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== Spring 2020 FreeSurfer Course: March 30th - April 2nd ==
=== 8:00 - 9:30am Registration Desk Open ===
* Indicates an optional technical talk. These talks have great content. They are related to, but not directly about, the !FreeSurfer processing stream. <<BR>> ** Indicates an optional talk that covers basic/beginner material. <<BR>> *** Indicates optional extra time to work on tutorials and/or ask questions about your own data. <<BR>> <<BR>> Research backgrounds of past and present staff members can be found on the [[https://www.martinos.org/lab/lcn/people|LCN website]].
==== Monday, March 30th - Introduction / Single Subject Analysis / ROI Analysis  ====
||'''Time''' ||'''Title''' ||'''Type''' ||'''Lecturer''' ||
||8:30 - 8:40 ||** Intro to Linux for !FreeSurfer Users ||talk/demo || Matthew Larrabee ||
||8:40 - 9:00 ||** [[https://surfer.nmr.mgh.harvard.edu/fswiki/UnixTutorial|Unix for FreeSurfer Users]] ||tutorial || ||
||9:00 - 9:15 ||** [[http://surfer.nmr.mgh.harvard.edu/pub/docs/fsjargon_clean.pptx|Intro to FreeSurfer Jargon]] || talk || Caroline Magnain ||
||9:15 - 9:25 ||'''break''' || || ||
||9:25 - 10:10 ||[[attachment:freesurfer.intro.apr.2019.ppt|Introduction to Freesurfer]] ||talk ||Bruce Fischl ||
||10:10 - 11:20 ||[[http://surfer.nmr.mgh.harvard.edu/pub/docs/fsrecon.pptx|Analyzing the Individual Subject]] ||talk ||Doug Greve ||
||11:20 - 11:40 ||'''break''' || || ||
||11:40 - 12:00 ||[[https://www.youtube.com/watch?v=Mv-ECowxq2o|Freeview demonstration]] ||[[FsTutorial/FreeviewDemo|demo]] || Bram Diamond ||
||12:00 - 12:30 ||[[FsTutorial/OutputData_freeview|Introduction to FreeSurfer Output]] ||tutorial ||staff ||
||12:30 - 1:30 ||'''Lunch''' [[https://surfer.nmr.mgh.harvard.edu/fswiki/CourseDescription?action=AttachFile&do=get&target=CourseMap.jpg|(Suggestions for where to eat)]] ||||||
||1:30 - 1:45 ||[[FsTutorial/OutputData_freeview|Introduction to FreeSurfer Output]] ||tutorial ||staff ||
||1:45 - 2:15 ||[[http://surfer.nmr.mgh.harvard.edu/pub/docs/fs.surface-based-analysis.ppt |Surface-based Analysis: Intersubject Registration & Smoothing  ]] ||talk || Diyva Varadarajan ||
||2:15 - 2:35 ||'''break''' || || ||
||2:35 - 3:05 ||[[http://surfer.nmr.mgh.harvard.edu/pub/docs/fs.roi.EB_wiki.pptx|ROI Analysis]] ||talk || Doug Greve ||
||3:05 - 3:50 ||[[FsTutorial/AnatomicalROIV6.0|ROI Analysis Tutorial]] ||tutorial ||staff ||
||3:50 - 4:20 || [[http://surfer.nmr.mgh.harvard.edu/pub/docs/freesurfer-struct-func04022018-handoutb.pdf| Structural & Functional Data Integration]] ||talk ||David Salat ||
||4:20 - 4:50 ||[[FsTutorial/Practice|Practice Working with Data]] ||tutorial ||staff ||
Answers to online questions [[http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/QuestionAnswers|here]]
