Diff for "FsTutorial/Sept2016CourseSchedule"

Differences between revisions 9 and 28 (spanning 19 versions)

FreeSurfer Course, September 26-29

Copy of all course slides compiled as a book can be found here.

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.

Monday, September 26th - Introduction / Single Subject Analysis / ROI Analysis / MR Acquisition

Time	Title	Type	Lecturer
8:30 - 9:00	** Intro to Linux for FreeSurfer Users	talk/demo	Zeke Kaufman
9:00 - 9:15	** Intro to FreeSurfer Jargon	talk	Allison Stevens & Lilla Zöllei
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	Allison Moreau
11:45 - 12:15	Interaction with Individual Subject Data Tutorial	tutorial	staff
12:15 - 1:15	Lunch (Suggestions for where to eat)	--	--
1:15 - 1:45	Interaction with Individual Subject Data Tutorial	tutorial	staff
1:45 - 2:15	Surface-based Analysis: Intersubject Registration & Smoothing	talk	Lilla Zöllei
2:15 - 2:35	break
2:35 - 3:05	ROI Analysis	talk	Doug Greve
3:05 - 3:55	ROI Analysis Tutorial	tutorial	staff
3:55 - 4:25	** A Non-physicist's Intro to MR (SpinBench)	talk	Dylan Tisdall
4:25 - 4:55	* MRI Acquisition Methods	talk	André van der Kouwe
4:55 - 5:15	* Motion-compensated Neuroanatomical Imaging	talk	Dylan Tisdall

Answers to online questions here

Tuesday, September 27th - Group Analysis / Longitudinal Analysis / Troubleshooting

Time	Title	Type	Lecturer
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 - 11:10	Multiple Comparisons	talk	Doug Greve
11:10 - 11:30	Multiple Comparisons Tutorial	tutorial	staff
11:30 - 11:50	QDEC demonstration	demo	Doug Greve
11:50 - 12:50	Lunch	--	--
12:50 - 1:30	QDEC Tutorial	tutorial	staff
1:30 - 2:15	Longitudinal FreeSurfer see also: LongitudinalProcessing	talk	Lilla Zöllei
2:15 - 2:55	Longitudinal Tutorial	tutorial	staff
2:55 - 3:25	FreeSurfer Troubleshooting	talk	Bruce Fischl
3:25 - 3:45	break
3:45 - 4:45	Troubleshooting Tutorial	tutorial	staff
4:45 - 5:45	Quality Checking a Recon	demo	Allison Stevens
6:30 - ?	Boston Beer Works	social activity	staff

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 28th - Multimodal Analysis / Diffusion Analysis / fMRI Analysis

Time	Title	Type	Lecturer
9:00 - 9:30	Multi-Modal Integration, Part 1: Registration	talk	Lilla Zöllei
9:30 - 10:00	Multi-Modal Integration Tutorial: Multimodal Registration	tutorial	staff
10:00 - 10:15	** A Non-Physicist's Intro to Diffusion MRI Physics	talk	Dylan Tisdall
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 - 2:00	TRActs Constrained by UnderLying Anatomy (TRACULA)	talk	Anastasia Yendiki
2:00 - 3:00	Tracula Tutorial	tutorial	staff
3:00 - 3:10	Longitudinal TRACULA	talk	Anastasia Yendiki
3:10 - 3:30	break
3:30 - 4:30	Basics of fMRI Analysis	talk	Jon Polimeni
4:30 - 5:10	FSFAST, Part 1: Preprocessing	talk	Doug Greve

Answers to online questions here

Thursday, September 29th - fMRI Analysis / Multimodal Analysis / Future Directions

Time	Title	Type	Lecturer
9:00 - 9:40	FSFAST, Part 2: GLM Analysis	talk	Doug Greve
9:40 - 10:40	FSFAST Tutorial	tutorial	staff
10:40 - 11:00	break & Evaluation
11:00 - 11:30	Multi-Modal Integration, Part 2	talk	Doug Greve
11:30 - 12:00	Multi-Modal Integration Tutorial: fMRI Integration & Surface-based Group fMRI Analysis	tutorial	staff
12:00 - 1:00	Lunch	--	--
1:00 - 1:40	* An Overview of Registration Methods	talk	Lilla Zöllei
1:40 - 2:25	Future Directions	talk	Bruce Fischl
2:25 - 2:45	Question & Answer Session	--	staff

