terça-feira, 13 de março de 2012

FSL & FREESURFER COURSE

 


This program has been endorsed by .

intro     registration     accommodation & location     reading     faculty     timetable     contact




Learn the theory and practice of functional and structural brain image analysis

We are pleased to announce the 2012 FSL & FreeSurfer Course, to be held in Auckland, New Zealand (May 14-18). It will run immediately after the ISMRM conference, which will be in Melbourne, Australia.
The intensive course covers both the theory and practice of functional and structural brain image analysis. Background concepts and the practicalities of analyses are taught in detailed lectures; these are interleaved with hands-on practical sessions where attendees learn how to carry out analysis for themselves on real data, with one computer provided for every two attendees. After completing the course, attendees should be able to analyse their own FMRI and MRI data sets.
The course is aimed at both new and existing users of these packages and will cover both basic and advanced features. The methods covered include
  • Functional MRI:
    • GLM analysis, including Bayesian multi-subject statistics (FSL - FEAT)
    • ICA Model-free analysis, RSNs, functional connectivity (FSL - MELODIC & dual-regression)
  • Structural MRI:
    • Image registration and unwarping (FSL - FLIRT/FNIRT/FUGUE & FreeSurfer - BBR)
    • Brain extraction and tissue-type segmentation (FSL - BET/FAST)
    • Structural spatial statistical analysis e.g. atrophy (FSL - SIENA/FSL-VBM)
    • Automatic subcortical segmentation / alignment (FreeSurfer - ASEG & FSL - FIRST)
  • Diffusion MRI:
    • Probabilistic diffusion modelling and tractography, including crossing-fibres (FSL - FDT)
    • Voxelwise multi-subject analysis (FSL - TBSS)
  • Cortical modelling and its applications (FreeSurfer):
    • Cortical flattening for improved FMRI analysis, including inter-subject averaging
    • Cortical labelling
    • Group studies of cortical morphometry; thickness, folding, surface area, volume
All lectures and printed material will be in English.



Registration

Registration (in UK pounds) is £550 for PhD/MSc students, £900 for postdocs and other non-student attendees, and £2000 for commercial attendees. Course registration includes lectures, computer practical sessions, coffee/tea breaks and a printed copy of the lecture slides. All course materials (lecture slide PDFs, practical instructions and practical datasets) will be available online after the course.
The registration fee does not include accommodation (see below), or lunches; there are plenty of local restaurants and cafés where course attendeees will be able to get lunch.
We are only able to take payment by credit card. To register and pay, visit the on-line registration page. Please note that your registration is not complete until you have finalised the payment (going to the shopping basket and then to checkout and payment).



Accommodation & Location Information

The course will take place in the centrally located Rydges Hotel, Auckland, New Zealand.
You will need to organise your own accommodation for the course.
A special rate at the Rydges Hotel has been arranged at NZ$119 per room per night for the week (normally NZ$142). Book online or use the code R-UOX130512 for email/phone bookings. Alternatively, there are many other hotels in central Auckland.
If you would like to try to arrange to share accommodation with another attendee, you can enter your contact information on our publicly-viewable wiki page.
For flights, ISMRM attendees should be able to have either Auckland or Melbourne as a stopover in a single return trip.



Preparatory Reading - Important

People with no previous experience of UNIX would benefit greatly from spending a few hours, before coming, working through at least the first 5 sections of A Basic UNIX Tutorial.
People with no background in FMRI experimentation and analysis would probably benefit from reading Chapters 1,9-16 from Functional MRI: An Introduction to Methods (or order at Amazon UK / USA).



Faculty

Local organisers     Joanne Lin, Laura Fogg, Reem Jan, Bruce Russell, Nick Gant; University of Auckland
Speakers
FMRIB, Oxford: Jesper Andersson, Mark Jenkinson, Saad Jbabdi, Karla Miller, Steve Smith
Donders Institute, Nijmegen: Christian Beckmann
MGH, Boston: Lilla Zollei, Allison Stevens, Nick Schmansky
Tutors     (in addition to the Speakers)
FMRIB, Oxford: Duncan Mortimer, Emma Robinson



Timetable: May 2012

Please note that there may be some minor changes to the timetable and faculty.

14
Monday
15
Tuesday
16
Wednesday
17
Thursday
18
Friday
8:30Course Registration


9:00-10:30
main lectures
Intro to Imaging, Overview of FSL, Brain-extraction (BET)
MJ
FMRI 1 - Preprocessing & Simple Stats
(FEAT)
MJ/JA
FMRI 3 - Advanced FMRI Analysis
(FEAT)
MJ/JA
ICA - Exploratory FMRI Analysis
(MELODIC)
CB
FreeSurfer
LZ/AS/NS
10:30-11:00 Tea & Coffee
11:00-12:30 Practical session
12:30-2:00 Lunch
2:00-3:30
main lectures
Registration & Unwarping
(FLIRT, FNIRT & FUGUE)
MJ
FMRI 2 - Permutation Testing & Multi-Subject Stats
(Randomise & FEAT)
JA/CB
Structural Segmentation
(FAST, FIRST, SIENA, FSL-VBM)
MJ
Diffusion MRI Analysis
(FDT & TBSS)
SJ/SS
FreeSurfer 2
LZ/AS
3:30-4:00 Tea & Coffee
4:00-5:30 Practical session
5:30-6:15
evening lectures
Intro to MRI acquisition
KM
Mapping the connectome with resting FMRI and DTI
TBC
Intro to DTI acquisition
KM
Intro to FreeSurfer
LZ
FSL & FreeSurfer Future Work
LZ/MJ
6:30-8:00 Drinks & nibbles reception




Contact Details

If you have any queries about the course, please email fslcourse@fmrib.ox.ac.uk
 

fonte: Universidade de Oxford

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