FreeSurfer Tutorial and Workshop
Overview
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!
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, December 12-14, 2011
MGH, Charlestown Navy Yard, Building 149, Conference Room A
Monday, December 12th - Introduction / Single Subject / Registration / Troubleshooting
Time |
Title |
Type |
Lecturer |
Give us your feedback |
8:00 - 8:30 |
optional - Unix Tutorial for FreeSurfer Users online practice |
tutorial |
Allison Stevens |
|
8:30 - 9:00 |
optional - Intro to FreeSurfer Jargon |
talk |
Allison Stevens |
|
8:30 - 9:00 |
Course Registration |
sign-in |
|
|
9:00 - 9:30 |
talk |
Bruce Fischl |
||
9:30 - 10:30 |
talk |
Doug Greve |
||
10:30 - 10:50 |
break |
|
|
|
10:50 - 11:20 |
Tkmedit/Tksurfer demonstration |
demo |
Doug Greve |
|
11:20 - 11:50 |
tutorial |
staff |
||
11:50 - 12:30 |
talk |
Doug Greve |
||
12:30 - 1:30 |
-- |
-- |
||
1:00 - 1:30 |
Optional Lunch Talk- A Non-physicist's Intro to MR SpinBench |
talk |
Dylan Tisdall |
|
1:30 - 2:15 |
talk |
Lilla Zollei |
||
2:15- 2:55 |
talk |
Bruce Fischl |
||
2:55 - 3:15 |
break |
|
|
|
3:15 - 3:35 |
Troubleshooting Demonstration |
demo |
Allison |
|
3:35 - 4:35 |
tutorial |
staff |
||
4:35 - 5:30 |
Quality Checking a Recon |
demo |
Allison Stevens |
|
5:30 - |
optional - FreeSurfer Installation on Personal Laptops |
one-on-one |
staff |
|
5:30 - |
optional - Start Processing Your Own Data |
one-on-one |
staff |
Boston Beer Works location information here and here.
Meet us at 6:40pm at the front of Building 149 (the entrance on the opposite side of the building from where the Course is held).
If you miss us, we are taking the 6:45pm MGH/Navy Yard shuttle to North Station (the next few buses depart at 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.
Tuesday, December 13th - ROIs / Longitudinal / Multimodal / Group Analysis
Time |
Title |
Type |
Lecturer |
Give us your feedback |
9:00 - 10:00 |
talk |
Doug Greve |
||
10:00 - 10:30 |
tutorial |
staff |
||
10:30 - 10:50 |
break |
|
|
|
10:50 - 11:20 |
talk |
Martin Reuter |
||
11:20 - 12:10 |
Freeview Demo, Longitudinal Tutorial |
tutorial |
staff |
|
12:10 - 1:10 |
Lunch |
-- |
-- |
|
12:40 - 1:10 |
Optional Lunch Talk- MRI Acquisition Methods for Morphometry |
talk |
Andre van der Kouwe |
|
1:10 - 1:40 |
Future Directions: Inferring architectonic boundaries from in-vivo MRI |
talk |
Bruce Fischl |
|
1:40 - 2:40 |
talk |
Doug Greve |
||
2:40 - 3:00 |
break |
|
|
|
3:00 - 3:45 |
tutorial |
staff |
||
3:45 - 4:45 |
talk |
J. Eugenio Iglesias |
||
4:45 - 5:15 |
QDEC demonstration |
demo |
Nick Schmansky |
|
5:15 - 6:15 |
tutorial |
staff |
||
5:15 - 6:15 |
tutorial |
staff |
Wednesday, December 14th - fMRI / Diffusion / Q&A
The Course Evaluation has been posted. Please feel free to start filling it out!
Time |
Title |
Type |
Lecturer |
Give us your feedback |
9:00 - 10:00 |
talk |
Jon Polimeni |
||
10:00 - 10:20 |
break |
|
|
|
10:20 - 11:40 |
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 - 2:40 |
talk |
Anastasia Yendiki |
||
2:40 - 3:25 |
tutorial |
staff |
||
3:25 - 3:45 |
break & Evaluation |
|
|
|
3:45 - 4:15 |
talk |
Anastasia Yendiki |
||
4:15 - 5:00 |
tutorial |
staff |
||
5:00 - 5:30 |
Question and Answer Session, FsQuiz |
talk |
staff |
Additional
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)
iSurf - iPhone/iPad app to view FreeSurfer segmentations