Answers to online questions here

FsTutorial/Sept2016CourseSchedule (last edited 2017-09-26 11:31:11 by MorganFogarty)

-  ⇤ ← Revision 9 as of 2016-09-19 16:19:20 → 
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+   ← Revision 28 as of 2017-09-26 11:31:11 → ⇥
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-Deletions are marked like this.
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+Copy of all course slides compiled as a book can be found [[http://surfer.nmr.mgh.harvard.edu/pub/docs/Course_Slides.pdf|here]].
<<BR>>
<<BR>>
Our awesome !FreeSurfer shirts can be purchased [[https://freesurfer.threadless.com|here]].
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+Line 11:
-* 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 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.
-Line 9:
+Line 13:
-==== Monday, September 26th - Introduction / Single Subject Analysis / ROI Analysis ====
+==== Monday, September 26th - Introduction / Single Subject Analysis / ROI Analysis / MR Acquisition ====
-Line 11:
+Line 15:
-||8:30 - 9:00 ||** [[http://surfer.nmr.mgh.harvard.edu/pub/docs/Unix_tutorial_zjk.pdf|Intro to Linux for FreeSurfer Users]] || talk/demo ||Zeke Kaufman ||
||9:00 - 9:15 ||** [[http://surfer.nmr.mgh.harvard.edu/pub/docs/fsjargon.ppt|Intro to FreeSurfer Jargon]] ||talk ||Allison Stevens & Lilla Zollei ||
+||8:30 - 9:00 ||** [[http://surfer.nmr.mgh.harvard.edu/pub/docs/Unix_tutorial_zjk.pdf|Intro to Linux for FreeSurfer Users]] ||talk/demo ||Zeke Kaufman ||
||9:00 - 9:15 ||** [[http://surfer.nmr.mgh.harvard.edu/pub/docs/fsjargon.ppt|Intro to FreeSurfer Jargon]] ||talk ||Allison Stevens & Lilla Z&#246;llei ||
-Line 17:
+Line 21:
-||11:30 - 11:45 ||Freeview demonstration ||[[FreeviewGuide|demo]] ||Allison Moreau ||
+||11:30 - 11:45 ||Freeview demonstration ||[[FsTutorial/FreeviewDemo|demo]] ||Allison Moreau ||
-Line 19:
+Line 23:
-||12:15 - 1:15 ||'''Lunch''' [[http://surfer.nmr.mgh.harvard.edu/pub/docs/lunch_map.jpg|(Suggestions for where to eat)]] ||-- ||-- ||
+||12:15 - 1:15 ||'''Lunch''' [[https://surfer.nmr.mgh.harvard.edu/fswiki/CourseDescription?action=AttachFile&do=get&target=CourseMap.jpg|(Suggestions for where to eat)]] ||-- ||-- ||
-Line 21:
+Line 25:
-||1:45 - 2:15 ||[[http://surfer.nmr.mgh.harvard.edu/pub/docs/fs.surface-based-analysis.ppt|Surface-based Analysis: Intersubject Registration & Smoothing]] ||talk ||Doug Greve ||
+||1:45 - 2:15 ||[[http://surfer.nmr.mgh.harvard.edu/pub/docs/fs.surface-based-analysis.ppt|Surface-based Analysis: Intersubject Registration & Smoothing]] ||talk ||Lilla Z&#246;llei ||
-Line 23:
+Line 27:
-||2:35 - 3:05 ||[[http://surfer.nmr.mgh.harvard.edu/pub/docs/fs.roi.ppt|ROI Analysis]] ||talk ||Doug Greve ||
+||2:35 - 3:05 ||[[http://surfer.nmr.mgh.harvard.edu/pub/docs/fs.roi.pptx|ROI Analysis]] ||talk ||Doug Greve ||
-Line 26:
+Line 30:
-||4:25 - 4:55 ||* [[http://surfer.nmr.mgh.harvard.edu/pub/docs/mri_acquisition.ppt|MRI Acquisition Methods]] ||talk ||Andre van der Kouwe ||
