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FreeSurfer Tutorial and Workshop in São Paulo, Brazil

16, 17, & 18 (Sat.,Sun.,Mon.) April 2011

The FreeSurfer Development Team is hosting a three-day course for beginner and experienced users of FreeSurfer. Topics are listed below. There are 40 available spots for this course (see course registration).

Computers will be provided to all pairs of registrants, which will have FreeSurfer and data already installed. Attendees will work in pairs (sharing a computer).

The course will be held at São Paulo healthcare complex of HCFMUSP.

Contact: Pedro Paulo de M. Oliveira Jr. ( ppj at netfilter dot com dot br )

Location

Hospital das Clínicas - Avenida Dr Eneas de Carvalho Aguiar, 44 - São Paulo - SP - Brazil - (hotel,map)

The course will be held at the Radiology Center Building, in the Amphitheatre C.

Saturday, 16 April - Introduction / Single Subject / Troubleshooting

Time	Title	Type	Lecturer
8:30 - 9:00	Course Registration	sign-in	staff
9:00 - 9:30	Unix Tutorial for FreeSurfer Users 1. Surrey, 2. O'Reilly	tutorial	Pedro Paulo de M. Oliveira Jr.
9:30 - 10:00	Intro to FreeSurfer Jargon	talk	Pedro Paulo de M. Oliveira Jr.
10:00 - 10:30	Introduction to Freesurfer	talk	Nick Schmansky
10:30 - 11:00	FreeSurfer Applications, Publications	talk	Nick Schmansky
11:00 - 11:30	break
11:30 - 12:30	Analyzing the Individual Subject	talk	Allison Stevens
12:30 - 1:30	lunch	--	--
1:30 - 2:00	Tkmedit/Tksurfer demonstration	demo	Nick Schmansky
2:00 - 3:00	Interaction with Individual Subject Data Tutorial	tutorial	staff
3:00 - 3:30	break
3:30- 4:00	Failure Modes	talk	Allison Stevens
4:00 - 4:30	Quality Checking a Recon	demo	Allison Stevens
4:30 - 5:30	Troubleshooting Demonstration, Troubleshooting Tutorial	tutorial	staff, Allison

Sunday, 17 April - Group Analysis / Registration / Longitudinal / ROIs

Time	Title	Type	Lecturer
9:00 - 10:00	Group Analysis / GLM / Multiple Comparisons	talk	Lilla Zollei
10:00 - 10:30	QDEC demonstration	demo	Nick Schmansky
10:30 - 10:45	break
10:45 - 11:15	Group Analysis / Multiple Comparisons - mri_glmfit Tutorial	tutorial	staff
11:15 - 11:45	Group Analysis - qdec Tutorial	tutorial	staff
11:45 - 1:00	lunch	--	--
1:00 - 1:45	Registration Methods	talk	Lilla Zollei
2:15 - 2:45	Longitudinal FreeSurfer see also: LongitudinalProcessing	talk	Lilla Zollei
2:45 - 3:00	break
3:00 - 3:30	ROI Analysis	talk	Allison Stevens
3:30 - 4:00	A Non-physicist's Intro to MR SpinBench	talk	Andre van der Kouwe
4:00 - 4:30	ROI Analysis Tutorial	tutorial	staff
4:30 - 5:00	Longitudinal Tutorial	tutorial	staff

Monday, 18 April - Diffusion / Tracula / MRI basics / Apps / Q&A

Time	Title	Type	Lecturer
9:00 - 9:30	Diffusion Data Processing,dtrecon intro	talk	Lilla Zollei
9:30 - 10:30	Diffusion Processing Tutorial	tutorial	staff
10:30 - 11:00	break and group photo
11:00 - 11:30	TRActs Constrained by UnderLying Anatomy (TRACULA)	talk	Lilla Zollei
11:30 - 12:30	Tracula Tutorial	tutorial	staff
12:30 - 1:30	lunch	--	--
1:30 - 2:00	MRI Acquisition Methods for Morphometry	talk	Andre van der Kouwe
2:00 - 2:30	break and evaluations
2:30 - 3:00	Motion-compensated neuroanatomical imaging	talk	Andre van der Kouwe
3:00 - 3:30	iSurf and local FreeSurfer Applications	talk	Pedro Paulo de M. Oliveira Jr.
3:30 - 4:00	Question and Answer Session, FsQuiz	talk	staff

FsTutorial/BrazilCourseSchedule (last edited 2011-03-11 08:53:24 by AllisonStevens)

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== FreeSurfer Tutorial and Workshop in São Paulo, Brazil ==
=== 11 & 12 March 2009 ===

The FreeSurfer Development Team is hosting a two-day course for beginner and experienced users of FreeSurfer. Day 1 will be an introduction to FreeSurfer (or a refresher for those more experienced). Day 2 will cover everything you need to know for analyzing your data. Topics are listed below. There are only 30 available spots for this course. The course will not cover FS-FAST or fMRI analysis.

Computers will be provided to all pairs of registrants, which will have FreeSurfer and data already installed. Attendees will work in pairs (sharing a computer). 

The course will be held at São Paulo healthcare complex of HCFMUSP.

