Diff for "FsTutorial/Spring2019CourseSchedule"

Differences between revisions 3 and 48 (spanning 45 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 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	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 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

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

* 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 covering basic/beginner material. *** Optional sessions are a time where you can work on finishing tutorials / work on your own data / ask basic questions in the presence of a few staff members

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

-  ⇤ ← Revision 3 as of 2018-07-26 14:13:58 → 
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+   ← Revision 48 as of 2019-04-04 07:16:59 → ⇥
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-Deletions are marked like this.
+Additions are marked like this.
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+## page was renamed from FsTutorial/October2018CourseSchedule
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-#acl LcnGroup:read,write,delete,revert All:read
'''!FreeSurfer Course, October 1-4, 2018'''
+'''!FreeSurfer Course, April 1-4, 2019'''
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-* 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.
+* 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.
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-==== Monday, October 1st - Introduction / Single Subject Analysis / ROI Analysis  ====
+==== Monday, April 1st - Introduction / Single Subject Analysis / ROI Analysis  ====
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-||8:30 - 9:00 ||** [[http://surfer.nmr.mgh.harvard.edu/pub/docs/Unix_LM.pptx|Intro to Linux for FreeSurfer Users]] ||talk/demo || Leah Morgan||
||9:00 - 9:15 ||** [[http://surfer.nmr.mgh.harvard.edu/pub/docs/fsjargon.pptx|Intro to FreeSurfer Jargon]] ||talk || Morgan Fogarty & Caroline Magnain ||
+||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 ||
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-||9:30 - 10:15 ||[[http://surfer.nmr.mgh.harvard.edu/pub/docs/freesurfer.intro.apr.2018.for_wiki.ppt|Introduction to Freesurfer]] ||talk ||Bruce Fischl ||
+||9:30 - 10:15 ||[[attachment:freesurfer.intro.apr.2019.ppt|Introduction to Freesurfer]] ||talk ||Bruce Fischl ||
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-||11:45 - 12:00 ||Freeview demonstration ||[[FsTutorial/FreeviewDemo|demo]] || Bram Diamond ||
||12:00 - 12:30 ||[[FsTutorial/OutputData_freeview|Interaction with Individual Subject Data Tutorial]] ||tutorial ||[[http://surfer.nmr.mgh.harvard.edu/pub/docs/staff2013.jpg|staff]] ||
+||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]] ||
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-||1:30 - 1:45 ||[[FsTutorial/OutputData_freeview|Interaction with Individual Subject Data Tutorial]] ||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 ||
+||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 ||
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-||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 ||[[https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Practice|Practice Working with Data]] ||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 ||
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-==== Tuesday, October 2nd - Group Analysis / Longitudinal Analysis / Troubleshooting ====
+==== Tuesday, April 2nd - Group Analysis / Longitudinal Analysis / Troubleshooting ====
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-||8:00 - 9:00 ||*** Optional time to work on tutorials / work on your own data / ask basic questions ||-- || Emma Boyd||
+||8:00 - 9:00 ||*** Optional session, extra support for structural processing and ROI analysis||-- || Research Techs ||
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-||1:00 - 1:45 ||[[http://surfer.nmr.mgh.harvard.edu/pub/docs/freesurfer.troubleshooting.ppt|FreeSurfer Troubleshooting]] ||talk ||Bruce Fischl ||
+||1:00 - 1:45 ||[[http://surfer.nmr.mgh.harvard.edu/pub/docs/freesurfer.troubleshooting.apr2019.ppt|FreeSurfer Troubleshooting]] ||talk ||Bruce Fischl ||
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-||3:05 - 4:05 ||Quality Checking a Recon ||demo ||Allison Stevens ||
||4:05 - 4:50 ||[[http://surfer.nmr.mgh.harvard.edu/pub/docs/fs.longitudinal.pptx|Longitudinal FreeSurfer]] ||talk ||Paul Wighton ||
||4:50 - 5:30 || [[FsTutorial/LongitudinalTutorialV6.0|LongitudinalTutorial]] ||tutorial ||staff ||
||5:30 - 6:15 ||*** Optional time to work on tutorials / work on your own data / ask basic questions ||-- || Emma Boyd||
||6:30 - ? ||Boston Beer Works ||social activity ||you! ||
+||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! ||
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-'''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, October 3rd - Multimodal Analysis / Diffusion Analysis / fMRI Analysis / MR Acquisition ====
+==== Wednesday, April 3rd - Multimodal Analysis / Diffusion Analysis / fMRI Analysis / MR Acquisition ====
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+Line 68:
-||8:00 - 9:00 ||*** Optional time to work on tutorials / work on your own data / ask basic questions ||-- || Emma Boyd||
||9:00 - 9:30 ||** [[http://surfer.nmr.mgh.harvard.edu/pub/docs/IntroMRI.pptx|A Non-physicist's Intro to MR]] ([[http://www.heartvista.com/SpinBench|SpinBench]])'' '' ||talk ||Robert Frost ||
+||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 ||
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-||10:50 - 11:05 ||** [[http://surfer.nmr.mgh.harvard.edu/pub/docs/IntroDiffusion.pptx|A Non-Physicist's Intro to Diffusion MRI Physics]] '' '' ||talk ||Robert Frost ||
||11:05 - 11:45 ||[[http://surfer.nmr.mgh.harvard.edu/pub/docs/BarcelonaSept2017/dmri,fs.ppt|Introduction to Diffusion MRI]] ||talk ||Anastasia Yendiki ||
+||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 ||
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+Line 81:
-||3:50 - 4:50 ||[[http://surfer.nmr.mgh.harvard.edu/pub/docs/fMRI_intro2018.ppt|Basics of fMRI Analysis]] ||talk ||Isik Karahanoglu ||
||4:50 - 5:50 ||*** Optional time to work on tutorials / work on your own data / ask basic questions ||-- || Emma Boyd||
+||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||
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-'''The !FreeSurfer Evaluation is [[ https://goo.gl/forms/o1D4r3j2Q3vEvOOD2|here]]!'''
==== Thursday, October 4th - fMRI Analysis / Multimodal Analysis / Future Directions ====
+##'''The !FreeSurfer Evaluation is [[ https://goo.gl/forms/o1D4r3j2Q3vEvOOD2|here]]!'''

