Contents
FreeSurfer Tutorial and Workshop
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 recommended workflow to execute these, and many of their component tools. 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). After completing the tutorials, you should be able to:
- perform surface reconstructions;
- generate subcortical segmentations;
- fix errors encountered during the volume or surface processing;
- overlay functional data onto surfaces;
- perform group analysis of structural (e.g. thickness) and functional data.
Note: During the tutorial sessions, you will be shown a variety of command strings on the tutorial wiki pages. Only those that appear between lines should be copy-and-pasted into the terminal for this tutorial. Those commands appear like this:
command arg1 arg2
Laptop damage policy: If liquid is spilled on a provided laptop, then you are liable for payment of the repair costs!
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.
Question / Suggestion Box
During the course, if you have questions or suggestions, please follow this link to submit them (anonymously, or not). We will process them during the course and give feedback at the end.
Course Schedule
FreeSurfer Course, April 29 - May 1, 2013
MGH, Charlestown Navy Yard, Building 114, Room D1
Fill out the Course evaluation here!!!
Monday, April 29th - Introduction / Single Subject / Registration / Troubleshooting
Time |
Title |
Type |
Lecturer |
8:00 - 8:30 |
optional - Unix Tutorial for FreeSurfer Users |
tutorial |
Maritza Ebling |
8:30 - 9:00 |
optional - Intro to FreeSurfer Jargon |
talk |
Melanie Ganz |
8:30 - 9:00 |
Course Registration |
sign-in |
|
9:00 - 9:30 |
talk |
Doug Greve |
|
9:30 - 10:30 |
talk |
Doug Greve |
|
10:30 - 10:50 |
break |
|
|
10:50 - 11:10 |
Freeview/Tksurfer demonstration |
demo |
Doug Greve |
11:10 - 11:40 |
tutorial |
staff |
|
11:40 - 12:20 |
Surface-based Analysis: Intersubject Smoothing & Registration |
talk |
Doug Greve |
12:20 - 1:20 |
-- |
-- |
|
12:35 - 1:20 |
Optional Lunch Talk- A Non-physicist's Intro to MR SpinBench |
talk |
Dylan Tisdall |
1:20 - 2:00 |
talk |
David Salat |
|
2:00 - 3:00 |
demo |
David Salat |
|
3:00 - 3:20 |
break |
|
|
3:20 - 3:40 |
Troubleshooting Demonstration |
demo |
Louis Vinke |
3:40 - 4:40 |
tutorial |
staff |
Tuesday, April 30th - ROIs / Longitudinal / Multimodal / Group Analysis
Time |
Title |
Type |
Lecturer |
9:00 - 9:40 |
talk |
Doug Greve |
|
9:40 - 10:10 |
tutorial |
staff |
|
10:10 - 10:30 |
break |
|
|
10:30 - 11:30 |
talk |
Melanie Ganz |
|
11:30 - 11:50 |
QDEC demonstration |
demo |
Nick Schmansky |
11:50 - 12:50 |
Lunch |
-- |
-- |
12:20 - 12:50 |
Optional Lunch Talk- MRI Acquisition Methods for Morphometry |
talk |
Andre van der Kouwe |
12:50 - 1:50 |
tutorial |
staff |
|
12:50 - 1:50 |
tutorial |
staff |
|
1:50 - 2:20 |
talk |
Martin Reuter |
|
2:20 - 2:40 |
break |
|
|
2:40 - 3:40 |
tutorial |
staff |
|
3:40 - 4:40 |
talk |
Doug Greve |
|
4:40 - 5:00 |
talk |
Lilla Zollei |
|
5:00 - 5:45 |
tutorial |
staff |
Boston Beer Works location information here and here.
Meet us at 6:10pm at the front of Building 149 (map to be provided soon).
If you miss us, we are taking the 6:15pm MGH/Navy Yard shuttle to North Station (the next few buses depart at 6:30pm, 6:45pm, 7pm, 7:15pm, and 7:45pm).
From there, you cross the street and go down Canal Street. Boston Beer Works will be on your right.
Wednesday, May 1st - fMRI / Diffusion / Q&A
The Course Evaluation has been posted. Please feel free to start filling it out!
Time |
Title |
Type |
Lecturer |
9:00 - 10:00 |
talk |
Jon Polimeni |
|
10:00 - 10:40 |
talk |
Doug Greve |
|
10:40 - 11:00 |
break |
|
|
11:00 - 11:40 |
FSFAST continued |
talk |
Doug Greve |
11:40 - 12:40 |
tutorial |
staff |
|
12:40 - 1:40 |
Lunch |
-- |
-- |
1:10 - 1:40 |
Optional Lunch Talk- Motion-compensated neuroanatomical imaging |
talk |
Dylan Tisdall |
1:40 - 2:20 |
talk |
Anastasia Yendiki |
|
2:20 - 2:50 |
tutorial |
staff |
|
2:50 - 3:10 |
break & Evaluation |
|
|
3:10 - 3:40 |
talk |
Anastasia Yendiki |
|
3:40 - 4:25 |
tutorial |
staff |
|
4:25 - 5:00 |
talk |
Caroline Magnain |
|
5:00 - 5:30 |
Question and Answer Session (Answers to online questions here), FsQuiz |
talk |
staff |
The FreeSurfer Evaluation is here!
Additional Useful Information
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
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.
iSurf - iPhone/iPad app to view FreeSurfer segmentations