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== Videos of Lectures == You can find videos of the lectures [[http://www.youtube.com/channel/UCruQerP8aa-gYttXkAcyveA|here]]. |
FreeSurfer Tutorial and Workshop
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 Evaluation
Please fill out our course evaluation here. You can fill it in throughout the remainder of the course but you can't save your answers and finish it later so be sure to submit it before you leave.
Videos of Lectures
You can find videos of the lectures here.
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
Commands on a Mac
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.
Course Schedule
FreeSurfer Course, November 4 - 6, 2013
MGH, Charlestown Navy Yard, Building 114, Room D1
8:00 - 9:30am Registration Desk Open
Monday, Nov 4th - Introduction / Single Subject Analysis /Troubleshooting
Time |
Title |
Type |
Lecturer |
8:30 - 9:00 |
optional - Unix Tutorial for FreeSurfer Users |
tutorial |
Maritza Ebling |
9:00 - 9:15 |
optional - Intro to FreeSurfer Jargon |
talk |
Allison Stevens |
9:15 - 9:30 |
break |
|
|
9:30 - 10:00 |
talk |
Bruce Fischl |
|
10:00 - 11:00 |
talk |
Doug Greve |
|
11:00 - 11:20 |
break |
|
|
11:20 - 12:05 |
optional - A Non-physicist's Intro to MR SpinBench |
talk |
Dylan Tisdall |
12:05 - 1:00 |
-- |
-- |
|
1:00 - 1:30 |
Freeview/Tksurfer demonstration |
demo |
Doug Greve |
1:30 - 2:00 |
tutorial |
||
2:00 - 2:30 |
talk |
Bruce Fischl |
|
2:30 - 2:50 |
break |
|
|
2:50 - 3:50 |
demo |
Allison Stevens |
|
3:50 - 5:00 |
tutorial |
staff |
|
5:00 - 5:15 |
Question and Answer Session (Answers to online questions here) |
talk |
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.
Tuesday, Nov 5th - Group Analysis / ROI Analysis / Multimodal
Time |
Title |
Type |
Lecturer |
9:00 - 9:40 |
Surface-based Analysis: Intersubject Smoothing & Registration |
talk |
Doug Greve |
9:40 - 10:20 |
talk |
Eugenio Iglesias |
|
10:20 - 10:40 |
break |
|
|
10:40 - 11:20 |
tutorial |
staff |
|
11:20 - 11:40 |
talk |
Eugenio Iglesias |
|
11:40 - 12:00 |
QDEC demonstration |
demo |
Eugenio Iglesias |
12:00 - 1:00 |
Lunch |
-- |
-- |
1:00 - 1:20 |
tutorial |
staff |
|
1:00 - 2:00 |
tutorial |
staff |
|
2:00 - 3:00 |
talk |
Doug Greve |
|
3:00 - 3:20 |
break |
|
|
3:20 - 3:50 |
tutorial |
staff |
|
3:50 - 4:20 |
talk |
Martin Reuter |
|
4:20 - 5:00 |
tutorial |
staff |
|
5:00 - 5:15 |
Question and Answer Session (Answers to online questions here) |
talk |
staff |
Wednesday, Nov 6th - Diffusion / Multimodal / Longitudinal / Future Directions / Q&A
Time |
Title |
Type |
Lecturer |
9:00 - 9:30 |
talk |
Doug Greve |
|
9:30 - 10:00 |
tutorial |
staff |
|
10:00 - 10:40 |
talk |
Anastasia Yendiki |
|
10:40 - 11:00 |
break |
|
|
11:00 - 11:30 |
tutorial |
staff |
|
11:30 - 12:00 |
talk |
Anastasia Yendiki |
|
12:00 - 1:00 |
Lunch |
-- |
-- |
1:00 - 1:45 |
tutorial |
staff |
|
1:45 - 2:15 |
talk |
Doug Greve |
|
2:15 - 3:00 |
tutorial |
staff |
|
3:00 - 3:20 |
break & Evaluation |
|
|
3:20 - 3:50 |
optional technical talk - MRI Acquisition Methods for Morphometry |
talk |
Andre van der Kouwe |
3:50 - 4:20 |
optional technical talk - Motion-compensated neuroanatomical imaging |
talk |
Dylan Tisdall |
4:20 - 4:45 |
optional technical talk - Registration Methods |
talk |
Lilla Zollei |
4:45 - 5:15 |
Future Directions |
talk |
Bruce Fischl, Lilla Zollei, Ender Konukoglu |
5:15 - 5:30 |
Question and Answer Session (Answers to online questions here), FsQuiz |
talk |
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.
Taxi Phone numbers can be found 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