh.harvard.edu
A full list of all FreeSurfer tutorials, including ones that may not have been included at this course
How to cite FreeSurfer is on the FreeSurferMethodsCitation page.
iSurf - iPhone/iPad app to view FreeSurfer segmentations