+||4:25 - 4:55 ||* [[http://surfer.nmr.mgh.harvard.edu/pub/docs/mri_acquisition.ppt|MRI Acquisition Methods]] ||talk ||Andr&#233; van der Kouwe ||
||4:55 - 5:15 ||* [[http://surfer.nmr.mgh.harvard.edu/pub/docs/FreeSurfer_Course_Apr_2013_Motion_Correction.pdf|Motion-compensated Neuroanatomical Imaging]] ||talk ||Dylan Tisdall ||
-Line 32:
+Line 36:
-==== Tuesday, September 27th - Group Analysis / Longitudinal Analysis / Multimodal Analysis ====
||'''Time''' ||'''Title''' ||'''Type''' ||'''Lecturer''' |
||9:00 - 9:50 ||[[http://surfer.nmr.mgh.harvard.edu/pub/docs/Copenhagen_Group_Analysis.pptx |Group Analysis]] ||talk ||Emily Lindemer ||
+==== Tuesday, September 27th - Group Analysis / Longitudinal Analysis / Troubleshooting ====
||'''Time''' ||'''Title''' ||'''Type''' ||'''Lecturer''' ||
||9:00 - 9:50 ||[[http://surfer.nmr.mgh.harvard.edu/pub/docs/Copenhagen_Group_Analysis.pptx|Group Analysis]] ||talk ||Emily Lindemer ||
-Line 38:
+Line 41:
-||10:50 - 11:10 ||[[http://surfer.nmr.mgh.harvard.edu/pub/docs/freesurfer.multiplecomparisons.ppt|Multiple Comparisons]] ||talk ||Doug Greve ||
+||10:50 - 11:10 ||[[http://surfer.nmr.mgh.harvard.edu/pub/docs/dng.Copenhagen_multiplecomparisons.ppt|Multiple Comparisons]] ||talk ||Doug Greve ||
-Line 43:
+Line 46:
-||1:30 - 2:15 ||[[http://surfer.nmr.mgh.harvard.edu/pub/docs/freesurfer.longitudinal.ppt|Longitudinal FreeSurfer]] see also:'' LongitudinalProcessing '' ||talk ||Lilla Zollei ||
||2:15 - 2:55 ||[[FsTutorial/LongitudinalTutorial_freeview|Longitudinal Tutorial]] ||tutorial ||staff ||
||2:55 - 3:15 ||'''break''' || ||
||3:15 - 3:45 ||[[http://surfer.nmr.mgh.harvard.edu/pub/docs/freesurfer.failure_modes.ppt|FreeSurfer Troubleshooting]] ||talk ||Bruce Fischl ||
+||1:30 - 2:15 ||[[http://surfer.nmr.mgh.harvard.edu/pub/docs/freesurfer.longitudinal.pptx|Longitudinal FreeSurfer]] see also:'' LongitudinalProcessing '' ||talk ||Lilla Z&#246;llei ||
||2:15 - 2:55 ||[[FsTutorial/LongitudinalTutorial|Longitudinal Tutorial]] ||tutorial ||staff ||
||2:55 - 3:25 ||[[http://surfer.nmr.mgh.harvard.edu/pub/docs/freesurfer.failure_modes.ppt|FreeSurfer Troubleshooting]] ||talk ||Bruce Fischl ||
||3:25 - 3:45 ||'''break''' || ||
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-||4:45 - 5:15 ||* [[http://surfer.nmr.mgh.harvard.edu/pub/docs/FreeSurfer_Course_Apr_2013_Motion_Correction.pdf|Motion-compensated Neuroanatomical Imaging]] ||talk ||Dylan Tisdall ||
||6:15 - ? ||Boston Beer Works ||social activity ||staff ||
+||4:45 - 5:45 ||Quality Checking a Recon ||demo ||Allison Stevens ||
||6:30 - ? ||Boston Beer Works ||social activity ||staff ||
-Line 53:
+Line 57:
-'''Boston Beer Works location information [[http://www.beerworks.net/html/locations_canal.html|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 6:15pm 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).
+'''Boston Beer Works location information [[http://www.beerworks.net/html/locations_canal.html|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).
