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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 2-5, 2018
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 extra time to work on tutorials and/or ask questions about your own data.
Monday, April 2nd - Introduction / Single Subject Analysis / ROI Analysis
Time |
Title |
Type |
Lecturer |
8:30 - 9:00 |
talk/demo |
Leah Morgan |
|
9:00 - 9:15 |
talk |
Morgan Fogarty & 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 |
Freeview demonstration |
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 3rd - Group Analysis / Longitudinal Analysis / Troubleshooting
Time |
Title |
Type |
Lecturer |
8:00 - 9:00 |
*** Optional time to work on tutorials / work on your own data / ask basic questions |
-- |
Emma Boyd |
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 |
Quality Checking a Recon |
demo |
Allison Stevens |
4:05 - 4:50 |
talk |
Paul Wighton |
|
4:50 - 5:30 |
tutorial |
staff |
|
5:30 - 6:15 |
*** Optional time to work on tutorials / work on your own data / ask basic questions |
-- |
Emma Boyd |
6:30 - ? |
Boston Beer Works |
social activity |
you! |
Answers to online questions here
Boston Beer Works location information here and here.
Meet us in front of Building 149 to catch the 6:30pm shuttle bus (it leaves on time!).
If you miss us, we are taking the MGH/Navy Yard shuttle to North Station. From there, cross the street to get to Canal Street.
Boston Beer Works will be down that street, on your right. (Shuttles depart every 15 minutes up until 7:15pm and every half hour after that).
Wednesday, April 4th - Multimodal Analysis / Diffusion Analysis / fMRI Analysis / MR Acquisition
Time |
Title |
Type |
Lecturer |
8:00 - 9:00 |
*** Optional time to work on tutorials / work on your own data / ask basic questions |
-- |
Emma Boyd |
9:00 - 9:30 |
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 |
Isik Karahanoglu |
|
4:50 - 5:50 |
*** Optional time to work on tutorials / work on your own data / ask basic questions |
-- |
Emma Boyd |
Answers to online questions here
The FreeSurfer Evaluation is here!
Thursday, April 5th - fMRI Analysis / Multimodal Analysis / Future Directions
Time |
Title |
Type |
Lecturer |
8:00 - 9:00 |
*** Optional time to work on tutorials / work on your own data / ask basic questions |
-- |
Emma Boyd |
9:00 - 9:30 |
talk |
Isik Karahanoglu |
|
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 |
Iman Aganj |
|
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 - 3:45 |
talk |
Doug Greve |
|
3:45 - 4:30 |
Future Directions |
talk |
Bruce Fischl |
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.
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