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fMRI Methods
Lecture1 - Introduction
http://www.weizmann.ac.il/neurobiology/labs/malach/ilan
Leonesco Bldg. room 208
Go over syllabus
Weekly exercises, final project (grades)
Office hours
Groups
Scanning (safety, Helsinki)
Matlab (experience, licenses)
Huettel et. al.
Course overview
Imaging
Contrast
Resolution(spatial, temporal)
Resolution scales
MRI scanner
What is the measurement in this image?
Hydrogen atoms
Physics
Sta
tic m
agne
tic fi
eld
dire
ctio
n
Physics
The voxel
First anatomical MRI
106 voxels took 4 hours to scan!
Damadian et. al. 1977
Anatomy
1T 2T
Anatomical measures
Gray/White matter Cortical thickness
Diffusion tensor imaging (DTI)
Tractography
Blue: up-down Green: fwd-bwd Yellow: right-left
Tractography
So far we didn’t care about temporal resolution.
Neurovascular coupling
Heeger et. al. 2002
Hemodynamics
Hemodynamic changes
Heeger et. al. 2002
Time
Hemodynamic response
Experiment
Experiment
scan/volume fMRI
R L
Front
Back
24 slices every 1.5 seconds
fMRI activation maps
Motor system
fMRI activation maps
Motor system
Visualsystem
fMRI activation maps
Motor system
Visualsystem
Obsession with localization!
With fMRI we care about temporal resolution.
Temporal sampling rate.
Limited by Hemodynamics
Break
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
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
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)
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….
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….
Example of a non-linear system
Are incredibly useful ways of representing data...
Vectors and matrices
For example images of the brain
Are incredibly useful ways of representing data...
Vectors and matrices
Or sound – voltage changes over time
And for manipulating the data...
Vectors and matrices
How would you increase the volume of this sound segment?
Go over handout
Open Matlab getting started section
“Geometric” linear algebra
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:http://www.weizmann.ac.il/neurobiology/labs/malach/ilan/lecture_notes.html
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”
Matlab Tutorials
Read Chapters 1 & 2 of Huettel et. al. (available in library)
Review Geometric linear algebra handout
Matlab exercise: email 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.
Homework!
