Diff for "FsTutorial/Spring2019CourseSchedule"

Differences between revisions 1 and 34 (spanning 33 versions)

FreeSurfer Course, April 1-4, 2019

Our awesome FreeSurfer shirts can be purchased here.

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.
** Indicates an optional talk that covers basic/beginner material.
*** Indicates extra time to work on tutorials and/or ask questions about your own data.

Monday, April 1st - Introduction / Single Subject Analysis / ROI Analysis

Time	Title	Type	Lecturer
8:30 - 9:00	** Intro to Linux for FreeSurfer Users	talk/demo	Andrew Hoopes
9:00 - 9:15	** Intro to FreeSurfer Jargon	talk	Caroline Magnain
9:15 - 9:30	break
9:30 - 10:15	Introduction to Freesurfer	talk	Bruce Fischl
10:15 - 11:25	Analyzing the Individual Subject	talk	Doug Greve
11:25 - 11:45	break
11:45 - 12:00	Freeview demonstration	demo	Bram Diamond
12:00 - 12:30	Introduction to FreeSurfer Output	tutorial	staff
12:30 - 1:30	Lunch (Suggestions for where to eat)	--	--
1:30 - 1:45	Introduction to FreeSurfer Output	tutorial	staff
1:45 - 2:15	Surface-based Analysis: Intersubject Registration & Smoothing	talk	Iman Aganj
2:15 - 2:35	break
2:35 - 3:05	ROI Analysis	talk	Emma Boyd
3:05 - 3:50	ROI Analysis Tutorial	tutorial	staff
3:50 - 4:20	Structural & Functional Data Integration	talk	David Salat
4:20 - 4:50	Practice Working with Data	tutorial	staff

Answers to online questions here

Tuesday, April 2nd - Group Analysis / Longitudinal Analysis / Troubleshooting

Time	Title	Type	Lecturer
8:00 - 9:00	*** Optional time to work on tutorials / work on your own data / ask basic questions	--	staff
9:00 - 9:50	Group Analysis	talk	Viviana Siless
9:50 - 10:30	Group Analysis Tutorial	tutorial	staff
10:30 - 10:50	break
10:50 - 11:30	Multiple Comparisons	talk	Doug Greve
11:30 - 12:00	Multiple Comparisons Tutorial	tutorial	staff
12:00 - 1:00	Lunch	--	--
1:00 - 1:45	FreeSurfer Troubleshooting	talk	Bruce Fischl
1:45 - 2:45	Troubleshooting Tutorial	tutorial	staff
2:45 - 3:05	break
3:05 - 4:05	Quality Checking a Recon	demo	Leah Morgan
4:05 - 4:50	Longitudinal FreeSurfer	talk	Malte Hoffmann
4:50 - 5:30	LongitudinalTutorial	tutorial	staff
5:30 - 6:15	*** Optional time to work on tutorials / work on your own data / ask basic questions	--	staff
6:30 - ?	Social Night, either at Boston Beer Works of Bldg. 149	social activity	you!

Answers to online questions here

Boston Beer Works location information here and here.
Meet us in front of Building 149 to catch the 6:30pm shuttle bus (it leaves on time!).
If you miss us, we are taking the MGH/Navy Yard shuttle to North Station. From there, cross the street to get to Canal Street.
Boston Beer Works will be down that street, on your right. (Shuttles depart every 15 minutes up until 7:15pm and every half hour after that).

Wednesday, April 3rd - Multimodal Analysis / Diffusion Analysis / fMRI Analysis / MR Acquisition