==== Thursday, April 4th - fMRI Analysis / Multimodal Analysis / Future Directions ====
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-||8:00 - 9:00 ||*** Optional time to work on tutorials / work on your own data / ask basic questions ||-- || Emma Boyd||
||9:00 - 9:30 ||[[http://surfer.nmr.mgh.harvard.edu/pub/docs/fsfast.ppt|FSFAST, Part 1: Preprocessing]] ||talk ||Isik Karahanoglu ||
+||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 ||
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-||10:00 - 10:20 ||'''break''' & [[https://goo.gl/forms/RY3xZpS2hoJDSEuu1|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 ||
+||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 ||
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-||1:00 - 1:30 ||* [[http://surfer.nmr.mgh.harvard.edu/pub/docs/FSCourse_ImageRegistration.pptx|An Overview of Image Registration]] ||talk || Iman Aganj||
+||1:00 - 1:30 ||[[http://surfer.nmr.mgh.harvard.edu/pub/docs/fs.registration.ppt|* An Overview of Registration Methods]] ||talk || Lilla Zöllei ||
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-||3:15 - 3:45 ||[[http://surfer.nmr.mgh.harvard.edu/pub/docs/fs.vbm.ppt|FreeSurfer vs. VBM]] ||talk ||Doug Greve ||
||3:45 - 4:30 ||Future Directions ||talk ||Bruce Fischl ||
+||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 ||
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-* 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.
+* 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. *** Optional sessions are a time where you can work on finishing tutorials / work on your own data / ask basic questions in the presence of a few staff members