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Follow the instructions on [[ DownloadAndInstall| this page]] to get FreeSurfer on your personal computer. <<BR >> Comments for Mac users: <<BR>> |
Follow the instructions on [[ DownloadAndInstall| this page]] to get FreeSurfer on your personal computer. <<BR >> Comments for Mac users: <<BR>> |
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. <<BR >> Comments for Mac users:
1) 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)
2) Follow these instructions for testing your mac installation and configuring the tutorial data
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 |
Upcoming Live Lectures |
Intro to Linux for FreeSurfer Users |
*Slides |
e.g. Monday March 30th 11:00 - 12:00 EST. Watch with Zoom [[|here]] |
||
Intro to FreeSurfer Jargon |
N/A |
|
||
Intro to FreeSurfer Software |
N/A |
|
||
Analyzing the Individual Subject |
|
|||
Intro to Freeview and the working with data |
N/A |
|
||
ROI Analysis |
|
Bonus Talks: Intro to MRI Presentation,Intro to MR Slides, MRI Aquisition Techniques for Morphometry, MRI Acquisition Methods Slides
Day 2: More Structural Processing and Troubleshooting
Subject |
Talk |
Slides |
Relevant Tutorials |
Upcoming Live Lectures |
Troubleshooting |
|
|||
Longitudinal Analysis |
|
|||
An Overview of Registration Methods |
N/A |
|
Day 3: Group Analysis and Statistics
Subject |
Talk |
Slides |
Relevant Tutorials |
Upcoming Live Lectures |
Surface-based analysis: Intersubject Registration & Smoothing |
N/A |
|
||
Group Analysis |
|
|||
Multiple Comparisons |
|
Day 4: Multimodal Analysis / Diffusion Analysis
Subject |
Talk |
Slides |
Relevant Tutorials |
Upcoming Live Lectures |
Intro to Diffusion |
|
|||
Multi-Modal Integration |
Multi-Modal Integration, Part 1: Registration, Multi-Modal Integration, Part 2: Group Analysis |
Multi-Modal Integration Tutorial, Part 1 ,Multi-Modal Integration Tutorial, Part 2 |
|
|
Tracts Constrained by Underlying Anatomy (TRACULA) |
|
Bonus Talks and Slides: Longitudinal TRACULA
Day 5: fMRI Analysis and FSFAST
Subject |
Talk |
Slides |
Relevant Tutorials |
Upcoming Live Lectures |
Basics of fMRI |
N/A |
|
||
Resting State fMRI |
N/A |
|
||
FSFAST |
|
Bonus Talks and Slides: Structural & Functional Data Integration
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
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.