Time	Title	Type	Lecturer
8:00 - 9:00	*** Optional time to work on tutorials / work on your own data / ask basic questions	--	Lilla Zöllei, other staff
9:00 - 9:30	** Intro to MR (SpinBench)	talk	Robert Frost
9:30 - 10:00	Multi-Modal Integration, Part 1: Registration	talk	Aina Frau-Pascual
10:00 - 10:30	Multi-Modal Integration Tutorial, Part 1	tutorial	staff
10:30 - 10:50	break
10:50 - 11:05	** Intro to Diffusion MRI Physics	talk	Robert Frost
11:05 - 11:45	Introduction to Diffusion MRI	talk	Anastasia Yendiki
11:45 - 12:30	Diffusion Processing Tutorial	tutorial	staff
12:30 - 1:30	Lunch	--	--
1:30 - 2:20	TRActs Constrained by UnderLying Anatomy (TRACULA)	talk	Anastasia Yendiki
2:20 - 3:20	Tracula Tutorial	tutorial	staff
3:20 - 3:40	break
3:40 - 3:50	Longitudinal TRACULA	talk	Anastasia Yendiki
3:50 - 4:50	Basics of fMRI Analysis	talk	Jingyuan Chen
4:50 - 5:30	* Running FreeSurfer in the cloud with AWS batch	talk	Paul Wighton

Answers to online questions here

Thursday, April 4th - fMRI Analysis / Multimodal Analysis / Future Directions

Time	Title	Type	Lecturer
8:00 - 9:00	*** Optional time to work on tutorials / work on your own data / ask basic questions	--	staff
9:00 - 9:30	FSFAST, Part 1: Preprocessing	talk	Doug Greve
9:30 - 10:00	FSFAST Tutorial, Part 1	tutorial	staff
10:00 - 10:20	break & Evaluation
10:20 - 11:20	FSFAST, Part 2: GLM Analysis	talk	Doug Greve
11:20 - 12:00	FSFAST Tutorial, Part 2	tutorial	staff
12:00 - 1:00	Lunch	--	--
1:00 - 1:30	* An Overview of Registration Methods	talk	Lilla Zöllei
1:30 - 1:45	Resting State fMRI	talk	Doug Greve
1:45 - 2:15	Multi-Modal Integration, Part 2: Group Analysis	talk	Doug Greve
2:15 - 3:00	Multi-Modal Integration Tutorial, Part 2	tutorial	staff
3:00 - 3:15	break
3:15 - 3:30	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 here

FsTutorial/Spring2019CourseSchedule (last edited 2019-09-17 12:53:10 by DougGreve)

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+'''!FreeSurfer Course, April 1-4, 2019'''

Our awesome !FreeSurfer shirts can be purchased [[https://freesurfer.threadless.com|here]].

=== 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 extra time to work on tutorials and/or ask questions about your own data.

==== Monday, April 1st - Introduction / Single Subject Analysis / ROI Analysis  ====
||'''Time''' ||'''Title''' ||'''Type''' ||'''Lecturer''' ||
||8:30 - 9:00 ||** [[http://surfer.nmr.mgh.harvard.edu/pub/docs/Unix_MF.pptx|Intro to Linux for FreeSurfer Users]] ||talk/demo || Andrew Hoopes||
||9:00 - 9:15 ||** [[http://surfer.nmr.mgh.harvard.edu/pub/docs/fsjargon_clean.pptx|Intro to FreeSurfer Jargon]] ||talk || Caroline Magnain ||
||9:15 - 9:30 ||'''break''' || || ||
||9:30 - 10:15 ||[[http://surfer.nmr.mgh.harvard.edu/pub/docs/freesurfer.intro.for_wiki.oct.2018.ppt|Introduction to Freesurfer]] ||talk ||Bruce Fischl ||
||10:15 - 11:25 ||[[http://surfer.nmr.mgh.harvard.edu/pub/docs/fsrecon.pptx|Analyzing the Individual Subject]] ||talk ||Doug Greve ||
||11:25 - 11:45 ||'''break''' || || ||
||11:45 - 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 ||[[http://surfer.nmr.mgh.harvard.edu/pub/docs/staff2013.jpg|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 ||[[http://surfer.nmr.mgh.harvard.edu/pub/docs/staff2013.jpg|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 || Iman Aganj ||
||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 ||Emma Boyd ||
||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-handout.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, April 2nd - Group Analysis / Longitudinal Analysis / Troubleshooting ====
||'''Time''' ||'''Title''' ||'''Type''' ||'''Lecturer''' ||
||8:00 - 9:00 ||*** Optional time to work on tutorials / work on your own data / ask basic questions ||-- || staff ||
||9:00 - 9:50 ||[[http://surfer.nmr.mgh.harvard.edu/pub/docs/GLM.pptx|Group Analysis]] ||talk || Viviana Siless ||
||9:50 - 10:30 ||[[FsTutorial/GroupAnalysisV6.0|Group Analysis Tutorial]] ||tutorial ||staff ||
||10:30 - 10:50 ||'''break''' || || ||
||10:50 - 11:30 ||[[http://surfer.nmr.mgh.harvard.edu/pub/docs/multiplecomparisons.ppt|Multiple Comparisons]] ||talk ||Doug Greve ||
||11:30 - 12:00 ||[[FsTutorial/MultipleComparisonsV6.0Perm|Multiple Comparisons Tutorial]] ||tutorial ||staff ||
||12:00 - 1:00 ||'''Lunch''' ||-- ||-- ||
||1:00 - 1:45 ||[[http://surfer.nmr.mgh.harvard.edu/pub/docs/freesurfer.troubleshooting.ppt|FreeSurfer Troubleshooting]] ||talk ||Bruce Fischl ||
||1:45 - 2:45 ||[[FsTutorial/TroubleshootingDataV6.0|Troubleshooting Tutorial]] ||tutorial ||staff ||
||2:45 - 3:05 ||'''break''' || || ||
||3:05 - 4:05 ||[[https://youtu.be/AR83_Bt04VQ|Quality Checking a Recon]] ||demo ||Leah Morgan||
||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||
||6:30 - ? ||Social Night, either at Boston Beer Works of Bldg. 149 ||social activity ||you! ||


