Deletions are marked like this. | Additions are marked like this. |
Line 19: | Line 19: |
##'''Laptop damage policy: If liquid is spilled on a provided laptop, then you are liable for payment of the repair costs!''' | '''Laptop damage policy: If liquid is spilled on a provided laptop, then you are liable for payment of the repair costs!''' |
Line 38: | Line 38: |
<<Include(FsTutorial/StLouis2010CourseSchedule)>> |
##<<Include(FsTutorial/StLouis2010CourseSchedule)>> <<Include(FsTutorial/Oct2010CourseSchedule)>> |
Line 52: | Line 53: |
## * [[ConferenceRoomA| Conference Room A]] | * [[ConferenceRoomA| Conference Room A]] |
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, October 4 and 5, 2010
MGH, Charlestown Navy Yard, Building 149, Conference Room A
Monday, October 4th - Introduction / Single Subject / Group Analysis
Time |
Title |
Type |
Lecturer |
8:00 - 8:30 |
optional - Unix Tutorial for FreeSurfer Users 1. Surrey, 2. O'Reilly |
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 - 10:00 |
talk |
David Salat |
|
10:00 - 11:00 |
talk |
Doug Greve |
|
11:00 - 11:15 |
break |
|
|
11:15 - 11:45 |
Tkmedit/Tksurfer demonstration |
demo |
Doug Greve |
11:45 - 12:15 |
tutorial |
staff |
|
12:15 - 1:15 |
Lunch |
-- |
-- |
12:30 - 1:00 |
Optional Lunch Talk- MRI Acquisition Methods for Morphometry |
talk |
Andre van der Kouwe |
1:15 - 2:00 |
talk |
David Salat |
|
2:00 - 2:30 |
talk |
Doug Greve |
|
2:30 - 2:45 |
break |
|
|
2:45 - 3:30 |
talk |
Mert Sabuncu |
|
3:30 - 4:30 |
tutorial |
staff |
|
4:30 - 4:45 |
QDEC demonstration |
demo |
Nick Schmansky |
4:45 - 5:30 |
tutorial |
staff |
|
5:30 - |
optional - FreeSurfer Installation on Personal Laptops |
one-on-one |
Nick Schmansky |
5:30 - |
optional - Start Processing Your Own Data |
one-on-one |
Allison Stevens |
Boston Beer Works location information here.
Meet us at 6:10pm 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 6:15pm MGH/Navy Yard shuttle to North Station. From there, you cross the street and go down Canal Street. Boston Beer Works will be on your left.
Tuesday, October 5th - ROIs / Troubleshooting / Multi-Modal / Q&A / Future Directions
Time |
Title |
Type |
Lecturer |
9:00 - 10:00 |
talk |
Doug Greve |
|
10:00 - 10:30 |
tutorial |
staff |
|
10:30 - 11:00 |
talk |
Martin Reuter |
|
11:00 - 11:15 |
break |
|
|
11:15 - 11:45 |
talk |
Bruce Fischl |
|
11:45 - 12:45 |
Troubleshooting Demonstration, Troubleshooting Tutorial |
tutorial |
staff, Allison |
12:45 - 1:45 |
Lunch |
-- |
-- |
12:45 - 1:15 |
Optional Lunch Talk- Quality Checking a Recon |
demo |
Allison Stevens |
1:45 - 3:00 |
talk |
Doug Greve |
|
3:00 - 3:45 |
tutorial |
staff |
|
3:45 - 4:00 |
break |
|
|
4:00 - 4:20 |
talk |
Lilla Zollei |
|
4:20 - 5:30 |
Future Directions of FreeSurfer: |
|
|
4:20 - 4:40 |
talk |
Dylan Tisdall |
|
4:40 - 5:10 |
talk |
Bruce Fischl |
|
5:10- 5:30 |
talk |
Lilla Zollei |
|
5:30 - 6:00 |
Question and Answer Session, FsQuiz............FsQuizAnswers |
talk |
staff |
The FreeSurfer Evaluation is here!
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)