Diff for "FsTutorial/Sept2017CourseSchedule"

Differences between revisions 7 and 25 (spanning 18 versions)

FreeSurfer Course, September 25-28, 2017

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, September 25th - Introduction / Single Subject Analysis / ROI Analysis

Time	Title	Type	Lecturer
8:30 - 9:00	** Intro to Linux for FreeSurfer Users	talk/demo	Emma Boyd
9:00 - 9:15	** Intro to FreeSurfer Jargon	talk	Caroline Magnain
9:15 - 9:30	break
9:30 - 10:00	Introduction to Freesurfer	talk	Bruce Fischl
10:00 - 11:10	Analyzing the Individual Subject	talk	Doug Greve
11:10 - 11:30	break
11:30 - 11:45	Freeview demonstration	demo	Andrew Hoopes
11:45 - 12:15	Interaction with Individual Subject Data Tutorial	tutorial	staff
12:15 - 1:15	Lunch (Suggestions for where to eat)	--	--
1:15 - 1:30	Interaction with Individual Subject Data Tutorial	tutorial	staff
1:30 - 2:00	Surface-based Analysis: Intersubject Registration & Smoothing	talk	Lilla Zöllei
2:00 - 2:20	break
2:20 - 3:20	ROI Analysis	talk	Doug Greve
3:20 - 4:00	ROI Analysis Tutorial	tutorial	staff
4:00 - 4:30	Practice Working with Data	tutorial	staff
4:30 - 5:00	* Running FreeSurfer in the cloud with AWS batch	talk	Paul Wighton

Answers to online questions here

Tuesday, September 26th - 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	--	Emma Boyd
9:00 - 9:50	Group Analysis	talk	Emily Lindemer
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	Allison Stevens
4:05 - 4:50	Longitudinal FreeSurfer see also: LongitudinalTutorial	talk	Lilla Zöllei
4:50 - 5:20	* An Overview of Registration Methods	talk	Lilla Zöllei
5:20 - 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!

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, September 27th - Multimodal Analysis / Diffusion Analysis / fMRI Analysis / MR Acquisition

Time	Title	Type	Lecturer
8:00 - 8:30	*** Optional time to work on tutorials / work on your own data / ask basic questions	--	Emma Boyd
8:30 - 9:00	** A Non-physicist's Intro to MR (SpinBench)	talk	Robert Frost
9:00 - 9:30	Multi-Modal Integration, Part 1: Registration	talk	Lilla Zöllei
9:30 - 10:00	Multi-Modal Integration Tutorial, Part 1	tutorial	staff
10:00 - 10:15	** A Non-Physicist's Intro to Diffusion MRI Physics	talk	Robert Frost
10:15 - 10:35	break
10:35 - 11:15	Introduction to Diffusion MRI	talk	Anastasia Yendiki
11:15 - 12:00	Diffusion Processing Tutorial	tutorial	staff
12:00 - 1:00	Lunch	--	--
1:00 - 1:50	TRActs Constrained by UnderLying Anatomy (TRACULA)	talk	Anastasia Yendiki
1:50 - 2:50	Tracula Tutorial	tutorial	staff
2:50 - 3:00	Longitudinal TRACULA	talk	Anastasia Yendiki
3:00 - 3:20	break
3:20 - 4:20	Basics of fMRI Analysis	talk	Isik Karahanoglu
4:20 - 5:20	*** Optional time to work on LongitudinalTutorial	tutorial	staff

Answers to online questions here

Thursday, September 28th - 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	--	Emma Boyd
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	Multi-Modal Integration, Part 2: Group Analysis	talk	Doug Greve
1:30 - 2:15	Multi-Modal Integration Tutorial, Part 2	tutorial	staff
2:15 - 2:45	Resting State fMRI	talk	Doug Greve
2:45 - 3:00	FreeSurfer vs. VBM	talk	Doug Greve
3:00 - 3:15	break
3:15 - 3:45	* MRI Acquisition Methods	talk	André van der Kouwe
3:45 - 4:30	Future Directions	talk	Bruce Fischl
4:30 - 5:00	Question & Answer Session	--	staff

Answers to online questions here

FsTutorial/Sept2017CourseSchedule (last edited 2017-09-28 07:30:36 by AllisonStevens)