Contact: Pedro Paulo de M. Oliveira Jr. ( ppj at netfilter dot com dot br )

=== Location ===

[[http://www.hcnet.usp.br/|Hospital das Clínicas]] - [[attachment:HospitaldasClinicas.kmz|.kmz|&do=get]] - [[http://maps.google.com/maps?q=Avenida%20Dr%20Eneas%20de%20Carvalho%20Aguiar%2C%2044%20-%20S%C3%A3o%20Paulo%20-%20SP%20-%20Brazil&oe=utf-8&rls=org.mozilla:en-US:official&client=firefox-a&um=1&ie=UTF-8&sa=N&hl=en&tab=wl|Avenida Dr Eneas de Carvalho Aguiar, 44 - São Paulo - SP - Brazil]] -  ([[http://www.atlanticahotels.com.br/atlantica%5Fing/hoteis/estrutura.asp?Numfuncionalidade=292&NumHotel=34&Cidade=S%E3o%20Paulo|hotel]],[[http://maps.google.com/maps?hl=en&q=rua%20Oscar%20Freire%2C%201948%20-%20Jardim%20Paulista%2C%20S%C3%A3o%20Paulo%20-%20SP%2C%2005409000%2C%20Brazil&um=1&ie=UTF-8&sa=N&tab=wl|map]])

The course will be held at the [[http://upload.wikimedia.org/wikipedia/commons/7/72/Hospitaldocancerdesp2.jpg|Cancer Center Building]], in the 6th floor auditorium.

=== Wednesday, March 11th - Introduction / Single Subject / Group Analysis ===

|| '''Time''' || '''Title''' || '''Type''' || '''Lecturer''' ||
|| 8:30 - 9:00 || Course Registration || sign-in || staff ||
|| 9:00 - 9:20 || Introductions, and Unix tutorial for !FreeSurfer || tutorial || Pedro Paulo in Portuguese ||
|| 9:20 - 9:50 || [[attachment:freesurfer.intro.2009.ppt|Introduction to Freesurfer|&do=get]]  || talk || Nick Schmansky  ||
|| 9:50 - 10:30 || [[attachment:freesurfer.applications.2009.ppt|FreeSurfer Applications|&do=get]] || talk || Nick Schmansky||
|| 10:30 - 10:45 || '''coffee break''' || || ||
|| 10:45 - 11:45 || [[attachment:course_individual_subject.ppt|Analyzing the Individual Subject|&do=get]] || talk|| Allison Stevens ||
|| 11:45 - 12:45 || '''lunch''' || ||  ||
|| 12:45 - 1:15  || Tkmedit/Tksurfer demonstration || demo || Nick Schmansky ||
|| 1:15 - 1:45 || [[FsTutorial/OutputData|Interaction with Individual Subject Data]] || tutorial || staff ||
|| 1:45 - 3:00 || [[attachment:freesurfer.groupanalysis.ppt|Group Analysis / GLM / Multiple Comparisons|&do=get]] || talk || Lilla Zollei ||
|| 3:00 - 3:15 || QDEC demonstration || demo || Nick Schmansky ||
|| 3:15 - 3:30 || '''coffee break''' || || ||
|| 3:15 - 4:15 || [[FsTutorial/GroupAnalysis|Group Analysis / Multiple Comparisons - mri_glmfit]] || tutorial || staff ||
|| 4:15 - 5:00 || [[FsTutorial/QdecGroupAnalysis|Group Analysis - qdec]] || tutorial || staff ||
## || 5:00 - || '''optional -''' [[DownloadAndInstall|FreeSurfer Installation on Personal Laptops]] || one-on-one || Nick Schmansky / Pedro Paulo ||
## || 5:00 - || '''optional -''' Start Processing Your Own Data || one-on-one || Allison Stevens / Lilla Zollei ||

=== Thursday, March 12th - ROIs / Troubleshooting / Multi-Modal / QA / Future Directions ===

|| '''Time''' || '''Title''' || '''Type''' || '''Lecturer''' ||
|| 9:00 - 10:00 || [[attachment:fs.roi.ppt|ROI Analysis|&do=get]] || talk || Allison Stevens ||
|| 10:00 - 10:45 || [[FsTutorial/AnatomicalROI|ROI Analysis]] || tutorial || staff ||
|| 10:45 - 11:00 || '''coffee break''' || || ||
|| 11:00 - 11:15 || [[attachment:freesurfer.failure_modes.2009.ppt|Failure Modes|&do=get]] || talk || Allison Stevens ||
|| 11:15 - 12:15 || [[FsTutorial/TroubleshootingData|Troubleshooting]] || tutorial || staff ||
|| 12:15 - 1:00 || '''lunch''' || || ||
|| 1:00 - 2:15 || [[attachment:fs.multimodal-integration.ppt|Multi-Modal Integration: ROI and Surface-based Analysis|&do=get]] || talk || Lilla Zollei ||
|| 2:15 - 3:15 || [[FsTutorial/MultiModal|Multi-Modal Integration]] || tutorial || staff ||
|| 3:15 - 3:30 || '''coffee break''' || || ||
|| 3:30 - 4:30 || [[attachment:LZ.future.directions.combined.short.ppt|Future Directions of FreeSurfer|&do=get]] || talk || Lilla Zollei ||
|| 4:30 - 5:30 || Question and Answer Session, FsQuiz || group session || staff ||
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