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== WARNING: The hyperlinks in the tables below used to download slides will NOT WORK in Google Chrome. Please use a different browser to access these slides. ==

= Suggested Steps for Conducting an at-home FreeSurfer Course =

=== Step 1: Download FreeSurfer For your Computer ===

Follow the instructions on [[ DownloadAndInstall| this page]] to get FreeSurfer on your personal computer. <<BR>>

Comments on Freeview for Mac users: <<BR>>
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 macOS operating systems<<BR>>
2) If you would like to use Freeview 6.0, follow [[https://surfer.nmr.mgh.harvard.edu/fswiki/MacOsInstall#ForMacOSsystemsrunningfreesurfer6.0.0|these]] instructions to install a necessary patch <<BR>>

=== Step 2: Download the tutorial data ===

Download the tutorial data [[FsTutorial/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: Prepare with the basics ===

We usually send [[http://ftp.nmr.mgh.harvard.edu/fswiki/CoursePrep|this]] page out to students before each course to help them find resources to cover the basics such as: Intro to unix and scripting, intro to neuroanatomy etc.

=== Step 5: Suggested Schedule (5 days) ===
##    '''''Which Live Lectures Would You Like to Watch?'''''
##For the next two weeks (March 16 - 27), we welcome you to indicate which lectures you would most like to hear/be able to have Q&A sessions on by filling out this [[https://docs.google.com/forms/d/e/1FAIpQLSd5mKVDXaZsS7Q-984FmCM1fEuX5RpZr3y20C_25auaBmDHmA/viewform?usp=sf_link|GoogleForm]]. Provided there is enough interest for a particular topic, we will be hosting live lectures and will publish those dates on the schedule below as soon as we know them. Additionally, over the coming few weeks we encourage students to attempt this schedule in their own time and the FreeSurfer team will be available to answer all of your questions and provide hands-on support whenever you need it.

##To help us curate a schedule of live lectures that will be most relevant to students partaking in this "Teach Yourself FreeSurfer" webpage, please fill out this [[https://docs.google.com/forms/d/e/1FAIpQLSd5mKVDXaZsS7Q-984FmCM1fEuX5RpZr3y20C_25auaBmDHmA/viewform?usp=sf_link|GoogleForm]] to rate which lectures you would most like to hear/be able to have Q&A sessions on. 

##We want to provide resources that are most needed, beneficial, and relevant to this semester's group of students. 

##Thank you for your interest ahead of time!

==== Day 1: Intro to FreeSurfer and Working with the Individual Subject ====

||'''Subject''' ||'''Talk''' ||'''Slides''' ||'''Relevant Tutorials''' || '''Upcoming/Recorded Live Lectures''' ||
|| Intro to FreeSurfer Jargon || [[https://www.youtube.com/watch?v=GywOKtfKZIU| Talk]] || [[http://surfer.nmr.mgh.harvard.edu/anonftp/pub/docs/fsjargon_DC.pptx|Slides]] || N/A || [[http://surfer.nmr.mgh.harvard.edu/anonftp/pub/docs/IntroToFSJargon_DC.mp4|Intro to FS Jargon Talk]] ||
|| Intro to Linux for !FreeSurfer Users || [[https://www.youtube.com/watch?v=6eJMxh7PlOY| Talk]] || [[http://surfer.nmr.mgh.harvard.edu/pub/docs/Unix_LM.pptx| Slides ]] || [[https://surfer.nmr.mgh.harvard.edu/fswiki/UnixTutorial|Tutorial]] || [[http://surfer.nmr.mgh.harvard.edu/anonftp/pub/docs/IntroToLinux_ML.mp4|Intro to Linux Talk]] ||
|| Intro to FreeSurfer Software || [[https://www.youtube.com/watch?v=eZcIHXXq_Uc&t=1452s| Talk ]] || [[http://surfer.nmr.mgh.harvard.edu/pub/docs/freesurfer.intro.apr.2020.MV.ppt| Slides ]] || N/A || [[http://surfer.nmr.mgh.harvard.edu/pub/docs/FreeSurferIntroduction.mp4|Introduction to FreeSurfer Talk]] ||
|| Analyzing the Individual Subject || [[ https://www.youtube.com/watch?v=8Ict0Erh7_c&t=1501s | Part 1]], [[ https://www.youtube.com/watch?v=KncPouQWAp0&t=1522s | Part 2]] ||  [[http://surfer.nmr.mgh.harvard.edu/pub/docs/IndividualSubject_03312020.pptx| Slides ]] || [[FsTutorial/OutputData_freeview|Introduction to FreeSurfer Output Tutorial]] || [[http://surfer.nmr.mgh.harvard.edu/pub/docs/IndividualAnalysis.mp4|Analyzing the Individual Subject Talk]] ||
|| Intro to Freeview and the working with data || [[https://www.youtube.com/watch?v=Mv-ECowxq2o|Freeview demonstration]] || N/A || [[FsTutorial/Practice|Practice Working with Data]] || [[http://surfer.nmr.mgh.harvard.edu/pub/docs/FreeViewDemo.mp4|FreeView Demo]] ||
|| ROI Analysis || [[https://www.youtube.com/watch?v=n5QkCwZZPko&t=294s | Talk]] || [[http://surfer.nmr.mgh.harvard.edu/pub/docs/fs.roi.EB_wiki.pptx| Slides]] || [[FsTutorial/AnatomicalROIV6.0|ROI Analysis Tutorial]] || [[http://surfer.nmr.mgh.harvard.edu/anonftp/pub/docs/ROItalk_ML.mp4|ROI Analysis talk]] ||
Bonus Talks: [[https://www.youtube.com/watch?v=SwsH64PBBZE|Intro to MRI Presentation]],[[http://surfer.nmr.mgh.harvard.edu/pub/docs/IntroMRI.pptx|Intro to MR Slides]], [[https://www.youtube.com/watch?v=aZfy8gsPxZE| MRI Aquisition Techniques for Morphometry]], [[http://surfer.nmr.mgh.harvard.edu/pub/docs/FreeSurfer_Acquisition_Sep2019.ppt|MRI Acquisition Methods Slides]]

