layout: post title: 'Freesurfer 2013 course: Videos and PPTs' date: '2014-01-21T09:17:00.001-09:00' author: Qingyang tags:
<div style="margin-bottom: 12px; margin-top: 16px;"><span style="font-size: large; font-weight: 600;">Intro</span></div><div style="margin-bottom: 12px; margin-top: 12px;">The developers of (FreeSurfer)[www.freesurfer.net] have put videos of their 2013 training course online to YouTube. The PowerPoint slides they used in the course are also freely distributed on their website. This gives the new Freesurfer users like me a great way to learn about this neuroimaging data processing and analysis tool. I am truly thankful for the generous of the FreeSerfer team for making the course lectures available online. It is really nice that I can take the courses in my own time and on my own pace. And it does not really cost me anything. All I need is, well, to fight with my procrastination.</div><div style="margin-bottom: 12px; margin-top: 12px;">One thing I found not very good is that the videos on <a href="http://www.youtube.com/channel/UCruQerP8aa-gYttXkAcyveA"><span style="color: blue;">the FreeSurfer YouTube channel</span></a> is not organized well enough. I had to constantly refer back to the <a href="http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Nov2013CourseSchedule"><span style="color: blue;">course schedule</span></a> to figure out which video should I watch after one ends. So I pulled all the links for the videos and corresponding slides together and arranged them according to the course schedule. The organized links are shared below.</div><div style="margin-bottom: 12px; margin-top: 12px;">Please note that only the talk session were put online. Most of the tutorials and demonstrations module of the course were not available in the form of videos. There are, however, the web links to the tutorial materials (which I also have the links) are available. It is very important to go through the tutorials if you really want to master the Freesurfer software. Hope the organized links are useful to you. Cheers~~</div><div style="margin-bottom: 12px; margin-top: 18px;"><span style="font-size: x-large; font-weight: 600;">Course Videos and Links</span></div><div style="margin-bottom: 12px; margin-top: 16px;"><span style="font-size: large; font-weight: 600;">Day 1</span></div><div style="margin-bottom: 12px; margin-top: 14px;"><span style="font-size: medium; font-weight: 600;">1.1 Tutorial: Unix Tutorial for FreeSurfer Users</span></div><ul style="-qt-list-indent: 1; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px;"><li style="margin: 12px 0px 0px;">Video: Not Available</li><li style="margin: 0px 0px 12px;">PPT: <a href="http://surfer.nmr.mgh.harvard.edu/pub/docs/unix_tutorial_FS_course.ppt"><span style="color: blue;">DownLoad</span></a></li></ul><div style="margin-bottom: 12px; margin-top: 14px;"><span style="font-size: medium; font-weight: 600;">1.2 Talk: Introduction To FreeSurfer Jargon</span></div><ul style="-qt-list-indent: 1; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px;"><li style="margin: 12px 0px 0px;">Video: <a href="http://www.youtube.com/watch?v=GywOKtfKZIU"><span style="color: blue;">Watch on Youtube</span></a></li><li style="margin: 0px 0px 12px;">PPT: <a href="http://surfer.nmr.mgh.harvard.edu/pub/docs/fsjargon.ppt.pptx"><span style="color: blue;">DownLoad</span></a></li></ul><div style="margin-bottom: 12px; margin-top: 14px;"><span style="font-size: medium; font-weight: 600;">1.3 Talk: Introduction To FreeSurfer</span></div><ul style="-qt-list-indent: 1; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px;"><li style="margin: 12px 0px 0px;">Video: <a href="http://www.youtube.com/watch?v=eZcIHXXq_Uc"><span style="color: blue;">Watch on Youtube</span></a></li><li style="margin: 0px 0px 12px;">PPT: <a href="http://surfer.nmr.mgh.harvard.edu/pub/docs/Nov2013/freesurfer.intro.ppt"><span