Deletions are marked like this. | Additions are marked like this. |
Line 72: | Line 72: |
==== Day 1 ==== | ==== Day 1: Intro to FreeSurfer and Working with the Individual Subject ==== |
Line 74: | Line 74: |
||'''Subject''' ||'''Talk''' ||'''Slides''' ||'''Tutorial''' || | ||'''Subject''' ||'''Talk''' ||'''Slides''' ||'''Relevant Tutorials''' || |
Line 82: | Line 82: |
|| ||[[http://surfer.nmr.mgh.harvard.edu/pub/docs/fs.surface-based-analysis.ppt |Surface-based Analysis: Intersubject Registration & Smoothing ]] ||talk || Diyva Varadarajan || |
=== Day 2: Working with Multiple Subjects === || Intersubject Registration & Smoothing || [[https://www.youtube.com/watch?v=8WPvXoORoAw&t=23s| YouTube Presentation]] ||[[http://surfer.nmr.mgh.harvard.edu/pub/docs/fs.surface-based-analysis.ppt |Slides]] || N/A || |
Upcoming FreeSurfer courses
If you would like to be notified about upcoming FreeSurfer courses, sign up for the course mailing list.. We host two Boston courses each year, typically in the first week of April and the last week of September.
Suggested Steps for Conducting an at-home FreeSurfer Course
Step 1: Download FreeSurfer For your Computer
Follow the instructions on this page to get FreeSurfer on your personal computer. We highly recommend downloading the standalone Dev version of Freeview to replace the Freeview application in the FreeSurfer v6.0 download package due to incompatabilites with newer operating systems (especially if you have a mac).
Step 2: Download the tutorial data
Download the tutorial data here (~ 8GB).
Step 3: test your FreeSurfer Install and Tutorial Data
These are some instructions written by Paul Wighton on how to run a script that will test some of the FreeSurfer tutorial commands on your laptop and ensure your install is working well enough to attempt the tutorials for the course.
FreeSurfer 6 can be downloaded from here: https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/6.0.0/freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0.tar.gz More insallation instructions can be found here: https://surfer.nmr.mgh.harvard.edu/fswiki/DownloadAndInstall The tutorial data can be downloaded from here: https://surfer.nmr.mgh.harvard.edu/pub/data/tutorial_data.tar.gz On my machine, I stored the downloaded `tar.gz` files in a directory called `/home/paul/lcn/data/fs-course-20200310`. After extracting the archives I have the following subdirectories in `/home/paul/lcn/data/fs-course-20200310` - `freesurfer` - `tutorial_data_20190918_1558` Next, edit the file `bashrc` in the `tutorial_data_20190918_1558` directory. (In my case, the full path of that file is `/home/paul/lcn/data/fs-course-20200310/tutorial_data_20190918_1558/bashrc`) and change lines 16 and 19 to match the location of freesurfer and the tutorial data on your machine. In my case, I edited the lines to read: - Line 16: `export TUTORIAL_DATA=/home/paul/lcn/data/fs-course-20200310/tutorial_data_20190918_1558` - Line 19: `export FREESURFER_HOME=/home/paul/lcn/data/fs-course-20200310/freesurfer` Next, change into the tutorial data directory: ``` cd /home/paul/lcn/data/fs-course-20200310/tutorial_data_20190918_1558 ``` and test the installation by running: ``` source bashrc test_commands.sh.15 ``` This may take a while (30 minutes to an hour) and the script will constantly "steal focus" so you will not be able to use your machine while the tests are running. If at some point, you see: ``` mean.practice.table (END) ``` Hit `q` so the script can continue (I had to do this twice) When you see `colortable with 14176 entries read (originally /autofs/cluster/freesurfer/centos7_x86_64/stable6/FreeSurferColorLUT.txt)` you can hit enter and the script will end.