-Line 55:
+Line 59:
+==== Wednesday, September 28th - Multimodal Analysis / Diffusion Analysis / fMRI Analysis ====
||'''Time''' ||'''Title''' ||'''Type''' ||'''Lecturer''' ||
||9:00 - 9:30 ||[[http://surfer.nmr.mgh.harvard.edu/pub/docs/fs.multimodal-integration.Part1.pptx|Multi-Modal Integration, Part 1: Registration]] ||talk ||Lilla Z&#246;llei ||
||9:30 - 10:00 ||[[FsTutorial/MultiModal_freeview|Multi-Modal Integration Tutorial: Multimodal Registration]] ||tutorial ||staff ||
||10:00 - 10:15 ||** [[http://surfer.nmr.mgh.harvard.edu/pub/docs/FreeSurfer_Course_Sep_2015_Diffusion.pdf|A Non-Physicist's Intro to Diffusion MRI Physics]] '' '' ||talk ||Dylan Tisdall ||
||10:15 - 10:35 ||'''break''' || ||
||10:35 - 11:15 ||[[http://surfer.nmr.mgh.harvard.edu/pub/docs/dmri,fs.ppt|Introduction to Diffusion MRI]] ||talk ||Anastasia Yendiki ||
||11:15 - 12:00 ||[[FsTutorial/Diffusion_DtiIntegration|Diffusion Processing Tutorial]] ||tutorial ||staff ||
||12:00 - 1:00 ||'''Lunch''' ||-- ||-- ||
||1:00 - 2:00 ||[[http://surfer.nmr.mgh.harvard.edu/pub/docs/tracula,fs.ppt|TRActs Constrained by UnderLying Anatomy (TRACULA)]] ||talk ||Anastasia Yendiki ||
||2:00 - 3:00 ||[[FsTutorial/Tracula|Tracula Tutorial]] ||tutorial ||staff ||
||3:00 - 3:10 ||[[http://surfer.nmr.mgh.harvard.edu/pub/docs/tracula,fs.ppt|Longitudinal TRACULA]] ||talk ||Anastasia Yendiki ||
||3:10 - 3:30 ||'''break''' || ||
||3:30 - 4:30 ||[[http://surfer.nmr.mgh.harvard.edu/pub/docs/fMRI_intro.ppt|Basics of fMRI Analysis]] ||talk ||Jon Polimeni ||
||4:30 - 5:10 ||[[http://surfer.nmr.mgh.harvard.edu/pub/docs/fsfast.april2011.ppt|FSFAST, Part 1: Preprocessing]] ||talk ||Doug Greve ||
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-==== Wednesday, September 28th - Diffusion Analysis / fMRI Analysis ====
||'''Time''' ||'''Title''' ||'''Type''' ||'''Lecturer''' ||
||9:00 - 10:00 ||Quality Checking a Recon ||demo ||Allison Stevens ||
||10:00 - 10:30 ||[[http://surfer.nmr.mgh.harvard.edu/pub/docs/fs.multimodal-integration.Part1.ppt|Multi-Modal Integration, Part 1]] ||talk ||Lilla Zollei ||
||10:30 - 10:50 ||'''break''' || ||
||10:50 - 11:20 ||[[FsTutorial/MultiModal_freeview|Multi-Modal Integration Tutorial: Multimodal Registration]] ||tutorial ||staff ||
||11:20 - 11:35 ||** [[http://surfer.nmr.mgh.harvard.edu/pub/docs/FreeSurfer_Course_Sep_2015_Diffusion.pdf|A Non-Physicist's Intro to Diffusion MRI Physics]] '' '' ||talk ||Dylan Tisdall ||
||12:00 - 1:00 ||'''Lunch''' ||-- ||-- ||
||9:15 - 10:00 ||[[http://surfer.nmr.mgh.harvard.edu/pub/docs/dmri,fs.ppt|Introduction to Diffusion MRI]] ||talk ||Anastasia Yendiki ||
||10:00 - 10:40 ||[[FsTutorial/Diffusion_DtiIntegration|Diffusion Processing Tutorial]] ||tutorial ||staff ||
||11:00 - 11:40 ||[[http://surfer.nmr.mgh.harvard.edu/pub/docs/tracula,fs.ppt|TRActs Constrained by UnderLying Anatomy (TRACULA)]] ||talk ||Anastasia Yendiki ||
||11:40 - 12:00 ||[[FsTutorial/Tracula|Tracula Tutorial]] ||tutorial ||staff ||