style="color: blue;">DownLoad</span></a></li></ul><div style="margin-bottom: 12px; margin-top: 14px;"><span style="font-size: medium; font-weight: 600;">1.4 Talk: Analyzing the Individual Subject</span></div><ul style="-qt-list-indent: 1; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px;"><li style="margin: 12px 0px 0px;">Video Part 1: <a href="http://youtu.be/8Ict0Erh7_c"><span style="color: blue;">Watch on Youtube</span></a></li><li style="margin: 0px;">Video Part 2: <a href="http://youtu.be/KncPouQWAp0"><span style="color: blue;">Watch on Youtube</span></a></li><li style="margin: 0px 0px 12px;">PPT: <a href="http://surfer.nmr.mgh.harvard.edu/pub/docs/Nov2013/fsrecon.ppt"><span style="color: blue;">DownLoad</span></a></li></ul><div style="margin-bottom: 12px; margin-top: 14px;"><span style="font-size: medium; font-weight: 600;">1.5 Talk: A Non-physicist’s Intro to MR</span></div><ul style="-qt-list-indent: 1; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px;"><li style="margin: 12px 0px 0px;">Video: <a href="http://youtu.be/SwsH64PBBZE"><span style="color: blue;">Watch on Youtube</span></a></li><li style="margin: 0px 0px 12px;">PPT: <a href="http://surfer.nmr.mgh.harvard.edu/pub/docs/FreeSurfer_Course_Apr_2013_MRI_Basics.pdf"><span style="color: blue;">DownLoad</span></a></li></ul><div style="margin-bottom: 12px; margin-top: 14px;"><span style="font-size: medium; font-weight: 600;">1.6 Demo: Freeview/Tksurfer Demostration</span></div><div style="margin-bottom: 12px; margin-top: 12px;">N/A</div><div style="margin-bottom: 12px; margin-top: 14px;"><span style="font-size: medium; font-weight: 600;">1.7 Tutorial: Interaction with Individual Subject Data Tutorial</span></div><ul style="-qt-list-indent: 1; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px;"><li style="margin: 12px 0px;">Tutorial: <a href="http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/OutputData_freeview"><span style="color: blue;">access</span></a></li></ul><div style="margin-bottom: 12px; margin-top: 14px;"><span style="font-size: medium; font-weight: 600;">1.8 Talk: FreeSurfer Troubleshooting</span></div><ul style="-qt-list-indent: 1; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px;"><li style="margin: 12px 0px 0px;">Video: <a href="http://www.youtube.com/watch?v=gf0BC0xs0tM"><span style="color: blue;">Watch on Youtube</span></a></li><li style="margin: 0px 0px 12px;">PPT: <a href="http://surfer.nmr.mgh.harvard.edu/pub/docs/Nov2013/freesurfer.failure_modes.ppt"><span style="color: blue;">DownLoad</span></a></li></ul><div style="margin-bottom: 12px; margin-top: 14px;"><span style="font-size: medium; font-weight: 600;">1.9 Demo: Quality Checking a Recon</span></div><ul style="-qt-list-indent: 1; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px;"><li style="margin: 12px 0px;">PPT: <a href="http://surfer.nmr.mgh.harvard.edu/pub/docs/QArecon.ppt"><span style="color: blue;">DownLoad</span></a></li></ul><div style="margin-bottom: 12px; margin-top: 14px;"><span style="font-size: medium; font-weight: 600;">1.10 Tutorial: Troubleshooting Tutorial</span></div><ul style="-qt-list-indent: 1; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px;"><li style="margin: 12px 0px;">Tutorial: <a href="http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TroubleshootingData"><span style="color: blue;">access</span></a></li></ul><div style="margin-bottom: 12px; margin-top: 14px;"><span style="font-size: medium; font-weight: 600;">1.11 Talk: Question and Answer Session (Answers to online questions here)</span></div><ul style="-qt-list-indent: 1; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px;"><li style="margin: 12px 0px 0px;">Video: N/A</li><li style="margin: 0px 0px 12px;">Questions Online: <a href="http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/QuestionAnswers"><span style="color: blue;">access</span></a></li></ul><div style="margin-bottom: 