Step 4: Suggested Schedule (5 days)
Day 1: Intro to FreeSurfer and Working with the Individual Subject
Subject |
Talk |
Slides |
Relevant Tutorials |
Intro to Linux for FreeSurfer Users |
*Slides |
||
Intro to FreeSurfer Jargon |
N/A |
||
Intro to FreeSurfer Software |
N/A |
||
Analyzing the Individual Subject |
N/A |
||
Intro to FreeView and the FreeSurfer Output |
N/A |
Introduction to FreeSurfer Output Tutorial, Practice Working with Data |
|
ROI Analysis |
Day 2: Working with Multiple Subjects
Intersubject Registration & Smoothing |
N/A |
|
talk |
David Salat |
Answers to online questions here
Tuesday, September 24th - Group Analysis / Longitudinal Analysis / Troubleshooting
Time |
Title |
Type |
Lecturer |
8:00 - 9:00 |
*** Morning Help Session |
|
research technicians |
9:00 - 9:45 |
talk |
Viviana Siless |
|
9:45 - 10:25 |
tutorial |
staff |
|
10:25 - 10:45 |
break |
|
|
10:45 - 11:30 |
talk |
Bruce Fischl |
|
11:30 - 12:30 |
tutorial |
staff |
|
12:30 - 1:30 |
Lunch |
|
|
1:30 - 2:15 |
Leah Morgan |
||
2:15 - 2:55 |
talk |
Doug Greve |
|
2:55 - 3:25 |
tutorial |
staff |
|
3:25 - 4:05 |
break |
|
|
4:05 - 4:50 |
talk |
Malte Hoffmann |
|
4:50 - 5:30 |
tutorial |
staff |
|
5:30 - 7:30 |
Social Night in the atrium of Bldg. 149 |
Snacks and Beverages Served |
|
Answers to online questions here
Wednesday, September 25th - Multimodal Analysis / Diffusion Analysis / fMRI Analysis / MR Acquisition
Time |
Title |
Type |
Lecturer |
8:00 - 9:00 |
*** Morning Help Session |
|
research technicians |
9:00 - 9:30 |
talk |
Robert Frost |
|
9:30 - 10:00 |
talk |
Aina Frau-Pascual |
|
10:00 - 10:30 |
tutorial |
staff |
|
10:30 - 10:50 |
break |
|
|
10:50 - 11:05 |
talk |
Robert Frost |
|
11:05 - 11:45 |
talk |
Anastasia Yendiki |
|
11:45 - 12:30 |
tutorial |
staff |
|
12:30 - 1:30 |
Lunch |
-- |
-- |
1:30 - 2:20 |
talk |
Anastasia Yendiki |
|
2:20 - 3:20 |
tutorial |
staff |
|
3:20 - 3:40 |
break |
|
|
3:40 - 3:50 |
talk |
Anastasia Yendiki |
|
3:50 - 4:50 |
talk |
Jingyuan Chen |
|
4:50 - 5:30 |
talk |
Andre van der Kouwe |
Answers to online questions here
The FreeSurfer Evaluation is here!
Thursday, September 26th - fMRI Analysis / Multimodal Analysis / Future Directions
Youtube Link |
Title |
Type |
Slides |
9:00 - 9:30 |
talk |
Doug Greve |
|
9:30 - 10:00 |
tutorial |
staff |
|
10:00 - 10:20 |
break & Evaluation |
|
|
10:20 - 11:20 |
talk |
Doug Greve |
|
11:20 - 12:00 |
tutorial |
staff |
|
12:00 - 1:00 |
Lunch |
|
|
1:00 - 1:30 |
talk |
Lilla Zöllei |
|
1:30 - 1:45 |
talk |
Doug Greve |
|
1:45 - 2:15 |
talk |
Doug Greve |
|
2:15 - 3:00 |
tutorial |
staff |
|
3:00 - 3:15 |
break |
|
|
3:15 - 3:30 |
talk |
Doug Greve |
|
3:30 - 4:30 |
* Future Directions |
talk |
FS Development Team |
4:30 - 5:00 |
Question & Answer Session |
|
staff |
Getting the Help and Support you need
For questions related to your own data processing and for troubleshooting help, please contact the FreeSurfer mailing list: freesurfer@nmr.mgh.harvard.edu and attach your recon-all.log file to your email.
For tutorial-specific questions, over the next two weeks (March 23 - April 3rd) our FreeSurfer tutorial support team will be extra available to set up video chats or answer your questions over email. Feel free to email the addresses on the list below for help:
mlarrabee1@mgh.harvard.edu, dccordero@mgh.harvard.edu, mvera2@mgh.harvard.edu, lmorgan6@mgh.harvard.edu, brd15@mgh.harvard.edu