= FreeSurfer Tutorials =
The !FreeSurfer tutorials provided below are designed to give users an introduction to using !FreeSurfer, as well as get you acquainted with the concepts needed to perform its various modes of analysis and processing of MRI data.  The tutorials are designed to be followed along in a terminal window, where commands can be copy/pasted into the terminal window instead of typed.

In order to run any of the !FreeSurfer tutorials, you must have a valid [[DownloadAndInstall|FreeSurfer]] installation on your machine, and a local copy of the [[FsTutorial/Data|tutorial data]]. Be sure to set the '''TUTORIAL_DATA''' environment variable properly as specified on the [[FsTutorial/Data|tutorial data]] page.

== 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. ==

=== version 7.0+ ===
Basics:
 * [[FsTutorial/OutputData_freeview|Introduction to FreeSurfer Output]]

=== version 6.0+ ===
Basics:

 * [[FsTutorial/OutputData_freeviewV6.0|Introduction to FreeSurfer Output]] ([[http://surfer.nmr.mgh.harvard.edu/pub/docs/fsrecon.sep2022.pptx|slides]], [[https://www.youtube.com/watch?v=8Ict0Erh7_c|video]])
 * [[FsTutorial/PracticeV6.0| Practice Working with Data]]
 * [[FsTutorial/TroubleshootingDataV6.0|Troubleshooting FreeSurfer Output]] ([[http://surfer.nmr.mgh.harvard.edu/pub/docs/freesurfer.troubleshooting.sep2022.ppt|slides]], [[https://www.youtube.com/watch?v=gf0BC0xs0tM|video]])
 * [[FsTutorial/GroupAnalysisV6.0|Group Analysis]] ([[http://surfer.nmr.mgh.harvard.edu/pub/docs/GLM.pptx|slides]], [[https://www.youtube.com/watch?v=EJewud8obuo|video]])
 * [[FsTutorial/MultipleComparisonsV6.0Perm|Multiple Comparisons via command-line (Permutation)]]
 ([[http://surfer.nmr.mgh.harvard.edu/pub/docs/GLM.pptx|slides]])
 * [[FsTutorial/QdecGroupAnalysisV6.0|Qdec Group Analysis via GUI]]
 * [[FsTutorial/AnatomicalROIV6.0|ROI Analysis]] ( [[http://surfer.nmr.mgh.harvard.edu/pub/docs/fs.roi.EB_wiki.pptx|slides]], [[https://www.youtube.com/watch?v=n5QkCwZZPko|video]])
 * [[MultiModalTutorialV6.0|Multimodal Analysis]] ([[http://surfer.nmr.mgh.harvard.edu/pub/docs/fs.multimodal1_2018.pptx|slides- Part 1]], [[http://surfer.nmr.mgh.harvard.edu/pub/docs/fs.multimodal-integration.Part2.pptx|slides- Part 2]], [[https://www.youtube.com/watch?v=gRl6bYF06hg|video]])

Specialized topics:

 * [[FsTutorial/LongitudinalTutorial|Longitudinal Processing, Edits and Post-Processing]] ([[http://surfer.nmr.mgh.harvard.edu/pub/docs/fs.longitudinal.pptx|slides]], [[https://www.youtube.com/watch?v=vxJODPBLd3M|video]])
 * [[FsTutorial/DiffusionV6.0|Diffusion Analysis]] ([[http://surfer.nmr.mgh.harvard.edu/pub/docs/dmri,fs.ppt|slides]], [[https://www.youtube.com/watch?v=BKjBdeWYllk|video]])
 * [[FsTutorial/Tracula|TRACULA]] ([[http://surfer.nmr.mgh.harvard.edu/pub/docs/tracula,fs.ppt|slides]], [[https://www.youtube.com/watch?v=LpdYbe4pJK0|video]])
 * [[FsFastTutorialV6.0|FS-Fast - fMRI Analysis]] ([[http://surfer.nmr.mgh.harvard.edu/pub/docs/fsfast.ppt|slides]])

Other:
 * [[FsTutorial/MultipleComparisonsV6.0|Multiple Comparisons via command-line]]
 ([[http://surfer.nmr.mgh.harvard.edu/pub/docs/multiplecomparisons.ppt|slides]], [[https://www.youtube.com/watch?v=EJewud8obuo|video]])

----
=== version 5.1/5.3 ===

Data for the 5.1/5.3 tutorials can be found on the bottom of the [[FsTutorial/Data#FreeSurferTutorialDatasets5.1.2BAC8-5.3|tutorial data]] page.