==== Tuesday, March 31st - Group Analysis / Longitudinal Analysis / Troubleshooting ====
||'''Time''' ||'''Title''' ||'''Type''' ||'''Lecturer''' ||
||8:00 - 9:00 ||*** Morning Help Session|| || research technicians ||
||9:00 - 9:45 ||[[http://surfer.nmr.mgh.harvard.edu/pub/docs/GLM.pptx|Group Analysis]] ||talk || Viviana Siless ||
||9:45 - 10:25 ||[[FsTutorial/GroupAnalysisV6.0|Group Analysis Tutorial]] ([[FsgdExamples|FSGD Examples]]) ||tutorial ||staff ||
||10:25 - 10:45 ||'''break''' || || ||
||10:45 - 11:30 ||[[http://surfer.nmr.mgh.harvard.edu/pub/docs/freesurfer.troubleshooting.apr2019.ppt|FreeSurfer Troubleshooting]] ||talk ||Bruce Fischl ||
||11:30 - 12:30 ||[[FsTutorial/TroubleshootingDataV6.0|Troubleshooting Tutorial]] ||tutorial ||staff ||
||12:30 - 1:30 ||'''Lunch''' || || ||
||1:30 - 2:15 ||[[https://youtu.be/AR83_Bt04VQ|Quality Checking a Recon]] || [[https://zoom.us/wc/join/369478461?pwd=|talk]] ||Leah Morgan ||
||2:15 - 2:55 ||[[http://surfer.nmr.mgh.harvard.edu/pub/docs/multiplecomparisons.ppt|Multiple Comparisons]] ||talk ||Doug Greve||
||2:55 - 3:25 ||[[FsTutorial/MultipleComparisonsV6.0Perm|Multiple Comparisons Tutorial]] ||tutorial ||staff ||
||3:25 - 4:05 ||'''break''' || || ||
||4:05 - 4:50 ||[[http://surfer.nmr.mgh.harvard.edu/pub/docs/fs.longitudinal.pptx|Longitudinal FreeSurfer]] ||talk ||Malte Hoffmann ||
||4:50 - 5:30 || [[FsTutorial/LongitudinalTutorial|LongitudinalTutorial]] ||tutorial ||staff ||
##||5:30 - 6:15 ||*** Optional time to work on tutorials / work on your own data / ask basic questions ||-- || staff||
||5:30 - 7:30 ||Social Night in the atrium of Bldg. 149|| Snacks and Beverages Served ||  ||
Answers to online questions [[http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/QuestionAnswers|here]]
==== Wednesday, April 1st - Multimodal Analysis / Diffusion Analysis / fMRI Analysis / MR Acquisition ====
||'''Time''' ||'''Title''' ||'''Type''' ||'''Lecturer''' ||
||8:00 - 9:00 ||*** Morning Help Session || ||research technicians ||
||9:00 - 9:30 ||* [[http://surfer.nmr.mgh.harvard.edu/pub/docs/IntroMRI.pptx|Intro to MR]] ([[http://www.heartvista.com/SpinBench|SpinBench]])'' '' ||talk ||Robert Frost ||
||9:30 - 10:00 ||[[http://surfer.nmr.mgh.harvard.edu/pub/docs/fs.multimodal1_2018.pptx|Multi-Modal Integration, Part 1: Registration]] ||talk || Aina Frau-Pascual||
||10:00 - 10:30 ||[[MultiModalTutorialV6.0|Multi-Modal Integration Tutorial, Part 1]] ||tutorial ||staff ||
||10:30 - 10:50 ||'''break''' || || ||
||10:50 - 11:05 ||* [[http://surfer.nmr.mgh.harvard.edu/pub/docs/IntroDiffusion.pptx|Intro to Diffusion MRI Physics]] '' '' ||talk ||Robert Frost ||
||11:05 - 11:45 ||[[http://surfer.nmr.mgh.harvard.edu/pub/docs/dmri,fs.ppt|Introduction to Diffusion MRI]] ||talk ||Anastasia Yendiki ||
