Diff for "FsTutorial/Fall2019CourseSchedule"

Differences between revisions 2 and 28 (spanning 26 versions)

[Spring2020CourseSchedule]

#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.
** 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.

Research backgrounds of past and present staff members can be found on the LCN website.

Monday, September 23rd - Introduction / Single Subject Analysis / ROI Analysis

Time	Title	Type	Lecturer
8:30 - 8:40	** Intro to Linux for FreeSurfer Users	talk/demo	Matthew Larrabee
8:40 - 9:00	** Unix for FreeSurfer Users	tutorial
9:00 - 9:15	** Intro to FreeSurfer Jargon	talk	Caroline Magnain
9:15 - 9:25	break
9:25 - 10:10	Introduction to Freesurfer	talk	Bruce Fischl
10:10 - 11:20	Analyzing the Individual Subject	talk	Doug Greve
11:20 - 11:40	break
11:40 - 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	Diyva Varadarajan
2:15 - 2:35	break
2:35 - 3:05	ROI Analysis	talk	Doug Greve
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, September 24th - Group Analysis / Longitudinal Analysis / Troubleshooting

Time	Title	Type	Lecturer
8:00 - 9:00	*** Morning Help Session		research technicians
9:00 - 9:45	Group Analysis	talk	Viviana Siless
9:45 - 10:25	Group Analysis Tutorial (FSGD Examples)	tutorial	staff
10:25 - 10:45	break
10:45 - 11:30	FreeSurfer Troubleshooting	talk	Bruce Fischl
11:30 - 12:30	Troubleshooting Tutorial	tutorial	staff
12:30 - 1:30	Lunch
1:30 - 2:15	Quality Checking a Recon	talk	Leah Morgan
2:15 - 2:55	Multiple Comparisons	talk	Doug Greve
2:55 - 3:25	Multiple Comparisons Tutorial	tutorial	staff
3:25 - 4:05	break
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

Answers to online questions here

Wednesday, September 25th - Multimodal Analysis / Diffusion Analysis / fMRI Analysis / MR Acquisition

Time	Title	Type	Lecturer
8:00 - 9:00	*** Morning Help Session		research technicians
9:00 - 9:30	* Intro to MR	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	* MRI Acquisition Methods	talk	Andre van der Kouwe

Answers to online questions here

The FreeSurfer Evaluation is here!

Thursday, September 26th - fMRI Analysis / Multimodal Analysis / Future Directions

Time	Title	Type	Lecturer
8:00 - 9:00	*** Morning Help Session		research technicians
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)