Answers to online questions [[http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/QuestionAnswers|here]]

'''Boston Beer Works location information [[https://www.beerworks.net/locations-hours|here]] and [[http://maps.google.com/maps?f=q&source=s_q&hl=en&geocode=&q=112+Canal+Street+Boston,+MA+02114&aq=&sll=37.0625,-95.677068&sspn=44.25371,54.228516&ie=UTF8&hq=&hnear=112+Canal+St,+Boston,+Massachusetts+02114&ll=42.367359,-71.058776&spn=0.010131,0.013239&z=16|here]].'''<<BR>> Meet us in front of [[http://surfer.nmr.mgh.harvard.edu/fswiki/CourseDescription#Map|Building 149]] to catch the 6:30pm shuttle bus (it leaves on time!). <<BR>> If you miss us, we are taking the MGH/Navy Yard shuttle to North Station. From there, cross the street to get to Canal Street. <<BR>>Boston Beer Works will be down that street, on your right. (Shuttles depart every 15 minutes up until 7:15pm and every half hour after that).

==== Wednesday, April 3rd - Multimodal Analysis / Diffusion Analysis / fMRI Analysis / MR Acquisition ====
||'''Time''' ||'''Title''' ||'''Type''' ||'''Lecturer''' ||
||8:00 - 9:00 ||*** Optional time to work on tutorials / work on your own data / ask basic questions ||-- ||Lilla Zöllei, other staff||
||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/fs-cloud-presentation.ppt|Running FreeSurfer in the cloud with AWS batch]] || talk || Paul Wighton||

Answers to online questions [[http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/QuestionAnswers|here]]

##'''The !FreeSurfer Evaluation is [[ https://goo.gl/forms/o1D4r3j2Q3vEvOOD2|here]]!'''

==== Thursday, April 4th - fMRI Analysis / Multimodal Analysis / Future Directions ====
||'''Time''' ||'''Title''' ||'''Type''' ||'''Lecturer''' ||
||8:00 - 9:00 ||*** Optional time to work on tutorials / work on your own data / ask basic questions ||-- ||staff||
||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''' & [[https://goo.gl/forms/AGh3kKXH14E86yeF2|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 ||

##||3:15 - 3:45 ||* [[http://surfer.nmr.mgh.harvard.edu/pub/docs/mri_acquisition.ppt|MRI Acquisition Methods]] ||talk ||André van der Kouwe ||


Answers to online questions [[http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/QuestionAnswers|here]]

* 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 covering basic/beginner material.