==== Day 2: More Structural Processing and Troubleshooting ====
||'''Subject''' ||'''Talk''' ||'''Slides''' ||'''Relevant Tutorials''' || '''Upcoming Live Lectures''' ||
|| Troubleshooting || [[ https://www.youtube.com/watch?v=gf0BC0xs0tM | Talk ]], [[https://www.youtube.com/watch?v=AR83_Bt04VQ| Demo]] || [[http://surfer.nmr.mgh.harvard.edu/pub/docs/Troubleshooting_Leah.pptx|FreeSurfer Troubleshooting]] || [[FsTutorial/TroubleshootingDataV6.0|Troubleshooting Tutorial]] || [[http://surfer.nmr.mgh.harvard.edu/anonftp/pub/docs/Troubleshooting_LMnew.mp4|Troubleshooting Talk]] ||
|| Longitudinal Analysis || [[ https://www.youtube.com/watch?v=vxJODPBLd3M&t=147s| Talk]] || [[http://surfer.nmr.mgh.harvard.edu/pub/docs/fs.longitudinal.pptx|Longitudinal FreeSurfer]] ||  [[FsTutorial/LongitudinalTutorial|LongitudinalTutorial]] || ||
|| An Overview of Registration Methods || [[https://www.youtube.com/watch?v=DQOmdLpf82k&t=834s| Talk ]] || [[http://surfer.nmr.mgh.harvard.edu/pub/docs/fs.registration.ppt|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 || [[https://www.youtube.com/watch?v=8WPvXoORoAw&t=23s| Talk]] ||[[http://surfer.nmr.mgh.harvard.edu/pub/docs/fs.surface-based-analysis.ppt |Slides]] || N/A || ||
|| Group Analysis || [[https://www.youtube.com/watch?v=EJewud8obuo&t=10s| Part 1]], [[https://www.youtube.com/watch?v=9111bn-XVsA&t=22s|Part 2]] || [[https://drive.google.com/open?id=1KXhj30THfLv6LH_WP4fOC6DHqX0_tK5z79szHfhYQfw|Group Analysis]] || [[FsTutorial/GroupAnalysisV6.0|Group Analysis Tutorial]] ||[[http://surfer.nmr.mgh.harvard.edu/pub/docs/GroupAnalysis_PW.mp4|Group Analysis Talk]] ||
|| Multiple Comparisons || [[ https://www.youtube.com/watch?v=s87--3yG6mU&t=1114s| Talk]] || [[https://drive.google.com/open?id=11PAHrSOnAY_d6RVj-1_dLKVAauv8gUN3-mQYVobaLmY|Multiple Comparisons Slides]] || [[FsTutorial/MultipleComparisonsV6.0Perm|Multiple Comparisons Tutorial]] ||[[http://surfer.nmr.mgh.harvard.edu/pub/docs/MultipleComparisons_PW.mp4|Multiple Comparisons Talk]] ||

