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| The !FreeSurfer tutorials provided below are designed to give users an introduction to using !FreeSurfer, as well get you acquainted with the concepts needed to perform its various modes of MRI data analysis and image processing. This includes performing a full recon of your raw image data, troubleshooting problem data sets and examples on making edits to the data, performing group analysis, ROI analysis, longitudinal studies, diffusion analysis, TRACULA, and more. 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. The presentation slides that normally proceed the tutorial as the course are provided here as well. In some cases, a link to the actual video presentation is provided as well. In order to run any of the freesurfer tutorials you must have valid 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. |
The !FreeSurfer tutorials provided below are designed to give users an introduction to using !FreeSurfer, as well 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 valid 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. |
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| *[[FsTutorial/TroubleshootingData|Troubleshooting FreeSurfer Output]] *[[FsTutorial/GroupAnalysis|Group Analysis via command-line]] |
*[[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 via command-line]] ([[http://surfer.nmr.mgh.harvard.edu/pub/docs/freesurfer.groupanalysis.ERL.ppt|slides]], [[https://www.youtube.com/watch?v=EJewud8obuo|video]]) |
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| *[[FsTutorial/AnatomicalROI|ROI Analysis]] | *[[FsTutorial/AnatomicalROI|ROI Analysis]] ( [[http://surfer.nmr.mgh.harvard.edu/pub/docs/fs.roi.ppt|slides]], [[https://www.youtube.com/watch?v=n5QkCwZZPko|video]]) |
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| * [[FsTutorial/LongitudinalTutorial_freeview|Longitudinal Processing, Edits and Post-Processing]] * [[FsTutorial/Diffusion|Diffusion Analysis]] * [[FsTutorial/Tracula|Tracula Analysis]] * [[FsFastTutorial|FS-Fast, fMRI Analysis]] |
* [[FsTutorial/LongitudinalTutorial_freeview|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 Analysis]] ([[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]]) |
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| Old versions of tutorials which use tkmedit or tksurfer (no longer updated 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]] |
## 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]] |
FreeSurfer Tutorials
The FreeSurfer tutorials provided below are designed to give users an introduction to using FreeSurfer, as well 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 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.
Basics:
ROI Analysis ( slides, video)
Specialized topics:
Longitudinal Processing, Edits and Post-Processing (slides, video)
Diffusion Analysis Diffusion and DTI Integration (slides, video)