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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. |
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
Multimodal Short Course, FreeSurfer/FS-FAST, April 30 & May 1, 2015
MGH- Charlestown Navy Yard
Thursday, April 30 - Introduction / Single Subject / Troubleshooting
Time |
Title |
Type |
Lecturer |
2:00 - 2:30 |
talk |
Doug Greve |
|
2:30 - 3:40 |
talk |
Doug Greve |
|
3:40 - 4:00 |
break |
|
|
4:00 - 4:20 |
Freeview demonstration |
demo |
Allison Moreau |
4:20 - 5:00 |
tutorial |
staff |
|
5:00 - 5:30 |
talk |
Allison Moreau |
|
5:30 - 6:00 |
tutorial |
staff |
Friday, May 1 - Surface-based Smoothing and Registration / Group Analysis / FS-FAST
Time |
Title |
Type |
Lecturer |
9:00 - 9:40 |
talk |
Doug Greve |
|
9:40 - 10:20 |
talk |
Martin Reuter |
|
10:20 - 10:35 |
break |
|
|
10:35 - 10:55 |
talk |
Martin Reuter |
|
10:55 - 11:15 |
QDEC demonstration |
demo |
Martin Reuter |
11:15 - 12:00 |
tutorial |
staff |
|
12:00 - 12:45 |
tutorial |
staff |
|
12:45 - 2:00 |
lunch |
|
|
2:00 - 3:15 |
talk |
Doug Greve |
|
3:15 - 4:00 |
talk |
Doug Greve |
|
4:00 - 4:15 |
break |
|
|
4:15 - 5:00 |
talk |
Doug Greve |
|
5:00 - 6:00 |
tutorial |
staff |
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.
After the Course
Home page: http://surfer.nmr.mgh.harvard.edu
Mailing list: send mail to majordomo@surfer.nmr.mgh.harvard.edu with the following command in the body of your email message: subscribe freesurfer
How to cite FreeSurfer is on the FreeSurferMethodsCitation page.
iSurf - iPhone/iPad app to view FreeSurfer segmentations
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.
After the Course
Home page: http://surfer.nmr.mgh.harvard.edu
Mailing list: send mail to majordomo@surfer.nmr.mgh.harvard.edu with the following command in the body of your email message: subscribe freesurfer
How to cite FreeSurfer is on the FreeSurferMethodsCitation page.
iSurf - iPhone/iPad app to view FreeSurfer segmentations