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**fMRI Methods Lecture1 - Introduction**

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**http://www. weizmann. ac. il/neurobiology/labs/malach/ilan ilan**

Leonesco Bldg. room 208

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

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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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**Static magnetic field direction**

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 1T 2T

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Anatomical measures Gray/White matter Cortical thickness

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**Diffusion tensor imaging (DTI)**

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**Blue: up-down Green: fwd-bwd Yellow: right-left**

Tractography Blue: up-down Green: fwd-bwd Yellow: right-left

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Tractography

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**So far we didn’t 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 Time Heeger et. al. 2002

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Hemodynamic response

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Experiment

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Experiment

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scan/volume fMRI R L Front Back 24 slices every 1.5 seconds

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**fMRI activation maps Motor system**

When judging about stimulus speed there are differences in motor/decision areas

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fMRI activation maps Visual system Motor system

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**Obsession with localization!**

fMRI activation maps Visual system Motor system Obsession with localization!

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**With fMRI we care about temporal resolution. Temporal sampling rate**

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

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Break

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Matlab 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?

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Linearity 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?

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**a*x + b*y + c*z scaling/weighting**

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

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**Example of a non-linear system**

The response of a single neuron at any given time is non-linear. It’s 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….

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**Example of a non-linear system**

The response of a single neuron at any given time is non-linear. It’s 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….

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**Are incredibly useful ways of representing data...**

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

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**Are incredibly useful ways of representing data...**

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

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**And for manipulating the data...**

Vectors and matrices And for manipulating the data... 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 Go over handout Open Matlab getting started section

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Matlab Tutorials 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 you’ve created and unzip. Open Matlab. Change the “current directory” to the directory you’ve created. Open: “Lab1_VisualizingBrain.m” When done open: “Lab1_CreatingStimuli.m”

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Homework! 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, don’t forget to also send me the movie you’ve created.

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Announcements a3 is out, due 2/15 11:59pm Please please please start early quiz will be graded in about a week. a1 will be graded shortly—use glookup to.

Announcements a3 is out, due 2/15 11:59pm Please please please start early quiz will be graded in about a week. a1 will be graded shortly—use glookup to.

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