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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>> Current staff members can be found on our [[https://www.martinos.org/lab/lcn/people|website]].
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||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 - 8:45 ||** [[http://surfer.nmr.mgh.harvard.edu/pub/docs/Unix_MF.pptx|Intro to Linux for FreeSurfer Users]] ||talk/demo || ||
||8:45 - 9:15 ||** [[http://surfer.nmr.mgh.harvard.edu/pub/docs/Unix_MF.pptx|Unix for FreeSurfer Users]] ||tutorial || ||
||9:15 - 9:30 ||** [[http://surfer.nmr.mgh.harvard.edu/pub/docs/
fsjargon_clean.pptx|Intro to FreeSurfer Jargon]] || talk || Caroline Magnain ||
||9:30 - 9:45 ||'''break''' || || ||
||
9:45 - 10:00 ||[[attachment:freesurfer.intro.apr.2019.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 ||
||11:10 - 11:30 ||'''break''' || || ||
||11:30
- 11:45 ||[[https://www.youtube.com/watch?v=Mv-ECowxq2o|Freeview demonstration]] ||[[FsTutorial/FreeviewDemo|demo]] || Bram Diamond ||
||11:45 - 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 ||  ||
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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 || Matthew Vera ||
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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 ||
||4:50 - 5:30 || [[FsTutorial/LongitudinalTutorial|LongitudinalTutorial]] ||tutorial ||staff ||
||8:00 - 9:00 ||*** Morning Help Session|| || Research Techs ||
||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]] ||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]] ||talk ||Leah Morgan, Allison Stevens ||
||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 ||
||4:50 - 5:30 || [[FsTutorial/LongitudinalTutorial|LongitudinalTutorial]] ||tutorial ||Malte Hoffmann ||
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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|| ||8:00 - 9:00 ||*** Morning Help Session || ||Research Techs ||
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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 ||** MRI Acquisition Methods || talk ||Andre van der Kouwe||
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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 Techs||
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||12:00 - 1:00 ||'''Lunch''' ||-- ||-- || ||12:00 - 1:00 ||'''Lunch''' || || ||
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||4:30 - 5:00 ||Question & Answer Session ||-- ||staff || ||4:30 - 5:00 ||Question & Answer Session || ||staff ||

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.

Current staff members can be found on our website.

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

Time

Title

Type

Lecturer

8:30 - 8:45

** Intro to Linux for FreeSurfer Users

talk/demo

8:45 - 9:15

** Unix for FreeSurfer Users

tutorial

9:15 - 9:30

** Intro to FreeSurfer Jargon

talk

Caroline Magnain

9:30 - 9:45

break

9:45 - 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

Bram Diamond

11:45 - 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

2:15 - 2:35

break

2:35 - 3:05

ROI Analysis

talk

Matthew Vera

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 Techs

9:00 - 9:45

Group Analysis

talk

Viviana Siless

9:45 - 10:25

Group Analysis Tutorial

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, Allison Stevens

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

Malte Hoffmann

5:30 - 7:30

Social Night in the atrium of Bldg. 149

Snacks and Beverages Served

you!

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 Techs

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

** 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 Techs

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


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