||11:45 - 12:30 ||[[FsTutorial/DiffusionV6.0|Diffusion Processing Tutorial]] ||tutorial ||staff ||
||12:30 - 1:30 ||'''Lunch''' ||-- ||-- ||
||1:30 - 2:20 ||[[http://surfer.nmr.mgh.harvard.edu/pub/docs/tracula,fs.ppt|Tracts Constrained by UnderLying Anatomy (TRACULA)]] ||talk ||Anastasia Yendiki ||
||2:20 - 3:20 ||[[FsTutorial/Tracula|TRACULA Tutorial]] ||tutorial ||staff ||
||3:20 - 3:40 ||'''break''' || || ||
||3:40 - 3:50 ||[[http://surfer.nmr.mgh.harvard.edu/pub/docs/tracula,fs.ppt|Longitudinal TRACULA]] ||talk ||Anastasia Yendiki ||
||3:50 - 4:50 ||[[http://surfer.nmr.mgh.harvard.edu/pub/docs/fMRI_intro2018.ppt|Basics of fMRI Analysis]] ||talk ||Jingyuan Chen ||
||4:50 - 5:30 ||* [[http://surfer.nmr.mgh.harvard.edu/pub/docs/FreeSurfer_Acquisition_Sep2019.ppt|MRI Acquisition Methods]] || talk ||Andre van der Kouwe||
Answers to online questions [[http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/QuestionAnswers|here]]
'''The !FreeSurfer Evaluation is [[ https://forms.gle/HmxDSXMopTdNMJKu7|here]]!'''
==== Thursday, April 2nd - fMRI Analysis / Multimodal Analysis / Future Directions ====
||'''Time''' ||'''Title''' ||'''Type''' ||'''Lecturer''' ||
||8:00 - 9:00 ||*** Morning Help Session || ||research technicians||
||9:00 - 9:30 ||[[http://surfer.nmr.mgh.harvard.edu/pub/docs/fsfast.ppt|FSFAST, Part 1: Preprocessing]] ||talk ||Doug Greve ||
||9:30 - 10:00 ||[[FsFastTutorialV6.0|FSFAST Tutorial, Part 1]] ||tutorial ||staff ||
||10:00 - 10:20 ||'''break''' & Evaluation || || ||
||10:20 - 11:20 ||[[http://surfer.nmr.mgh.harvard.edu/pub/docs/fsfast.ppt|FSFAST, Part 2: GLM Analysis]] ||talk || Doug Greve ||
||11:20 - 12:00 ||[[FsFastTutorialV6.0|FSFAST Tutorial, Part 2]] ||tutorial || staff ||
||12:00 - 1:00 ||'''Lunch''' || || ||
||1:00 - 1:30 ||* [[http://surfer.nmr.mgh.harvard.edu/pub/docs/fs.registration.ppt|An Overview of Registration Methods]] ||talk || Lilla Zöllei ||
||1:30 - 1:45 || [[http://surfer.nmr.mgh.harvard.edu/pub/docs/resting-state.fmri.ppt|Resting State fMRI]] ||talk ||Doug Greve ||
||1:45 - 2:15 ||[[http://surfer.nmr.mgh.harvard.edu/pub/docs/fs.multimodal-integration.Part2.pptx|Multi-Modal Integration, Part 2: Group Analysis]] ||talk ||Doug Greve ||
||2:15 - 3:00 ||[[MultiModalTutorialV6.0|Multi-Modal Integration Tutorial, Part 2]] ||tutorial ||staff ||
||3:00 - 3:15 ||'''break''' || || ||
||3:15 - 3:30 ||* [[http://surfer.nmr.mgh.harvard.edu/pub/docs/fs.vbm.ppt|FreeSurfer vs. VBM]] ||talk ||Doug Greve ||
||3:30 - 4:30 ||* Future Directions ||talk || FS Development Team ||
||4:30 - 5:00 ||Question & Answer Session || ||staff ||
Answers to online questions [[http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/QuestionAnswers|here]]
<<BR>>
'''!FreeSurfer Merchandise'''
Enjoyed our course? Purchase our awesome !FreeSurfer T-shirts [[https://freesurfer.threadless.com|here]].