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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.
+* 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.
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-||8:30 - 9:00 ||** [[http://surfer.nmr.mgh.harvard.edu/pub/docs/Unix_tutorial_zjk.pdf|Intro to Linux for FreeSurfer Users]] ||talk/demo || Emma Boyd||
||9:00 - 9:15 ||** [[http://surfer.nmr.mgh.harvard.edu/pub/docs/fsjargon.ppt|Intro to FreeSurfer Jargon]] ||talk || Caroline Magnain ||
+||8:30 - 9:00 ||** [[http://surfer.nmr.mgh.harvard.edu/pub/docs/BarcelonaSept2017/Unix_EB_clean.pptx|Intro to Linux for FreeSurfer Users]] ||talk/demo || Emma Boyd||
||9:00 - 9:15 ||** [[http://surfer.nmr.mgh.harvard.edu/pub/docs/BarcelonaSept2017/fsjargon_EB_clean.ppt|Intro to FreeSurfer Jargon]] ||talk || Caroline Magnain ||
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-||9:30 - 10:00 ||[[http://surfer.nmr.mgh.harvard.edu/pub/docs/freesurfer.intro.ppt|Introduction to Freesurfer]] ||talk ||Bruce Fischl ||
||10:00 - 11:10 ||[[http://surfer.nmr.mgh.harvard.edu/pub/docs/fsrecon.ppt|Analyzing the Individual Subject]] ||talk ||Doug Greve ||
+||9:30 - 10:00 ||[[http://surfer.nmr.mgh.harvard.edu/pub/docs/Antonia_slides/freesurfer.intro.ppt|Introduction to Freesurfer]] ||talk ||Bruce Fischl ||
||10:00 - 11:10 ||[[http://surfer.nmr.mgh.harvard.edu/pub/docs/fsrecon.pptx|Analyzing the Individual Subject]] ||talk ||Doug Greve ||
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-||4:00 - 4:30 ||** [[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 ||
+||4:00 - 4:30 ||Practice Working with Data ||tutorial ||staff ||
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-Line 33:
+Line 34:
-||9:00 - 9:50 ||[[http://surfer.nmr.mgh.harvard.edu/pub/docs/Copenhagen_Group_Analysis.pptx|Group Analysis]] ||talk || ||
+||8:00 - 9:00 ||*** Optional time to work on tutorials / work on your own data / ask basic questions ||-- || Emma Boyd||
||9:00 - 9:50 ||[[http://surfer.nmr.mgh.harvard.edu/pub/docs/Copenhagen_Group_Analysis.pptx|Group Analysis]] ||talk || Emily Lindemer ||
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+Line 38:
-||10:50 - 11:10 ||[[http://surfer.nmr.mgh.harvard.edu/pub/docs/dng.Copenhagen_multiplecomparisons.ppt|Multiple Comparisons]] ||talk ||Doug Greve ||
||11:10 - 11:30 ||[[http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysisV6.0#ClusterwiseCorrectionforMultipleComparisons|Multiple Comparisons Tutorial]] ||tutorial ||staff ||
||11:30 - 11:50 ||QDEC demonstration ||demo ||Doug Greve ||
||11:50 - 12:50 ||'''Lunch''' ||-- ||-- ||
||12:50 - 1:30 ||[[FsTutorial/QdecGroupAnalysisV6.0|QDEC Tutorial]] ||tutorial ||staff ||
||1:30 - 2:00 ||[[http://surfer.nmr.mgh.harvard.edu/pub/docs/freesurfer.troubleshooting.ppt|FreeSurfer Troubleshooting]] ||talk ||Bruce Fischl ||
||2:00 - 3:00 ||[[FsTutorial/TroubleshootingDataV6.0|Troubleshooting Tutorial]] ||tutorial ||staff ||
||3:00 - 3:20 ||'''break''' || || ||
||3:20 - 4:20 ||Quality Checking a Recon ||demo ||Allison Stevens ||
||4:20 - 5:05 ||[[http://surfer.nmr.mgh.harvard.edu/pub/docs/fs.longitudinal.pptx|Longitudinal FreeSurfer]] see also:'' [[FsTutorial/LongitudinalTutorial|LongitudinalTutorial]]'' ||talk ||Lilla Zöllei ||
||5:05 - 5:35 ||* [[http://surfer.nmr.mgh.harvard.edu/pub/docs/fs.registration.ppt|An Overview of Registration Methods]] ||talk ||Lilla Zöllei ||
+||10:50 - 11:30 ||[[http://surfer.nmr.mgh.harvard.edu/pub/docs/multiplecomparisons.ppt|Multiple Comparisons]] ||talk ||Doug Greve ||
