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fMRI Methods Lecture1 - Introduction

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Leonesco Bldg. room 208

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

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Imaging Contrast Resolution (spatial, temporal)

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Resolution scales

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MRI scanner What is the measurement in this image?

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Hydrogen atoms

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Physics Static magnetic field direction

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Physics

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The voxel

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

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Anatomy 1T1T2T2T

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Anatomical measures Gray/White matterCortical thickness

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Diffusion tensor imaging (DTI)

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

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Tractography

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So far we didnt care about temporal resolution.

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Neurovascular coupling Heeger et. al. 2002

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Hemodynamics

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Hemodynamic changes Heeger et. al Time

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Hemodynamic response

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Experiment

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

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fMRI activation maps Motor system

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fMRI activation maps Motor system Visual system

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fMRI activation maps Motor system Visual system Obsession with localization!

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

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Break

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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

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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

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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)

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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

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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

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

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

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

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Go over handout Open Matlab getting started section Geometric linear algebra

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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

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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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