==== Day 4: Multimodal Analysis / Diffusion Analysis ====
||'''Subject''' ||'''Talk''' ||'''Slides''' ||'''Relevant Tutorials''' ||
|| Intro to Diffusion || [[https://www.youtube.com/watch?v=BKjBdeWYllk&t=66s| Part 1]], [[https://www.youtube.com/watch?v=efsxszjPmpc&t=42s|Part 2]]|| [[http://surfer.nmr.mgh.harvard.edu/pub/docs/dmri,fs.ppt|Introduction to Diffusion MRI]] || [[FsTutorial/DiffusionV6.0|Diffusion Processing Tutorial]] ||
|| Multi-Modal Integration || [[https://www.youtube.com/watch?v=gRl6bYF06hg| Part 1]], [[https://www.youtube.com/watch?v=2vPjMBYMM0E&t=1s | Part 2 ]] || [[http://surfer.nmr.mgh.harvard.edu/pub/docs/fs.multimodal1_2018.pptx|Multi-Modal Integration, Part 1: Registration]], [[http://surfer.nmr.mgh.harvard.edu/pub/docs/fs.multimodal-integration.Part2.pptx|Multi-Modal Integration, Part 2: Group Analysis]] || [[MultiModalTutorialV6.0|Multi-Modal Integration Tutorial, Part 1]] ,[[MultiModalTutorialV6.0|Multi-Modal Integration Tutorial, Part 2]] ||
||Tracts Constrained by Underlying Anatomy (TRACULA) || [[https://www.youtube.com/watch?v=LpdYbe4pJK0&t=79s| Part 1]], [[https://www.youtube.com/watch?v=BvTi7B4rneU| Part 2]] || [[http://surfer.nmr.mgh.harvard.edu/pub/docs/tracula,fs.ppt|Slides]] || [[FsTutorial/Tracula|TRACULA Tutorial]] ||

Bonus Talks and Slides: [[http://surfer.nmr.mgh.harvard.edu/pub/docs/tracula,fs.ppt|Longitudinal TRACULA]]

==== Day 5: fMRI Analysis and FSFAST ====
||'''Subject''' ||'''Talk''' ||'''Slides''' ||'''Relevant Tutorials''' ||
|| Basics of fMRI || [[https://www.youtube.com/watch?v=cAkdey4SH7o&t=138s| Intro to fMRI Talk]] || [[http://surfer.nmr.mgh.harvard.edu/pub/docs/fMRI_intro2018.ppt|Slides]] || N/A ||
|| Resting State fMRI || [[https://www.youtube.com/watch?v=DavxePlS94w&t=7s| Resting State fMRI Presentation ]] || [[http://surfer.nmr.mgh.harvard.edu/pub/docs/resting-state.fmri.ppt|Resting State fMRI Slides]] || N/A ||
|| FSFAST || [[https://www.youtube.com/watch?v=Q1RoThGmuxk| FSFAST Presentation]] || [[http://surfer.nmr.mgh.harvard.edu/pub/docs/fsfast.ppt|FSFAST, Part 1 and 2]] || [[FsFastTutorialV6.0|FSFAST Tutorial, Part 1]], [[FsFastTutorialV6.0|FSFAST Tutorial, Part 2]] ||

Bonus Talks and Slides: [[http://surfer.nmr.mgh.harvard.edu/pub/docs/freesurfer-struct-func04022018-handoutb.pdf| Structural & Functional Data Integration]]

=== Getting the Help and Support you need ===
You can email the FreeSurfer Help mailing list with questions related to your own data processing and troubleshooting. The address to email for all questions is: freesurfer@nmr.mgh.harvard.edu. For troubleshooting your data processing, be sure to attach your recon-all.log file to your email. For questions specifically related to any of the above lectures or tutorials, feel free to email the speaker of the lecture, you can find their emails below. <<BR>>

||'''Lecture Topic''' ||'''Lecturer''' ||'''Email Address''' ||
|| Intro to FreeSurfer Jargon || Dev Cordero || dccordero@mgh.harvard.edu ||
|| Intro to Linux for Freesurfer Users <<BR>> ROI Analysis || Matt Larrabee || mlarrabee1@mgh.harvard.edu ||
|| Intro to FreeSurfer Software || Matt Vera || mvera2@mgh.harvard.edu ||
|| Analyzing the Individual Subject || Bram Diamond || brdiamond@mgh.harvard.edu ||
|| Intro to FreeView & Working with Data || Kim Nestor || knestor1@mgh.harvard.edu ||
|| Troubleshooting || Leah Morgan || lmorgan6@mgh.harvard.edu ||
|| Group Analysis <<BR>> Multiple Comparisons || Paul Wighton || paul@corticometrics.com ||

=== Upcoming FreeSurfer courses ===
If you would like to be notified about upcoming !FreeSurfer courses, sign up for the [[http://surfer.nmr.mgh.harvard.edu/cgi-bin/fsurfer/interest.cgi|course mailing list.]]. We host two Boston courses each year, typically in the first week of April and the last week of September.<<BR>>