||11:30 - 12:00 ||[[FsTutorial/MultipleComparisonsV6.0|Multiple Comparisons Tutorial]] ||tutorial ||staff ||
||12:00 - 1:00 ||'''Lunch''' ||-- ||-- ||
||1:00 - 1:45 ||[[http://surfer.nmr.mgh.harvard.edu/pub/docs/Antonia_slides/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 ||Quality Checking a Recon ||demo ||Allison Stevens ||
||4:05 - 4:50 ||[[http://surfer.nmr.mgh.harvard.edu/pub/docs/fs.longitudinal.pptx|Longitudinal FreeSurfer]] see also:'' [[FsTutorial/LongitudinalTutorial|LongitudinalTutorial]]'' ||talk ||Lilla Zöllei ||
||4:50 - 5:20 ||* [[http://surfer.nmr.mgh.harvard.edu/pub/docs/fs.registration.ppt|An Overview of Registration Methods]] ||talk ||Lilla Zöllei ||
||5:20 - 6:15 ||*** Optional time to work on tutorials / work on your own data / ask basic questions ||-- || Emma Boyd||
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+Line 57:
+||8:00 - 8:30 ||*** Optional time to work on tutorials / work on your own data / ask basic questions ||-- || Emma Boyd||
||8:30 - 9:00 ||** [[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 ||
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+Line 63:
-||10:35 - 11:15 ||[[http://surfer.nmr.mgh.harvard.edu/pub/docs/dmri,fs.ppt|Introduction to Diffusion MRI]] ||talk ||Anastasia Yendiki ||
+||10:35 - 11:15 ||[[http://surfer.nmr.mgh.harvard.edu/pub/docs/BarcelonaSept2017/dmri,fs.ppt|Introduction to Diffusion MRI]] ||talk ||Anastasia Yendiki ||
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+Line 70:
-||3:20 - 4:20 ||[[http://surfer.nmr.mgh.harvard.edu/pub/docs/fMRI_intro.ppt|Basics of fMRI Analysis]] ||talk ||Jon Polimeni ||
+||3:20 - 4:20 ||[[http://surfer.nmr.mgh.harvard.edu/pub/docs/BarcelonaSept2017/fMRI_intro.ppt|Basics of fMRI Analysis]] ||talk ||Isik Karahanoglu ||
||4:20 - 5:20 ||*** Optional time to work on [[FsTutorial/LongitudinalTutorial|LongitudinalTutorial]] ||tutorial ||staff ||
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+Line 78:
-||9:00 - 9:30 ||[[http://surfer.nmr.mgh.harvard.edu/pub/docs/fsfast.april2011.ppt|FSFAST, Part 1: Preprocessing]] ||talk ||Doug Greve ||
+||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 ||Doug Greve ||
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+Line 82:
-||10:20 - 11:20 ||[[http://surfer.nmr.mgh.harvard.edu/pub/docs/fsfast.april2011.ppt|FSFAST, Part 2: GLM Analysis]] ||talk ||Doug Greve ||
+||10:20 - 11:20 ||[[http://surfer.nmr.mgh.harvard.edu/pub/docs/fsfast.ppt|FSFAST, Part 2: GLM Analysis]] ||talk ||Doug Greve ||
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-||1:30 - 2:00 ||[[MultiModalTutorialV6.0|Multi-Modal Integration Tutorial, Part 2]] ||tutorial ||staff ||
||2:00 - 2:30 ||* [[http://surfer.nmr.mgh.harvard.edu/pub/docs/mri_acquisition.ppt|MRI Acquisition Methods]] ||talk ||André van der Kouwe ||
||2:30 - 3:00 ||Future Directions ||talk ||Bruce Fischl ||
##||2:25 - 2:45 ||Question & Answer Session ||-- ||staff ||
+||1:30 - 2:15 ||[[MultiModalTutorialV6.0|Multi-Modal Integration Tutorial, Part 2]] ||tutorial ||staff ||
||2:15 - 2:45 ||[[http://surfer.nmr.mgh.harvard.edu/pub/docs/resting-state.fmri.ppt|Resting State fMRI]] ||talk ||Doug Greve ||
||2:45 - 3:00 ||[[http://surfer.nmr.mgh.harvard.edu/pub/docs/fs.vbm.ppt|FreeSurfer vs. VBM]] ||talk ||Doug Greve ||
||3:00 - 3:15 ||'''break''' || || ||
||3:15 - 3:45 ||* [[http://surfer.nmr.mgh.harvard.edu/pub/docs/mri_acquisition.ppt|MRI Acquisition Methods]] ||talk ||André van der Kouwe ||
||3:45 - 4:30 ||Future Directions ||talk ||Bruce Fischl ||
||4:30 - 5:00 ||Question & Answer Session ||-- ||staff ||