||1:00 - 1:30 ||[[FsTutorial/Tracula|Tracula Tutorial]] ||tutorial ||staff ||
||1:30 - 1:40 ||[[http://surfer.nmr.mgh.harvard.edu/pub/docs/tracula,fs.ppt|Longitudinal TRACULA]] ||talk ||Anastasia Yendiki ||
||1:40 - 1:55 ||'''break''' || ||
||1:55 - 2:55 ||[[http://surfer.nmr.mgh.harvard.edu/pub/docs/fMRI_intro.ppt|Basics of fMRI Analysis]] ||talk ||Jon Polimeni ||
||2:55 - 3:35 ||[[http://surfer.nmr.mgh.harvard.edu/pub/docs/fsfast.april2011.ppt|FSFAST]] ||talk ||Doug Greve ||
||3:35 - 3:50 ||'''break''' || ||
||3:50 - 4:30 ||[[http://surfer.nmr.mgh.harvard.edu/pub/docs/fsfast.april2011.ppt|FSFAST]] ||talk ||Doug Greve ||
||4:30 - 5:30 ||[[FsFastTutorialV5.1_freeview|FSFAST Tutorial]] ||tutorial ||staff ||
||4:30 - 5:10 ||* [[http://surfer.nmr.mgh.harvard.edu/pub/docs/fs.registration.ppt|An Overview of Registration Methods]] ||talk ||Lilla Zollei ||
-Line 82:
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-==== Thursday, September 29th - Multimodal Analysis / Troubleshooting / Future Directions ====
+==== Thursday, September 29th - fMRI Analysis / Multimodal Analysis / Future Directions ====
-Line 84:
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-||9:00 - 9:30 ||[[http://surfer.nmr.mgh.harvard.edu/pub/docs/fs.multimodal-integration.Part2.ppt|Multi-Modal Integration, Part 2]] ||talk || Doug Greve ||
||9:30 - 10:00 ||[[FsTutorial/MultiModal_freeview|Multi-Modal Integration Tutorial: fMRI Integration & Surface-based Group fMRI Analysis]] ||tutorial ||staff ||
||10:30 - 11:00 ||'''break''' & [[http://goo.gl/forms/xyGk2iJbp1|Evaluation]]  || ||
+||9:00 - 9:40 ||[[http://surfer.nmr.mgh.harvard.edu/pub/docs/fsfast.april2011.ppt|FSFAST, Part 2: GLM Analysis]] ||talk ||Doug Greve ||
||9:40 - 10:40 ||[[FsFastTutorialV5.1_freeview|FSFAST Tutorial]] ||tutorial ||staff ||
||10:40 - 11:00 ||'''break''' & [[https://docs.google.com/forms/d/e/1FAIpQLSeEvgB6Yr-MC3I131_nmOPVrKtrhKHjjoymY050VTbXq0PtRg/viewform|Evaluation]] || ||
||11:00 - 11:30 ||[[http://surfer.nmr.mgh.harvard.edu/pub/docs/fs.multimodal-integration.Part2.pptx|Multi-Modal Integration, Part 2]] ||talk ||Doug Greve ||
||11:30 - 12:00 ||[[FsTutorial/MultiModal_freeview|Multi-Modal Integration Tutorial: fMRI Integration & Surface-based Group fMRI Analysis]] ||tutorial ||staff ||
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-||2:00 - 2:50 ||Future Directions ||talk ||Bruce Fischl ||
||2:50 - 3:00 ||Question & Answer session ||-- ||staff ||
+||1:00 - 1:40 ||* [[http://surfer.nmr.mgh.harvard.edu/pub/docs/fs.registration.ppt|An Overview of Registration Methods]] ||talk ||Lilla Z&#246;llei ||
||1:40 - 2:25 ||Future Directions ||talk ||Bruce Fischl ||
||2:25 - 2:45 ||Question & Answer Session ||-- ||staff ||