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Introduction / Overview

2009. Introduction / Overview. 15th October 2009. Maria Joao Rosa and Antoinette Nicolle Wellcome Trust Centre for Neuroimaging, UCL. Overview. Introduction What’s MfD Programme for 2009 How to prepare your presentation Where to find information and help Experts Overview for dummies.

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Introduction / Overview

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  1. 2009 Introduction / Overview 15th October 2009 Maria Joao Rosa and Antoinette Nicolle Wellcome Trust Centre for Neuroimaging, UCL

  2. Overview • Introduction • What’s MfD • Programme for 2009 • How to prepare your presentation • Where to find information and help • Experts • Overview for dummies Introduction to MfD 2009

  3. Methods for Dummies 2009 Aim: to give a basic introduction to human brain imaging analysis methods, focusing on fMRI and M/EEG Wednesdays / 13h00 – 14h00 / FIL Seminar Room Areas covered in MfD • Basic Statistics • fMRI (BOLD) • EEG / MEG • Connectivity • VBM Introduction to MfD 2009

  4. PROGRAMME 2009 Autumn Introduction to MfD 2009

  5. I. Basic Statistics21st Oct – 18th Nov • Linear Algebra & Matrices (Elvina Chu and Flavia Mancini) • T-tests, ANOVA’s & Regression (Carles Falcon and Suz Prejawa) • General Linear Model (Catherine Tur and Ashawin Jha) • Bayes for beginners (Raphael Kaplan and Jason Stretton) • Random Field Theory (Friederike Schuur and Anne-Lise Goddings) Introduction to MfD 2009

  6. II. What are we measuring?25th Nov – 2nd Dec • Basis of the BOLD signal (Miriam Klein and Ciara O’Mahony) • Basis of the M/EEG signal (Jordi Costa Faidella and Tal Machover) Introduction to MfD 2009

  7. III. fMRI Analysis9th Dec – 16th Dec • Preprocessing: • Realigning and un-warping (Idalmis Santusteban and Rebecca Knight) • Co-registration & spatial normalisation (Ana Csaraiva and Britt Hoffland) Continues after Christmas break… Introduction to MfD 2009

  8. PROGRAMME 2009 Spring 2010 Introduction to MfD 2009

  9. III. fMRI Analysis (cont.)13th Jan – 3rd Feb • Study design and efficiency (Heidi Bonnici and Sinead Mullally) • 1st level analysis – Design matrix contrasts and inference (Loreili Howard and Rumana Chowdury) • 1st level analysis – Basis functions, parametric modulation and correlated regressors (Crystal Goh and one other) • 2nd level analysis – between-subject analysis (Jennifer Marchant and Tessa Dekker) Introduction to MfD 2009

  10. IV. EEG & MEG10th Feb – 17th Feb • Pre-processing and experimental design (Thomas Ditye and Lena Kaestner) • Contrasts, inference and source localisation (Diana Omigie and Stjepana Kovac) Introduction to MfD 2009

  11. V. Connectivity 24th Feb – 10th March • Intro to connectivity - PPI & SEM (Melissa Stockbridge and Dean Dsouza) • DCM for fMRI – theory & practice (Marie-Helene Boudrais and Jorge Ivan Castillo-Quan) • DCM for ERP / ERF – theory & practice (Flavia Cardini and Darren McGuinness) Introduction to MfD 2009

  12. VI. Structural MRI Analysis17th March • Voxel Based Morphometry (Nikos Gorgoraptis and one other) Introduction to MfD 2009

  13. How to prepare your presentation Very important!!!: Read thePresenter’s guide (available on the website) • 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 2009

  14. 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 Maria or Antoinette as soon as possible (at least 3 weeks before the talk). Introduction to MfD 2009

  15. Where to find help MfD Home Resources http://www.fil.ion.ucl.ac.uk/mfd/page2/page2.html • 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 2009

  16. Experts • Will Penny – Head of Methods • John Ashburner • Jean Daunizeau • Guillaume Flandin • James Kilner • Rosalyn Moran • Andre Marreiros • Vladimir Litvak • Chloe Hutton • Maria Joao Rosa • Antoinette Nicolle Contact the expert: discuss presentation and other issues (1 week before talk) Expert will be present in the session Introduction to MfD 2009

  17. Website http://www.fil.ion.ucl.ac.uk/mfd/ Where you can find all the information about MfD 2009: Programme Contacts Presenter’s guide Resources (Help) Etc… Introduction to MfD 2009

  18. Other helpful courses • Matlab for Cognitive Neuroscience (ICN) • Run by Christian Ruff • http://www.icn.ucl.ac.uk/courses/MATLAB-Tutorials/index.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 Introduction to MfD 2009

  19. Overview for Dummies Introduction to MfD 2009

  20. Outline • SPM & your (fMRI) data • Preprocessing • Analysis • Connectivity • Getting started with an experiment • Acronyms Introduction to MfD 2009

  21. Pre-processing

  22. Preprocessing Possibilities… • These steps basically get your imaging data to a state where you can start your analysis • Realignment & Unwarping • Segmentation and Normalisation • Smoothing

  23. Model specification and estimation

  24. 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 experiment E.g. ‘visual stimulus on = 1’ ‘visual stimulus off = 0’ Design matrix General Linear Model

  25. Inference

  26. 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

  27. Write up and publish…

  28. 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

  29. Statistical Parametric Mapping • MfD 2009 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

  30. 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 2009

  31. 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 2009

  32. 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 2009

  33. 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 2009

  34. 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 2009

  35. 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

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