Diff for "FsTutorial/Fall2019CourseSchedule"

Differences between revisions 1 and 2

Fall 2019 FreeSurfer Course: September 23rd - 26th

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 optional 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
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 session, extra support for structural processing and ROI analysis	--	Research Techs
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, Allison Stevens
4:05 - 4:50	Longitudinal FreeSurfer	talk	Malte Hoffmann
4:50 - 5:30	LongitudinalTutorial	tutorial	staff
5:30 - 7:30	Social Night in the atrium of Bldg. 149	Snacks and Beverages Served	you!

Answers to online questions here

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

Time	Title	Type	Lecturer
8:00 - 9:00	*** Optional session, extra support for questions on longitudinal processing and working with pediatric data	--	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

The FreeSurfer Evaluation is here!

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

Time	Title	Type	Lecturer
8:00 - 9:00	*** Optional session, extra support for fMRI and Diffusion 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

FreeSurfer Merchandise

Enjoyed our course? Purchase our awesome FreeSurfer T-shirts here.

FsTutorial/Fall2019CourseSchedule (last edited 2020-02-28 09:23:37 by DevaniCordero)

Deletions are marked like this.	Additions are marked like this.
Line 1:	Line 1:
*Subject to change	## page was renamed from FsTutorial/Spring2019CourseSchedule ## Please edit system and help pages ONLY in the master wiki! ## For more information, please see MoinMoin:MoinDev/Translation. ## IMPORTANT NOTE: ## When you use this page as a template for creating your project page: ## * please remove all lines starting with two hashes (##) ## * except the acl line, please keep that, but remove one hash, so it reads #acl ... ## * fix the acl line so it has the correct page instead of the sample Project/...Group ##acl Project/AdminGroup:admin,read,write,delete,revert Project/ReadWriteGroup:read,write Project/ReadGroup:read ##master-page:Unknown-Page ##master-date:Unknown-Date #format wiki #language en == Fall 2019 FreeSurfer Course: September 23rd - 26th == === 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. ==== 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 \|\|[[attachment:freesurfer.intro.apr.2019.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 \|\| \|\| \|\|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, April 2nd - Group Analysis / Longitudinal Analysis / Troubleshooting ==== \|\|'''Time''' \|\|'''Title''' \|\|'''Type''' \|\|'''Lecturer''' \|\| \|\|8:00 - 9:00 \|\|* Optional session, extra support for structural processing and ROI analysis\|\|-- \|\| Research Techs \|\| \|\|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.apr2019.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, Allison Stevens\|\| \|\|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 \|\|you! \|\| Answers to online questions [[http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/QuestionAnswers\|here]] ==== Wednesday, April 3rd - Multimodal Analysis / Diffusion Analysis / fMRI Analysis / MR Acquisition ==== \|\|'''Time''' \|\|'''Title''' \|\|'''Type''' \|\|'''Lecturer''' \|\| \|\|8:00 - 9:00 \|\|* Optional session, extra support for questions on longitudinal processing and working with pediatric data \|\|-- \|\|Lilla Zöllei, other staff\|\| \|\|9:00 - 9:30 \|\| [[http://surfer.nmr.mgh.harvard.edu/pub/docs/IntroMRI.apr2019.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.apr2019.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 \|\|* [[attachment:fs-cloud-prsentation_20190403.pdf\|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://forms.gle/HmxDSXMopTdNMJKu7\|here]]!''' ==== Thursday, April 4th - fMRI Analysis / Multimodal Analysis / Future Directions ==== \|\|'''Time''' \|\|'''Title''' \|\|'''Type''' \|\|'''Lecturer''' \|\| \|\|8:00 - 9:00 \|\|*** Optional session, extra support for fMRI and Diffusion 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''' & 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]] <<BR>> '''!FreeSurfer Merchandise''' Enjoyed our course? Purchase our awesome !FreeSurfer T-shirts [[https://freesurfer.threadless.com\|here]].