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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 optional 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. <<BR>> <<BR>> Research backgrounds of past and present staff members can be found on the [[https://www.martinos.org/lab/lcn/people|LCN website]].
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-==== Monday, April 1st - Introduction / Single Subject Analysis / ROI Analysis  ====
+==== Monday, September 23rd - Introduction / Single Subject Analysis / ROI Analysis  ====
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+Line 24:
-||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 ||
+||8:30 - 8:40 ||** Intro to Linux for !FreeSurfer Users ||talk/demo || Matthew Larrabee ||
||8:40 - 9:00 ||** [[https://surfer.nmr.mgh.harvard.edu/fswiki/UnixTutorial|Unix for FreeSurfer Users]] ||tutorial || ||
||9:00 - 9:15 ||** [[http://surfer.nmr.mgh.harvard.edu/pub/docs/fsjargon_clean.pptx|Intro to FreeSurfer Jargon]] || talk || Caroline Magnain ||
||9:15 - 9:25 ||'''break''' || || ||
||9:25 - 10:10 ||[[attachment:freesurfer.intro.apr.2019.ppt|Introduction to Freesurfer]] ||talk ||Bruce Fischl ||
||10:10 - 11:20 ||[[http://surfer.nmr.mgh.harvard.edu/pub/docs/fsrecon.pptx|Analyzing the Individual Subject]] ||talk ||Doug Greve ||
||11:20 - 11:40 ||'''break''' || || ||
||11:40 - 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 ||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 ||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 || Diyva Varadarajan ||
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-||2:35 - 3:05 ||[[http://surfer.nmr.mgh.harvard.edu/pub/docs/fs.roi.EB_wiki.pptx|ROI Analysis]] ||talk || ||
+||2:35 - 3:05 ||[[http://surfer.nmr.mgh.harvard.edu/pub/docs/fs.roi.EB_wiki.pptx|ROI Analysis]] ||talk || Doug Greve ||
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-==== Tuesday, April 2nd - Group Analysis / Longitudinal Analysis / Troubleshooting ====
+==== Tuesday, September 24th - Group Analysis / Longitudinal Analysis / Troubleshooting ====
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-||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 ||
+||8:00 - 9:00 ||*** Morning Help Session|| || research technicians ||
||9:00 - 9:45 ||[[http://surfer.nmr.mgh.harvard.edu/pub/docs/GLM.pptx|Group Analysis]] ||talk || Viviana Siless ||
||9:45 - 10:25 ||[[FsTutorial/GroupAnalysisV6.0|Group Analysis Tutorial]] ([[FsgdExamples|FSGD Examples]]) ||tutorial ||staff ||
||10:25 - 10:45 ||'''break''' || || ||
||10:45 - 11:30 ||[[http://surfer.nmr.mgh.harvard.edu/pub/docs/freesurfer.troubleshooting.apr2019.ppt|FreeSurfer Troubleshooting]] ||talk ||Bruce Fischl ||
||11:30 - 12:30 ||[[FsTutorial/TroubleshootingDataV6.0|Troubleshooting Tutorial]] ||tutorial ||staff ||
||12:30 - 1:30 ||'''Lunch''' || || ||
||1:30 - 2:15 ||[[https://youtu.be/AR83_Bt04VQ|Quality Checking a Recon]] || [[https://zoom.us/wc/join/369478461?pwd=|talk]] ||Leah Morgan ||
||2:15 - 2:55 ||[[http://surfer.nmr.mgh.harvard.edu/pub/docs/multiplecomparisons.ppt|Multiple Comparisons]] ||talk ||Doug Greve||
||2:55 - 3:25 ||[[FsTutorial/MultipleComparisonsV6.0Perm|Multiple Comparisons Tutorial]] ||tutorial ||staff ||
||3:25 - 4:05 ||'''break''' || || ||
||4:05 - 4:50 ||[[http://surfer.nmr.mgh.harvard.edu/pub/docs/fs.longitudinal.pptx|Longitudinal FreeSurfer]] ||talk ||Malte Hoffmann ||
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-||5:30 - 7:30 ||Social Night in the atrium of Bldg. 149|| Snacks and Beverages Served ||you! ||
+||5:30 - 7:30 ||Social Night in the atrium of Bldg. 149|| Snacks and Beverages Served ||  ||
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-==== Wednesday, April 3rd - Multimodal Analysis / Diffusion Analysis / fMRI Analysis / MR Acquisition ====
+==== Wednesday, September 25th - Multimodal Analysis / Diffusion Analysis / fMRI Analysis / MR Acquisition ====
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-||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 ||
+||8:00 - 9:00 ||*** Morning Help Session || ||research technicians ||
||9:00 - 9:30 ||* [[http://surfer.nmr.mgh.harvard.edu/pub/docs/IntroMRI.pptx|Intro to MR]] '' '' ||talk ||Robert Frost ||
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-||10:50 - 11:05 ||** [[http://surfer.nmr.mgh.harvard.edu/pub/docs/IntroDiffusion.apr2019.pptx|Intro to Diffusion MRI Physics]] '' '' ||talk ||Robert Frost ||
+||10:50 - 11:05 ||* [[http://surfer.nmr.mgh.harvard.edu/pub/docs/IntroDiffusion.pptx|Intro to Diffusion MRI Physics]] '' '' ||talk ||Robert Frost ||
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-||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 ||
+||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 ||
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-||4:50 - 5:30 ||* [[attachment:fs-cloud-prsentation_20190403.pdf|Running FreeSurfer in the cloud with AWS batch]] || talk || Paul Wighton||
+||4:50 - 5:30 ||* [[http://surfer.nmr.mgh.harvard.edu/pub/docs/FreeSurfer_Acquisition_Sep2019.ppt|MRI Acquisition Methods]] || talk ||Andre van der Kouwe||
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-==== Thursday, April 4th - fMRI Analysis / Multimodal Analysis / Future Directions ====
+==== Thursday, September 26th - fMRI Analysis / Multimodal Analysis / Future Directions ====
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-||8:00 - 9:00 ||*** Optional session, extra support for fMRI and Diffusion Questions ||-- ||staff||
+||8:00 - 9:00 ||*** Morning Help Session || ||research technicians||
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-||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 ||
+||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 ||
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-||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 - 3:30 ||* [[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 ||
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-##||3:15 - 3:45 ||* [[http://surfer.nmr.mgh.harvard.edu/pub/docs/mri_acquisition.ppt|MRI Acquisition Methods]] ||talk ||André van der Kouwe ||