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==== Day 1 ==== ||'''Youtube Link''' ||'''Title''' ||'''Type''' ||'''Slides''' || || [[https://www.youtube.com/watch?v=6eJMxh7PlOY| Video]] ||** Intro to Linux for !FreeSurfer Users ||talk/demo || N/A || || ||** [[https://surfer.nmr.mgh.harvard.edu/fswiki/UnixTutorial|Unix for FreeSurfer Users]] ||tutorial || || || ||** [[http://surfer.nmr.mgh.harvard.edu/pub/docs/fsjargon_clean.pptx|Intro to FreeSurfer Jargon]] || talk || Caroline Magnain || || ||'''break''' || || || || ||[[attachment:freesurfer.intro.apr.2019.ppt|Introduction to Freesurfer]] ||talk ||Bruce Fischl || || ||[[http://surfer.nmr.mgh.harvard.edu/pub/docs/fsrecon.pptx|Analyzing the Individual Subject]] ||talk ||Doug Greve || || ||'''break''' || || || || ||[[https://www.youtube.com/watch?v=Mv-ECowxq2o|Freeview demonstration]] ||[[FsTutorial/FreeviewDemo|demo]] || Bram Diamond || || ||[[FsTutorial/OutputData_freeview|Introduction to FreeSurfer Output]] ||tutorial ||staff || || ||'''Lunch''' [[https://surfer.nmr.mgh.harvard.edu/fswiki/CourseDescription?action=AttachFile&do=get&target=CourseMap.jpg|(Suggestions for where to eat)]] |||||| || ||[[FsTutorial/OutputData_freeview|Introduction to FreeSurfer Output]] ||tutorial ||staff || || ||[[http://surfer.nmr.mgh.harvard.edu/pub/docs/fs.surface-based-analysis.ppt |Surface-based Analysis: Intersubject Registration & Smoothing ]] ||talk || Diyva Varadarajan || || ||'''break''' || || || || ||[[http://surfer.nmr.mgh.harvard.edu/pub/docs/fs.roi.EB_wiki.pptx|ROI Analysis]] ||talk || Doug Greve || || ||[[FsTutorial/AnatomicalROIV6.0|ROI Analysis Tutorial]] ||tutorial ||staff || || || [[http://surfer.nmr.mgh.harvard.edu/pub/docs/freesurfer-struct-func04022018-handoutb.pdf| Structural & Functional Data Integration]] ||talk ||David Salat || || ||[[FsTutorial/Practice|Practice Working with Data]] ||tutorial ||staff || Answers to online questions [[http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/QuestionAnswers|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 ||[[http://surfer.nmr.mgh.harvard.edu/pub/docs/GLM.pptx|Group Analysis]] ||talk || Viviana Siless || ||9:45 - 10:25 ||[[FsTutorial/GroupAnalysisV6.0|Group Analysis Tutorial]] ([[FsgdExamples|FSGD Examples]]) ||tutorial ||staff || ||10:25 - 10:45 ||'''break''' || || || ||10:45 - 11:30 ||[[http://surfer.nmr.mgh.harvard.edu/pub/docs/freesurfer.troubleshooting.apr2019.ppt|FreeSurfer Troubleshooting]] ||talk ||Bruce Fischl || ||11:30 - 12:30 ||[[FsTutorial/TroubleshootingDataV6.0|Troubleshooting Tutorial]] ||tutorial ||staff || ||12:30 - 1:30 ||'''Lunch''' || || || ||1:30 - 2:15 ||[[https://youtu.be/AR83_Bt04VQ|Quality Checking a Recon]] || [[https://zoom.us/wc/join/369478461?pwd=|talk]] ||Leah Morgan || ||2:15 - 2:55 ||[[http://surfer.nmr.mgh.harvard.edu/pub/docs/multiplecomparisons.ppt|Multiple Comparisons]] ||talk ||Doug Greve|| ||2:55 - 3:25 ||[[FsTutorial/MultipleComparisonsV6.0Perm|Multiple Comparisons Tutorial]] ||tutorial ||staff || ||3:25 - 4:05 ||'''break''' || || || ||4:05 - 4:50 ||[[http://surfer.nmr.mgh.harvard.edu/pub/docs/fs.longitudinal.pptx|Longitudinal FreeSurfer]] ||talk ||Malte Hoffmann || ||4:50 - 5:30 || [[FsTutorial/LongitudinalTutorial|LongitudinalTutorial]] ||tutorial ||staff || ##||5:30 - 6:15 ||*** Optional time to work on tutorials / work on your own data / ask basic questions ||-- || staff|| ||5:30 - 7:30 ||Social Night in the atrium of Bldg. 149|| Snacks and Beverages Served || || Answers to online questions [[http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/QuestionAnswers|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 ||* [[http://surfer.nmr.mgh.harvard.edu/pub/docs/IntroMRI.pptx|Intro to MR]] '' '' ||talk ||Robert Frost || ||9:30 - 10:00 ||[[http://surfer.nmr.mgh.harvard.edu/pub/docs/fs.multimodal1_2018.pptx|Multi-Modal Integration, Part 1: Registration]] ||talk || Aina Frau-Pascual|| ||10:00 - 10:30 ||[[MultiModalTutorialV6.0|Multi-Modal Integration Tutorial, Part 1]] ||tutorial ||staff || ||10:30 - 10:50 ||'''break''' || || || ||10:50 - 11:05 ||* [[http://surfer.nmr.mgh.harvard.edu/pub/docs/IntroDiffusion.pptx|Intro to Diffusion MRI Physics]] '' '' ||talk ||Robert Frost || ||11:05 - 11:45 ||[[http://surfer.nmr.mgh.harvard.edu/pub/docs/dmri,fs.ppt|Introduction to Diffusion MRI]] ||talk ||Anastasia Yendiki || ||11:45 - 12:30 ||[[FsTutorial/DiffusionV6.0|Diffusion Processing Tutorial]] ||tutorial ||staff || ||12:30 - 1:30 ||'''Lunch''' ||-- ||-- || ||1:30 - 2:20 ||[[http://surfer.nmr.mgh.harvard.edu/pub/docs/tracula,fs.ppt|Tracts Constrained by UnderLying Anatomy (TRACULA)]] ||talk ||Anastasia Yendiki || ||2:20 - 3:20 ||[[FsTutorial/Tracula|TRACULA Tutorial]] ||tutorial ||staff || ||3:20 - 3:40 ||'''break''' || || || ||3:40 - 3:50 ||[[http://surfer.nmr.mgh.harvard.edu/pub/docs/tracula,fs.ppt|Longitudinal TRACULA]] ||talk ||Anastasia Yendiki || ||3:50 - 4:50 ||[[http://surfer.nmr.mgh.harvard.edu/pub/docs/fMRI_intro2018.ppt|Basics of fMRI Analysis]] ||talk ||Jingyuan Chen || ||4:50 - 5:30 ||* [[http://surfer.nmr.mgh.harvard.edu/pub/docs/FreeSurfer_Acquisition_Sep2019.ppt|MRI Acquisition Methods]] || talk ||Andre van der Kouwe|| Answers to online questions [[http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/QuestionAnswers|here]] '''The !FreeSurfer Evaluation is [[ https://forms.gle/HmxDSXMopTdNMJKu7|here]]!''' ==== Thursday, September 26th - fMRI Analysis / Multimodal Analysis / Future Directions ==== ||'''Youtube Link''' ||'''Title''' ||'''Type''' ||'''Slides''' || ||9:00 - 9:30 ||[[http://surfer.nmr.mgh.harvard.edu/pub/docs/fsfast.ppt|FSFAST, Part 1: Preprocessing]] ||talk ||Doug Greve || ||9:30 - 10:00 ||[[FsFastTutorialV6.0|FSFAST Tutorial, Part 1]] ||tutorial ||staff || ||10:00 - 10:20 ||'''break''' & Evaluation || || || ||10:20 - 11:20 ||[[http://surfer.nmr.mgh.harvard.edu/pub/docs/fsfast.ppt|FSFAST, Part 2: GLM Analysis]] ||talk || Doug Greve || ||11:20 - 12:00 ||[[FsFastTutorialV6.0|FSFAST Tutorial, Part 2]] ||tutorial || staff || ||12:00 - 1:00 ||'''Lunch''' || || || ||1:00 - 1:30 ||* [[http://surfer.nmr.mgh.harvard.edu/pub/docs/fs.registration.ppt|An Overview of Registration Methods]] ||talk || Lilla Zöllei || ||1:30 - 1:45 || [[http://surfer.nmr.mgh.harvard.edu/pub/docs/resting-state.fmri.ppt|Resting State fMRI]] ||talk ||Doug Greve || ||1:45 - 2:15 ||[[http://surfer.nmr.mgh.harvard.edu/pub/docs/fs.multimodal-integration.Part2.pptx|Multi-Modal Integration, Part 2: Group Analysis]] ||talk ||Doug Greve || ||2:15 - 3:00 ||[[MultiModalTutorialV6.0|Multi-Modal Integration Tutorial, Part 2]] ||tutorial ||staff || ||3:00 - 3:15 ||'''break''' || || || ||3:15 - 3:30 ||* [[http://surfer.nmr.mgh.harvard.edu/pub/docs/fs.vbm.ppt|FreeSurfer vs. VBM]] ||talk ||Doug Greve || ||3:30 - 4:30 ||* Future Directions ||talk || FS Development Team || ||4:30 - 5:00 ||Question & Answer Session || ||staff || |
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For tutorial-specific questions, over the next two weeks (March 23 - April 3rd) our FreeSurfer 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:<<BR>> | 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:<<BR>> |
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
Youtube Link |
Title |
Type |
Slides |
** Intro to Linux for FreeSurfer Users |
talk/demo |
N/A |
|
|
tutorial |
|
|
|
talk |
Caroline Magnain |
|
|
break |
|
|
|
talk |
Bruce Fischl |
|
|
talk |
Doug Greve |
|
|
break |
|
|
|
Bram Diamond |
||
|
tutorial |
staff |
|
|
|||
|
tutorial |
staff |
|
|
Surface-based Analysis: Intersubject Registration & Smoothing |
talk |
Diyva Varadarajan |
|
break |
|
|
|
talk |
Doug Greve |
|
|
tutorial |
staff |
|
|
talk |
David Salat |
|
|
tutorial |
staff |
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