Basics:

 * [[FsTutorial/OutputData_freeviewV6.0|Introduction to FreeSurfer Output]] ([[http://surfer.nmr.mgh.harvard.edu/pub/docs/fsrecon.ppt|slides]], [[https://www.youtube.com/watch?v=8Ict0Erh7_c|video]])
 * [[FsTutorial/TroubleshootingData|Troubleshooting FreeSurfer Output]] ([[http://surfer.nmr.mgh.harvard.edu/pub/docs/freesurfer.failure_modes.ppt|slides]], [[https://www.youtube.com/watch?v=gf0BC0xs0tM|video]])
 * [[FsTutorial/GroupAnalysis|Group Analysis/ Multiple Comparisons via command-line]] ([[http://surfer.nmr.mgh.harvard.edu/pub/docs/freesurfer.groupanalysis.ERL.ppt|slides]], [[https://www.youtube.com/watch?v=EJewud8obuo|video]])
 * [[FsTutorial/QdecGroupAnalysis_freeview|Qdec Group Analysis via GUI]]
 * [[FsTutorial/AnatomicalROI|ROI Analysis]] ( [[http://surfer.nmr.mgh.harvard.edu/pub/docs/fs.roi.ppt|slides]], [[https://www.youtube.com/watch?v=n5QkCwZZPko|video]])
 * [[FsTutorial/MultiModal_freeview|Multimodal Analysis]] ([[http://surfer.nmr.mgh.harvard.edu/pub/docs/fs.multimodal-integration.Part1.ppt|slides- Part 1]], [[http://surfer.nmr.mgh.harvard.edu/pub/docs/fs.multimodal-integration.Part2.ppt|slides- Part 2]], [[https://www.youtube.com/watch?v=gRl6bYF06hg|video]])

Specialized topics:

 * [[FsTutorial/LongitudinalTutorialV5|Longitudinal Processing, Edits and Post-Processing]] ([[http://surfer.nmr.mgh.harvard.edu/pub/docs/freesurfer.longitudinal.ppt|slides]], [[https://www.youtube.com/watch?v=vxJODPBLd3M|video]])
 * [[FsTutorial/Diffusion|Diffusion Analysis]] [[FsTutorial/Diffusion_DtiIntegration|Diffusion and DTI Integration]] ([[http://surfer.nmr.mgh.harvard.edu/pub/docs/dmri,fs.ppt|slides]], [[https://www.youtube.com/watch?v=BKjBdeWYllk|video]])
 * [[FsTutorial/Tracula|TRACULA]] ([[http://surfer.nmr.mgh.harvard.edu/pub/docs/tracula,fs.ppt|slides]], [[https://www.youtube.com/watch?v=LpdYbe4pJK0|video]])
 * [[FsFastTutorial|FS-Fast - fMRI Analysis]] ([[http://surfer.nmr.mgh.harvard.edu/pub/docs/fsfast.april2011.ppt|slides]])

## Old versions of tutorials which use tkmedit or tksurfer (deprecated as of May 2014):
## *[[FsTutorial/OutputData_tktools|Intro to FreeSurfer Output]]
##  *[[FsTutorial/GroupAnalysis_tktools|Group Analysis via command-line]]
##  *[[FsTutorial/QdecGroupAnalysis_tktools|Group Analysis via GUI]]
##  *[[FsTutorial/AnatomicalROI_tktools|ROI Analysis]]
##  *[[FsTutorial/MultiModal_tktools|Multimodal Analysis]]
##  *[[FsTutorial/LongitudinalTutorial_tktools|Longitudinal Processing, Edits and Post-Processing]]