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FMRI Methods Lecture1 - Introduction.

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Presentation on theme: "FMRI Methods Lecture1 - Introduction."— Presentation transcript:

1 fMRI Methods Lecture1 - Introduction

2 Leonesco Bldg. room 208

3 Go over syllabus Weekly exercises, final project (grades) Office hours Groups Scanning (safety, Helsinki) Matlab (experience, licenses) Huettel et. al. Course overview

4 Imaging Contrast Resolution (spatial, temporal)

5 Resolution scales

6 MRI scanner What is the measurement in this image?

7 Hydrogen atoms

8 Physics Static magnetic field direction

9 Physics

10 The voxel

11 First anatomical MRI 106 voxels took 4 hours to scan! Damadian et. al. 1977

12 Anatomy 1T1T2T2T

13 Anatomical measures Gray/White matterCortical thickness

14 Diffusion tensor imaging (DTI)

15 Tractography Blue: up-downGreen: fwd-bwdYellow: right-left

16 Tractography

17 So far we didnt care about temporal resolution.

18 Neurovascular coupling Heeger et. al. 2002

19 Hemodynamics

20 Hemodynamic changes Heeger et. al Time

21 Hemodynamic response

22 Experiment

23

24 scan/volume fMRI RL Front Back 24 slices every 1.5 seconds

25 fMRI activation maps Motor system

26 fMRI activation maps Motor system Visual system

27 fMRI activation maps Motor system Visual system Obsession with localization!

28 With fMRI we care about temporal resolution. Temporal sampling rate. Limited by Hemodynamics

29 Break

30 A tool for manipulating vectors and matrices. Matlab offers an immense number of functions with which one can do these manipulations quickly. Generally we will assume that our data (neural and hemodynamic responses) are generated by a linear system. What does it mean to be linear? Matlab

31 A linear system is one that satisfies the following two conditions: 1. Additivity/Superposition – f(x+y) = f(x) + f(y) 2. Homogeneity – f(ax) = af(x) What does this mean? Linearity

32 a*x + b*y + c*z scaling/weighting Example of a linear system X Y Stimulus and neural response: X (stimulus) = a*Y (neural response)

33 The response of a single neuron at any given time is non-linear. Its an all or nothing response with a certain threshold – a spike. A linear system has to output graded responses of consistently increasing/decreasing amplitudes. However, the summed response of a neuron across time windows of a given length (i.e. compute its firing rate) may be linear…. Example of a non-linear system

34 The response of a single neuron at any given time is non-linear. Its an all or nothing response with a certain threshold – a spike. A linear system has to output graded responses of consistently increasing/decreasing amplitudes. However, the summed response of a neuron across time windows of a given length (i.e. compute its firing rate) may be linear…. Example of a non-linear system

35 Are incredibly useful ways of representing data... Vectors and matrices For example images of the brain

36 Are incredibly useful ways of representing data... Vectors and matrices Or sound – voltage changes over time

37 And for manipulating the data... Vectors and matrices How would you increase the volume of this sound segment?

38 Go over handout Open Matlab getting started section Geometric linear algebra

39 Open a folder for your code on the local computer. Try to keep the path name simple (e.g. C:\Your_name). Download code and MRI data from: Save Lab1.zip in the folder youve created and unzip. Open Matlab. Change the current directory to the directory youve created. Open: Lab1_VisualizingBrain.m When done open: Lab1_CreatingStimuli.m Matlab Tutorials

40 Read Chapters 1 & 2 of Huettel et. al. (available in library) Review Geometric linear algebra handout Matlab exercise: me the report as a word document. The report should include answers, figures, and the actual Matlab code used to generate them (copy it into word). This week, dont forget to also send me the movie youve created. Homework!


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