12px; margin-top: 16px;"><span style="font-size: large; font-weight: 600;">Day 2:</span></div><div style="margin-bottom: 12px; margin-top: 14px;"><span style="font-size: medium; font-weight: 600;">2.1 Talk: Surface-based Analysis: Intersubject Smoothing & Registration</span></div><ul style="-qt-list-indent: 1; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px;"><li style="margin: 12px 0px 0px;">Video: <a href="http://youtu.be/8WPvXoORoAw"><span style="color: blue;">Watch on Youtube</span></a></li><li style="margin: 0px 0px 12px;">PPT: <a href="http://surfer.nmr.mgh.harvard.edu/pub/docs/Nov2013/fs.surface-based-analysis.ppt"><span style="color: blue;">DownLoad</span></a></li></ul><div style="margin-bottom: 12px; margin-top: 14px;"><span style="font-size: medium; font-weight: 600;">2.2 Talk: Group Analysis</span></div><ul style="-qt-list-indent: 1; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px;"><li style="margin: 12px 0px 0px;">Video part 1: <a href="http://youtu.be/EJewud8obuo"><span style="color: blue;">Watch on Youtube</span></a></li><li style="margin: 0px;">Video part 2: <a href="http://youtu.be/9111bn-XVsA"><span style="color: blue;">Watch on Youtube</span></a></li><li style="margin: 0px 0px 12px;">PPT: <a href="http://surfer.nmr.mgh.harvard.edu/pub/docs/Nov2013/freesurfer.groupanalysis.ppt"><span style="color: blue;">DownLoad</span></a></li></ul><div style="margin-bottom: 12px; margin-top: 14px;"><span style="font-size: medium; font-weight: 600;">2.3 Tutorial: Group Analysis Tutorial:</span></div><ul style="-qt-list-indent: 1; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px;"><li style="margin: 12px 0px;">Tutorial: <a href="http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis"><span style="color: blue;">access</span></a></li></ul><div style="margin-bottom: 12px; margin-top: 14px;"><span style="font-size: medium; font-weight: 600;">2.4 Talk: Multiple Comparisons</span></div><ul style="-qt-list-indent: 1; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px;"><li style="margin: 12px 0px 0px;">Video: <a href="http://youtu.be/s87--3yG6mU"><span style="color: blue;">Watch on Youtube</span></a></li><li style="margin: 0px 0px 12px;">PPT: <a href="http://surfer.nmr.mgh.harvard.edu/pub/docs/Nov2013/freesurfer.multipecomparisons.ppt"><span style="color: blue;">DownLoad</span></a></li></ul><div style="margin-bottom: 12px; margin-top: 14px;"><span style="font-size: medium; font-weight: 600;">2.5 Demo: QDEC demonstration</span></div><ul style="-qt-list-indent: 1; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px;"><li style="margin: 12px 0px;">N/A</li></ul><div style="margin-bottom: 12px; margin-top: 14px;"><span style="font-size: medium; font-weight: 600;">2.6 Tutorial: Multiple Comparisons Tutorial</span></div><ul style="-qt-list-indent: 1; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px;"><li style="margin: 12px 0px;">Tutorial: <a href="http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis#ClusterwiseCorrectionforMultipleComparisons"><span style="color: blue;">access</span></a></li></ul><div style="margin-bottom: 12px; margin-top: 14px;"><span style="font-size: medium; font-weight: 600;">2.7 Tutorial: QDEC Tutorial</span></div><ul style="-qt-list-indent: 1; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px;"><li style="margin: 12px 0px;">Tutorial: <a href="http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/QdecGroupAnalysis_freeview"><span style="color: blue;">access</span></a></li></ul><div style="margin-bottom: 12px; margin-top: 14px;"><span style="font-size: medium; font-weight: 600;">2.8 Talk: ROI Analysis</span></div><ul style="-qt-list-indent: 1; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px;"><li style="margin: 12px 0px 0px;">Video: <a href="http://youtu.be/n5QkCwZZPko"><span style="color: blue;">Watch on Youtube</span></a></li><li style="margin: 0px 0px 12px;">PPT: <a