introduction / overview 6th october 2010 suz prejawa chris lambert wellcome trust centre for...
DESCRIPTION
Methods for Dummies 2009 Basic Statistics fMRI (BOLD) EEG / MEG Connectivity VBM & DTI (a new addition) Introduction to MfD 2010 Areas covered in MfD Wednesdays / 13h00 – 14h00 / FIL Seminar Room Aim: to give a basic introduction to human brain imaging analysis methods, focusing on fMRI and M/EEGTRANSCRIPT
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Introduction / Overview6th October 2010
Suz Prejawa & Chris Lambert
Wellcome Trust Centre for Neuroimaging, UCL
2010
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Overview• Introduction
• What’s MfD
• Programme for 2010
• How to prepare your presentation
• Where to find information and help
• Experts
• Overview for dummies
Introduction to MfD 2010
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Methods for Dummies 2009
• Basic Statistics
• fMRI (BOLD)
• EEG / MEG
• Connectivity
• VBM & DTI (a new addition)
Introduction to MfD 2010
Areas covered in MfD
Wednesdays / 13h00 – 14h00 / FIL Seminar Room
Aim: to give a basic introduction to human brain imaging analysis methods, focusing on fMRI and M/EEG
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PROGRAMME 2010Autumn
Introduction to MfD 2010
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I. Basic Statistics 20th Oct – 17th Nov
• Linear Algebra & Matrices (Philip Glass & Melanie Boly)
• T-tests, ANOVA’s & Regression (Jennifer Siegel & Varun Sethi)
• General Linear Model (Holly Rossiter & Philip Glass)
• Bayes for beginners (Rik Adams & Yen Yu)
• Random Field Theory (Rumana Chowdhury & Nagako Murase)
Introduction to MfD 2010
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II. What are we measuring?Part I: 24th Nov
• Basis of the BOLD signal (Louise McDonald & Yen Yu)
Introduction to MfD 2010
A nice one week break…
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III. fMRI Analysis8th Dec – 15th Dec
• Preprocessing:– Realigning and un-warping (Matteo Pugnaghi & Rebecca Lawson)
– Co-registration & spatial normalisation (Rebecca Lawson & Matteo Pugnaghi
Introduction to MfD 2010
Continues after Christmas break…
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PROGRAMME 2009Winter/ Spring 2010
Introduction to MfD 2010
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Introduction to MfD 2010
• Study design and efficiency (Rumana Chowdhury & Robin Carhart Harris)
• 1st level analysis – Design matrix contrasts and inference (Stephane de Brito
& Fiona McNab)
• 1st level analysis – Basis functions, parametric modulation and correlated
regressors (Klaartje Heinen & Paul Rogerson)
• 2nd level analysis – between-subject analysis (Fiona McNab & Stephane de
Brito)
III. fMRI Analysis (cont.)12th Jan – 2nd Feb
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II. What are we measuring?Part II: 9th Feb
• Basis of the M/EEG signal (Rik Adams & Louise McDonald)
Introduction to MfD 2010
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IV. EEG & MEG16th Feb – 23rd Feb
• Pre-processing and experimental design (Jennifer Siegel & Tabish Saifee)
• Contrasts, inference and source localisation (Tabish Saifee & Paul Rogerson)
Introduction to MfD 2010
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V. Connectivity 2nd March – 16th March
• Intro to connectivity - PPI & SEM (Nagako Murase & Klaartje Heinen)
• DCM for fMRI – theory & practice (Peter Zeidman & Laura Madeley)
• DCM for ERP / ERF – theory & practice (Niall Lally & Holly Rossiter)
Introduction to MfD 2010
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Introduction to MfD 2010
VI. Structural MRI Analysis 23rd March- 30th March
• Voxel Based Morphometry (Laura Madeley & Sabeena Chaudry)
• Basic DTI (Niall Lally & Sabeena Chaudry)
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How to prepare your presentation
• Remember your audience are not experts…
• The aim of the sessions is to
– introduce the concepts and explain why they are important to imaging analysis
– familiarise people with the basic theory and standard methods
• Time: 45min. + 15min. questions – 2 presenters per session
• Don’t just copy last year’s slides!!!...
• Start preparing your talk with your co-presenter at least 2 weeks in advance
• Talk to the allocated expert 1 week in advance
Introduction to MfD 2010
Very important!!!: Read the Presenter’s guide (http://www.fil.ion.ucl.ac.uk/mfd/guide.pdf)
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What if I can’t make my presentation?
• If you want to change / swap your topic, try and find someone else to swap with….
• …if you still can’t find a solution, then get in touch with Chris, Maria or Suz as soon as possible (at least 3 weeks before the talk).
