Differences between revisions 107 and 110 (spanning 3 versions)

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 FreeSurfer installation on your machine, and a local copy of the tutorial data. Be sure to set the TUTORIAL_DATA environment variable properly as specified on the 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:

Introduction to FreeSurfer Output

version 6.0+

Basics:

Specialized topics:

Other:

Multiple Comparisons via command-line (slides, video)

version 5.1/5.3

Data for the 5.1/5.3 tutorials can be found on the bottom of the tutorial data page.

Basics:

Specialized topics:

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-= Virtual FreeSurfer Course for Boston Veterans Administration Feb 17, 2026 =

This is a 4 hour shortened version of our [[https://surfer.nmr.mgh.harvard.edu/fswiki/VirtualCourse|Full 2-Day Course]]. 

== Schedule ==

 Tuesday, Feb 17 - Introduction / Single Subject Analysis / Group Analysis 
||12:00 - 12:30 ||[[attachment:va2026.fs.intro.pptx|Introduction to Freesurfer]] ||talk ||Doug Greve ||
||12:30 -  1:30 ||[[attachment:va2026.fsrecon.pptx|Analyzing the Individual Subject]] ||talk ||Doug Greve ||
|| 1:30 -  2:00 ||[[FsTutorial/FreeviewDemo|Freeview Demo]] ||demo ||Doug Greve ||
|| 2:00 -  2:30 ||[[FsTutorial/OutputData_freeview|Tutorial: Individual Subject Output]] ||tutorial ||Nate Draudt ||
|| 2:30 -  3:15 ||[[attachment:va2026.GLM.pptx|Group Analysis]] ||talk ||Doug Greve ||
|| 3:15 -  4:00 ||[[FsTutorial/GroupAnalysisV6.0|Tutorial: Group Analysis]] ([[FsgdExamples|FSGD Examples]]) ||tutorial ||Nate Draudt||
|| 4:00 -  4:30 ||Self-paced Practice ||tutorial ||staff ||
|| 4:30 -  5:00 ||Q&A ||tutorial ||staff ||

[[https://surfer.nmr.mgh.harvard.edu/fswiki/CourseDescription/Remote_Qualify|Setting up the VM.]] This is already done for the course.

[[https://surfer.nmr.mgh.harvard.edu/fswiki/VirtualCourse|Full 2-Day Course can be found here]]. 

<<BR>><<BR>><<BR>><<BR>><<BR>><<BR>>
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- * [[FsTutorial/PracticeV6.0| Practice Working with Data]]
+ * [[FsTutorial/PracticeV6.0|Practice Working with Data]]
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- * [[FsTutorial/MultipleComparisonsV6.0Perm|Multiple Comparisons via command-line (Permutation)]]
 ([[http://surfer.nmr.mgh.harvard.edu/pub/docs/GLM.pptx|slides]])
+ * [[FsTutorial/MultipleComparisonsV6.0Perm|Multiple Comparisons via command-line (Permutation)]] ([[http://surfer.nmr.mgh.harvard.edu/pub/docs/GLM.pptx|slides]])
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- * [[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]])
+ * [[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]])
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