href="http://surfer.nmr.mgh.harvard.edu/pub/docs/Nov2013/fs.roi.ppt"><span style="color: blue;">DownLoad</span></a></li></ul><div style="margin-bottom: 12px; margin-top: 14px;"><span style="font-size: medium; font-weight: 600;">2.9 Tutorial: ROI Analysis Tutorial</span></div><ul style="-qt-list-indent: 1; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px;"><li style="margin: 12px 0px;">Tutorial: <a href="http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/AnatomicalROI"><span style="color: blue;">access</span></a></li></ul><div style="margin-bottom: 12px; margin-top: 14px;"><span style="font-size: medium; font-weight: 600;">2.10 Talk: Longitudinal FreeSurfer</span></div><ul style="-qt-list-indent: 1; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px;"><li style="margin: 12px 0px 0px;">Video: <a href="http://youtu.be/vxJODPBLd3M"><span style="color: blue;">Watch on Youtube</span></a></li><li style="margin: 0px;">PPT: <a href="http://surfer.nmr.mgh.harvard.edu/pub/docs/freesurfer.longitudinal.ppt"><span style="color: blue;">DownLoad</span></a></li><li style="margin: 0px 0px 12px;">Wiki: <a href="http://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalProcessing"><span style="color: blue;">access</span></a></li></ul><div style="margin-bottom: 12px; margin-top: 14px;"><span style="font-size: medium; font-weight: 600;">2.11 Tutorial: Longitudinal Tutorial</span></div><ul style="-qt-list-indent: 1; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px;"><li style="margin: 12px 0px;">Tutorial: <a href="http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/LongitudinalTutorial_freeview"><span style="color: blue;">access</span></a></li></ul><div style="margin-bottom: 12px; margin-top: 16px;"><span style="font-size: large; font-weight: 600;">Day 3</span></div><div style="margin-bottom: 12px; margin-top: 14px;"><span style="font-size: medium; font-weight: 600;">3.1 Talk: Multi-Modal Integration, Part 1</span></div><ul style="-qt-list-indent: 1; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px;"><li style="margin: 12px 0px 0px;">Video: <a href="http://youtu.be/gRl6bYF06hg"><span style="color: blue;">Watch on Youtube</span></a></li><li style="margin: 0px 0px 12px;">PPT: <a href="http://surfer.nmr.mgh.harvard.edu/pub/docs/Nov2013/fs.multimodal-integration.ppt"><span style="color: blue;">DownLoad</span></a></li></ul><div style="margin-bottom: 12px; margin-top: 14px;"><span style="font-size: medium; font-weight: 600;">3.2 Tutorial: Multi-Modal Integration Tutorial, Part 1</span></div><ul style="-qt-list-indent: 1; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px;"><li style="margin: 12px 0px;">Tutorial: <a href="http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/MultiModal_freeview"><span style="color: blue;">access</span></a></li></ul><div style="margin-bottom: 12px; margin-top: 14px;"><span style="font-size: medium; font-weight: 600;">3.3 Talk: Introduction to Diffusion MRI</span></div><ul style="-qt-list-indent: 1; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px;"><li style="margin: 12px 0px 0px;">Video Part 1: <a href="http://youtu.be/BKjBdeWYllk"><span style="color: blue;">Watch on Youtube</span></a></li><li style="margin: 0px;">Video Part 2: <a href="http://youtu.be/efsxszjPmpc"><span style="color: blue;">Watch on Youtube</span></a></li><li style="margin: 0px 0px 12px;">PPT: <a href="http://www.youtube.com/redirect?q=http%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Fpub%2Fdocs%2Fdmri%2Cfs.ppt&session_token=C9HlF0TSY-dRtytCILLZuM8MixR8MTM5MDMxODE1N0AxMzkwMjMxNzU3"><span style="color: blue;">DownLoad</span></a></li></ul><div style="margin-bottom: 12px; margin-top: 14px;"><span style="font-size: medium; font-weight: 600;">3.4 Tutorial: Diffusion Processing Tutorial</span></div><ul style="-qt-list-indent: 1; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px;"><li style="margin: 12px 0px;">Tutorial: <a href="http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Diffusion"><span style="color: blue;">access</span></a></li></ul><div style="margin-bottom: 12px; margin-top: 14px;"><span style="font-size: medium; font-weight: 600;">3.5 Talk: TRActs Constrained by UnderLying Anatomy (TRACULA)</span></div><ul style="-qt-list-indent: 1; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px;"><li style="margin: 12px 0px 0px;">Video part 1: <a href="http://youtu.be/LpdYbe4pJK0"><span style="color: blue;">Watch on Youtube</span></a></li><li style="margin: 0px;">Video part 2: <a href="http://youtu.be/BvTi7B4rneU"><span style="color: blue;">Watch on Youtube</span></a></li><li style="margin: 0px 0px 12px;">PPT: <a href="http://surfer.nmr.mgh.harvard.edu/pub/docs/tracula,fs.ppt"><span style="color: blue;">DownLoad</span></a></li></ul><div style="margin-bottom: 12px; margin-top: 14px;"><span style="font-size: medium; font-weight: 600;">3.6 Tutorial: Tracula Tutorial</span></div><ul style="-qt-list-indent: 1; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px;"><li style="margin: 12px 0px;">Tutorial: <a href="http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Tracula"><span style="color: blue;">access</span></a></li></ul><div style="margin-bottom: 12px; margin-top: 14px;"><span style="font-size: medium; font-weight: 600;">3.7 Talk: Multi-Modal Integration, Part 2</span></div><ul style="-qt-list-indent: 1; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px;"><li style="margin: 12px 0px 0px;">Video: Watch on Youtube</li><li style="margin: 0px 0px 12px;">PPT: <a href="http://surfer.nmr.mgh.harvard.edu/pub/docs/Nov2013/fs.multimodal-integration.ppt"><span style="color: blue;">DownLoad</span></a></li></ul><div style="margin-bottom: 12px; margin-top: 14px;"><span style="font-size: medium; font-weight: 600;">3.8 Tutorial: Multi-Modal Integration Tutorial, Part 2</span></div><ul style="-qt-list-indent: 1; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px;"><li style="margin: 12px 0px;">Tutorial: <a href="http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/MultiModal_freeview"><span style="color: blue;">access</span></a></li></ul><div style="margin-bottom: 12px; margin-top: 14px;"><span style="font-size: medium; font-weight: 600;">3.9 Talk: MRI Acquisition Methods For Morphometry</span></div><ul style="-qt-list-indent: 1; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px;"><li style="margin: 12px 0px 0px;">Video: <a href="http://youtu.be/aZfy8gsPxZE"><span style="color: blue;">Watch on Youtube</span></a></li><li style="margin: 0px 0px 12px;">PPT: <a href="http://surfer.nmr.mgh.harvard.edu/pub/docs/mri_acquisition.ppt"><span style="color: blue;">DownLoad</span></a></li></ul><div style="margin-bottom: 12px; margin-top: 14px;"><span style="font-size: medium; font-weight: 600;">3.10 Talk: Motion-compensated neuroanatomical imaging</span></div><ul style="-qt-list-indent: 1; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px;"><li style="margin: 12px 0px 0px;">Video: <a href="http://youtu.be/uZGie1XWKa8"><span style="color: blue;">Watch on Youtube</span></a></li><li style="margin: 0px 0px 12px;">PPT: <a href="http://surfer.nmr.mgh.harvard.edu/pub/docs/FreeSurfer_Course_Apr_2013_Motion_Correction.pdf"><span style="color: blue;">DownLoad</span></a></li></ul><div style="margin-bottom: 12px; margin-top: 14px;"><span style="font-size: medium; font-weight: 600;">3.11 Talk: Registration Methods</span></div><ul style="-qt-list-indent: 1; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; margin-top: 0px;"><li style="margin: 12px 0px 0px;">Video: <a href="http://youtu.be/DQOmdLpf82k"><span style="color: blue;">Watch on Youtube</span></a></li><li style="margin: 0px 0px 12px;">PPT: <a href="http://surfer.nmr.mgh.harvard.edu/pub/docs/Nov2013/fs.registration.ppt"><span style="color: blue;">DownLoad</span></a> <!--EndFragment--></li></ul>