Introduction to MfD 2010
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Where to find help
• Key papers• Previous years’ slides• Human Brain Function Textbook (online)• SPM course slides• Cambridge CBU homepage (Rik Henson’s slides)
• Methods Group Experts• Monday Methods Meetings (4th floor FIL, 12.30)• SPM email List
Introduction to MfD 2010
MfD Home
Resources http://www.fil.ion.ucl.ac.uk/mfd/page2/page2.html
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Experts• Will Penny – Head of Methods• John Ashburner• Dimitris Pinotsis• Guillaume Flandin• James Kilner• Rosalyn Moran• Andre Marreiros• Steve Fleming• Vladimir Litvak• Chloe Hutton• Antoine Lutti• Ged Ridgeway• Zoltan Nagy• Marta Garrido
Introduction to MfD 2010
Contact the expert: discuss presentation and other issues (1 week before talk)
Expert will be present in the session
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Website
http://www.fil.ion.ucl.ac.uk/mfd/
Introduction to MfD 2010
Where you can find all the information about MfD 2010:
Programme
Contacts
Presenter’s guide
Resources (Help)
Etc…
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Other helpful courses
Introduction to MfD 2010
• Matlab for Cognitive Neuroscience (ICN)– Run by Klaartje Heinen Jen Marchant [email protected]
& [email protected] – http://www.icn.ucl.ac.uk/courses/MATLAB-Tutorials/in
dex.htm– 4.30 pm, Thursday (not every week!)– 17 Queen Square, basement seminar room
• Physics lecture series– Run by FIL physics team– Details will be announced– 12 Queen Square, Seminar room
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Overview for Dummies
Introduction to MD 2010
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Outline
• SPM & your (fMRI) data– Preprocessing– Analysis– Connectivity
• Getting started with an experiment
• Acronyms
Introduction to MfD 2010
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Pre-processing
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Preprocessing Possibilities…
• These steps basically get your imaging data to a state where you can start your analysis
– Realignment & Unwarping
– Segmentation and Normalisation
– Smoothing
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Model specification and estimation
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Analysis
• Once you have carried out your pre-processing you can specify your design and data
– The design matrix is simply a mathematical description of your experimentE.g. ‘visual stimulus on = 1’ ‘visual stimulus off = 0’
Design matrix
General Linear Model
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Inference
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Contrasts & inference
• Contrasts allow us to test hypotheses about our data, using t & f tests
• 1st level analysis: activation over scans (within subject)• 2nd level analysis: activation over subjects
• Multiple Comparison Problem – Random Field Theory
SPM
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Write up and publish…
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Brain connectivity
• Functional integration – how one region influences another…subdivided into: – Functional connectivity: correlations among brain systems (e.g.
principal component analysis)– Effective connectivity: the influence of one region over another
(e.g. psycho-physiological interactions, or Dynamic Causal Modelling)
Causal interactions between brain areas, statistical dependencies
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Statistical Parametric Mapping
• MfD 2010 will focus on the use of SPM8• SPM software has been designed for the analysis of brain imaging
data in fMRI, PET, SPECT, EEG & MEG • It runs in Matlab… just type SPM at the prompt and all will be
revealed.• There are sample data sets available on the SPM website to play
with
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Getting started – Cogent
• http://www.vislab.ucl.ac.uk/Cogent/
– present scanner-synchronized visual stimuli, auditory stimuli, mechanical stimuli, taste and smell stimuli
– monitor key presses
– physiological recordings
– logging stimulus & scan onset times
• Try and get hold of one to modify rather than starting from scratch! People are more than happy to share scripts around.
• If you need help, talk to Eric Featherstone.
Introduction to MfD 2010
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Getting started - Setting up your experiment
If you need…• special equipment
– Peter Aston– Physics team
• special scanning sequences– Physics team
• They are very happy to help, but contact them in time!
Introduction to MfD 2010
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Getting started - scanning decisions to be made
• What are your scanning parameters: – how many conditions/sessions/blocks– Interstimulus interval– Scanning sequence– Scanning angle– How much brain coverage do you need
• how many slices• what slice thickness
– what TR
• Use the physics wiki page: http://cast.fil.ion.ucl.ac.uk/pmwiki/pmwiki.php
Introduction to MfD 2010
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Summary
• Get you script ready & working with the scanner
• Make sure it logs all the data you need for your analysis
• Back up your data from the stimulus PC! You can transfer it via the network after each scanning session…
• Get a scanning buddy if it’s your first scanning study
• Provide the radiographers with tea, biscuits, chocolate etc.
Introduction to MfD 2010
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Use the project presentations!
They are there to help you design a project that will get you
data that can actually be analyzed in a meaningful way
Introduction to MfD 2010
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Acronyms
• DCM – dynamic causal model• DTI – diffusion tensor imaging • FDR – false discovery rate• FFX – fixed effects analysis• FIR – finite impulse response• FWE – family wise error• FWHM – full width half maximum• GLM – general linear model• GRF – gaussian random field theory• HRF – haemodynamic response
function• ICA – independent component
analysis• ISI – interstimulus interval
• PCA – principal component analysis• PEB – parametric empirical bayes• PPI – psychophysiological interaction• PPM – posterior probability map• ReML – restricted maximum likelihood• RFT– random field theory• RFX – random effects analysis• ROI – region of interest• SOA – stimulus onset asynchrony• SPM – statistical parametric mapping• VBM – voxel-based morphometry